Starting phenix.real_space_refine on Thu Sep 18 22:09:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kht_62354/09_2025/9kht_62354.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kht_62354/09_2025/9kht_62354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kht_62354/09_2025/9kht_62354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kht_62354/09_2025/9kht_62354.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kht_62354/09_2025/9kht_62354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kht_62354/09_2025/9kht_62354.map" } resolution = 4.85 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= 0.004 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 51 5.16 5 C 12650 2.51 5 N 3399 2.21 5 O 3860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19960 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 539 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 556 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "d" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "e" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 556 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "f" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 568 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 528 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "c" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 528 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 6722 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 917, 6706 Classifications: {'peptide': 917} Incomplete info: {'truncation_to_alanine': 188} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 36, 'TRANS': 875} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 716 Unresolved non-hydrogen angles: 890 Unresolved non-hydrogen dihedrals: 586 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'TYR:plan': 7, 'ASN:plan1': 15, 'GLU:plan': 19, 'PHE:plan': 9, 'ARG:plan': 15, 'ASP:plan': 12, 'HIS:plan': 2, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 373 Conformer: "B" Number of residues, atoms: 917, 6705 Classifications: {'peptide': 917} Incomplete info: {'truncation_to_alanine': 188} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 36, 'TRANS': 875} Chain breaks: 9 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 719 Unresolved non-hydrogen angles: 895 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'TYR:plan': 7, 'ASN:plan1': 15, 'GLU:plan': 19, 'PHE:plan': 9, 'ARG:plan': 15, 'ASP:plan': 12, 'HIS:plan': 2, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 373 bond proxies already assigned to first conformer: 6817 Chain: "B" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1013 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 15, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 6, 'ARG:plan': 1, 'TYR:plan': 1, 'TRP:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 64 Chain: "a" Number of atoms: 6793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 922, 6777 Classifications: {'peptide': 922} Incomplete info: {'truncation_to_alanine': 182} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 37, 'TRANS': 879} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 690 Unresolved non-hydrogen angles: 856 Unresolved non-hydrogen dihedrals: 565 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'TYR:plan': 6, 'ASN:plan1': 11, 'GLU:plan': 21, 'PHE:plan': 10, 'ARG:plan': 13, 'ASP:plan': 11, 'HIS:plan': 1, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 350 Conformer: "B" Number of residues, atoms: 922, 6776 Classifications: {'peptide': 922} Incomplete info: {'truncation_to_alanine': 182} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 37, 'TRANS': 879} Chain breaks: 9 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 693 Unresolved non-hydrogen angles: 861 Unresolved non-hydrogen dihedrals: 567 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'TYR:plan': 6, 'ASN:plan1': 11, 'GLU:plan': 21, 'PHE:plan': 10, 'ARG:plan': 13, 'ASP:plan': 11, 'HIS:plan': 1, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 350 bond proxies already assigned to first conformer: 6891 Chain: "b" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1030 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 15, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 7, 'ARG:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N LEU D 73 " occ=0.45 ... (3 atoms not shown) pdb=" CB LEU D 73 " occ=0.45 residue: pdb=" N ARG D 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG D 74 " occ=0.45 residue: pdb=" N GLY D 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY D 75 " occ=0.25 residue: pdb=" N GLY D 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY D 76 " occ=0.25 residue: pdb=" N LEU d 73 " occ=0.45 ... (3 atoms not shown) pdb=" CB LEU d 73 " occ=0.45 residue: pdb=" N ARG d 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG d 74 " occ=0.45 residue: pdb=" N GLY d 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY d 75 " occ=0.25 residue: pdb=" N GLY d 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY d 76 " occ=0.25 Time building chain proxies: 7.72, per 1000 atoms: 0.39 Number of scatterers: 19960 At special positions: 0 Unit cell: (137.238, 155.902, 127.356, 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 51 16.00 O 3860 8.00 N 3399 7.00 C 12650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5246 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 17 sheets defined 59.9% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'D' and resid 22 through 28 Processing helix chain 'D' and resid 30 through 35 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.606A pdb=" N TYR D 59 " --> pdb=" O LEU D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 29 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 37 through 41 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.762A pdb=" N ASP E 58 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 35 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 55 through 60 removed outlier: 3.506A pdb=" N ASN F 60 " --> pdb=" O SER F 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 28 Processing helix chain 'd' and resid 30 through 35 Processing helix chain 'd' and resid 37 through 41 Processing helix chain 'd' and resid 55 through 60 removed outlier: 3.935A pdb=" N ASN d 60 " --> pdb=" O SER d 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 22 through 29 Processing helix chain 'e' and resid 30 through 35 Processing helix chain 'e' and resid 37 through 41 Processing helix chain 'f' and resid 22 through 35 Processing helix chain 'f' and resid 37 through 41 Processing helix chain 'f' and resid 55 through 60 removed outlier: 3.666A pdb=" N ASN f 60 " --> pdb=" O SER f 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 28 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'c' and resid 22 through 28 Processing helix chain 'c' and resid 37 through 41 Processing helix chain 'c' and resid 55 through 60 Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 38 through 48 removed outlier: 3.609A pdb=" N THR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 76 removed outlier: 3.575A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 102 removed outlier: 3.659A pdb=" N ILE A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.508A pdb=" N GLY A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.862A pdb=" N TYR A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.988A pdb=" N LEU A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 162 removed outlier: 4.212A pdb=" N PHE A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.994A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 4.116A pdb=" N ILE A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.785A pdb=" N PHE A 211 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A 212 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 242 through 273 removed outlier: 4.267A pdb=" N ALA A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 270 " --> pdb=" O PHE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 292 removed outlier: 3.584A pdb=" N LYS A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.529A pdb=" N ALA A 298 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.742A pdb=" N THR A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 removed outlier: 4.570A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.571A pdb=" N PHE A 342 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.656A pdb=" N ALA A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 396 removed outlier: 3.893A pdb=" N ASP A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 406 removed outlier: 3.799A pdb=" N SER A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.766A pdb=" N GLU A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 461 removed outlier: 3.570A pdb=" N LYS A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 485 removed outlier: 3.735A pdb=" N ARG A 482 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 485 " --> pdb=" O ILE A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 Processing helix chain 'A' and resid 528 through 542 Proline residue: A 534 - end of helix Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.547A pdb=" N GLU A 560 " --> pdb=" O GLY A 556 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 removed outlier: 4.060A pdb=" N LYS A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 613 through 625 removed outlier: 4.174A pdb=" N VAL A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 625 " --> pdb=" O PHE A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 636 through 652 removed outlier: 3.883A pdb=" N SER A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 669 removed outlier: 4.133A pdb=" N LYS A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 705 removed outlier: 3.595A pdb=" N PHE A 673 " --> pdb=" O ASN A 669 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 676 " --> pdb=" O PHE A 672 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE A 686 " --> pdb=" O ASN A 682 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU A 688 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 755 removed outlier: 3.696A pdb=" N ILE A 750 " --> pdb=" O LYS A 746 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A 754 " --> pdb=" O ILE A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 760 removed outlier: 4.390A pdb=" N PHE A 759 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 760 " --> pdb=" O PRO A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 760' Processing helix chain 'A' and resid 761 through 781 removed outlier: 4.179A pdb=" N TYR A 766 " --> pdb=" O PRO A 762 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ARG A 767 " --> pdb=" O GLU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 787 removed outlier: 3.681A pdb=" N GLY A 785 " --> pdb=" O GLY A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 814 removed outlier: 3.834A pdb=" N LEU A 813 " --> pdb=" O VAL A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 832 through 845 removed outlier: 3.604A pdb=" N VAL A 836 " --> pdb=" O ARG A 832 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 877 removed outlier: 3.633A pdb=" N GLU A 866 " --> pdb=" O ASN A 862 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN A 867 " --> pdb=" O LYS A 863 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 871 " --> pdb=" O GLN A 867 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 872 " --> pdb=" O ARG A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 917 Processing helix chain 'A' and resid 930 through 934 removed outlier: 3.661A pdb=" N VAL A 934 " --> pdb=" O LEU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 955 removed outlier: 3.654A pdb=" N ARG A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 17 removed outlier: 4.621A pdb=" N ILE B 7 " --> pdb=" O SER B 3 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 8 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS B 9 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 87 through 93 removed outlier: 4.181A pdb=" N LYS B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 121 through 131 Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'a' and resid 2 through 8 Processing helix chain 'a' and resid 35 through 37 No H-bonds generated for 'chain 'a' and resid 35 through 37' Processing helix chain 'a' and resid 38 through 49 Processing helix chain 'a' and resid 55 through 76 removed outlier: 3.599A pdb=" N ARG a 72 " --> pdb=" O GLN a 68 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN a 76 " --> pdb=" O ARG a 72 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 102 removed outlier: 3.680A pdb=" N ILE a 95 " --> pdb=" O ASP a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 112 through 123 removed outlier: 3.517A pdb=" N GLY a 119 " --> pdb=" O ASN a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 142 removed outlier: 3.821A pdb=" N TYR a 127 " --> pdb=" O ASN a 123 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP a 129 " --> pdb=" O ASN a 125 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE a 130 " --> pdb=" O SER a 126 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER a 132 " --> pdb=" O THR a 128 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU a 140 " --> pdb=" O GLN a 136 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU a 141 " --> pdb=" O ARG a 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 151 removed outlier: 3.540A pdb=" N ASN a 149 " --> pdb=" O LEU a 145 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 161 Processing helix chain 'a' and resid 173 through 187 removed outlier: 3.515A pdb=" N PHE a 181 " --> pdb=" O VAL a 177 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE a 184 " --> pdb=" O ILE a 180 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR a 186 " --> pdb=" O GLU a 182 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE a 187 " --> pdb=" O LEU a 183 " (cutoff:3.500A) Processing helix chain 'a' and resid 187 through 195 removed outlier: 4.064A pdb=" N ILE a 193 " --> pdb=" O PRO a 189 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 211 removed outlier: 3.779A pdb=" N PHE a 211 " --> pdb=" O PRO a 208 " (cutoff:3.500A) Processing helix chain 'a' and resid 227 through 235 Processing helix chain 'a' and resid 242 through 273 removed outlier: 3.592A pdb=" N ILE a 249 " --> pdb=" O GLN a 245 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA a 255 " --> pdb=" O GLU a 251 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU a 256 " --> pdb=" O SER a 252 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS a 270 " --> pdb=" O PHE a 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 275 through 292 removed outlier: 3.513A pdb=" N ILE a 289 " --> pdb=" O TYR a 285 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS a 292 " --> pdb=" O HIS a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 298 Processing helix chain 'a' and resid 302 through 306 Processing helix chain 'a' and resid 308 through 320 removed outlier: 3.785A pdb=" N THR a 316 " --> pdb=" O MET a 312 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU a 317 " --> pdb=" O SER a 313 " (cutoff:3.500A) Processing helix chain 'a' and resid 322 through 327 removed outlier: 4.436A pdb=" N PHE a 326 " --> pdb=" O PHE a 322 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 337 Processing helix chain 'a' and resid 338 through 343 removed outlier: 4.510A pdb=" N PHE a 342 " --> pdb=" O ALA a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 360 through 372 removed outlier: 3.660A pdb=" N ALA a 366 " --> pdb=" O LYS a 362 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG a 372 " --> pdb=" O TYR a 368 " (cutoff:3.500A) Processing helix chain 'a' and resid 380 through 395 removed outlier: 3.925A pdb=" N ASP a 384 " --> pdb=" O ASN a 380 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU a 390 " --> pdb=" O PHE a 386 " (cutoff:3.500A) Processing helix chain 'a' and resid 396 through 423 removed outlier: 3.647A pdb=" N ILE a 411 " --> pdb=" O MET a 407 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS a 412 " --> pdb=" O GLY a 408 " (cutoff:3.500A) Processing helix chain 'a' and resid 430 through 461 removed outlier: 3.851A pdb=" N GLN a 457 " --> pdb=" O ARG a 453 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY a 458 " --> pdb=" O PHE a 454 " (cutoff:3.500A) Processing helix chain 'a' and resid 464 through 485 removed outlier: 3.790A pdb=" N ARG a 482 " --> pdb=" O THR a 478 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL a 483 " --> pdb=" O PHE a 479 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL a 484 " --> pdb=" O LEU a 480 " (cutoff:3.500A) Processing helix chain 'a' and resid 522 through 526 Processing helix chain 'a' and resid 528 through 542 Proline residue: a 534 - end of helix Processing helix chain 'a' and resid 556 through 566 removed outlier: 3.607A pdb=" N GLU a 560 " --> pdb=" O GLY a 556 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE a 561 " --> pdb=" O SER a 557 " (cutoff:3.500A) Processing helix chain 'a' and resid 568 through 572 removed outlier: 4.128A pdb=" N VAL a 572 " --> pdb=" O PRO a 569 " (cutoff:3.500A) Processing helix chain 'a' and resid 574 through 590 removed outlier: 4.044A pdb=" N LYS a 578 " --> pdb=" O ASN a 574 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS a 580 " --> pdb=" O HIS a 576 " (cutoff:3.500A) Processing helix chain 'a' and resid 600 through 606 Processing helix chain 'a' and resid 607 through 612 Processing helix chain 'a' and resid 613 through 625 removed outlier: 4.101A pdb=" N VAL a 623 " --> pdb=" O LEU a 619 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE a 624 " --> pdb=" O ASP a 620 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL a 625 " --> pdb=" O PHE a 621 " (cutoff:3.500A) Processing helix chain 'a' and resid 626 through 628 No H-bonds generated for 'chain 'a' and resid 626 through 628' Processing helix chain 'a' and resid 636 through 655 removed outlier: 3.796A pdb=" N SER a 640 " --> pdb=" O ASP a 636 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU a 648 " --> pdb=" O ILE a 644 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU a 650 " --> pdb=" O ILE a 646 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR a 653 " --> pdb=" O GLU a 649 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE a 655 " --> pdb=" O LEU a 651 " (cutoff:3.500A) Processing helix chain 'a' and resid 655 through 669 removed outlier: 4.130A pdb=" N LYS a 659 " --> pdb=" O ILE a 655 " (cutoff:3.500A) Processing helix chain 'a' and resid 669 through 705 removed outlier: 3.556A pdb=" N PHE a 673 " --> pdb=" O ASN a 669 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG a 675 " --> pdb=" O ASP a 671 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE a 676 " --> pdb=" O PHE a 672 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU a 684 " --> pdb=" O MET a 680 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR a 685 " --> pdb=" O LEU a 681 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE a 686 " --> pdb=" O ASN a 682 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU a 688 " --> pdb=" O LEU a 684 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ASP a 689 " --> pdb=" O THR a 685 " (cutoff:3.500A) Processing helix chain 'a' and resid 720 through 755 removed outlier: 3.744A pdb=" N ILE a 750 " --> pdb=" O LYS a 746 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP a 754 " --> pdb=" O ILE a 750 " (cutoff:3.500A) Processing helix chain 'a' and resid 755 through 760 removed outlier: 4.405A pdb=" N PHE a 759 " --> pdb=" O ILE a 755 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL a 760 " --> pdb=" O PRO a 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 755 through 760' Processing helix chain 'a' and resid 761 through 781 removed outlier: 4.237A pdb=" N TYR a 766 " --> pdb=" O PRO a 762 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ARG a 767 " --> pdb=" O GLU a 763 " (cutoff:3.500A) Processing helix chain 'a' and resid 781 through 787 removed outlier: 3.645A pdb=" N GLY a 785 " --> pdb=" O GLY a 781 " (cutoff:3.500A) Processing helix chain 'a' and resid 798 through 814 removed outlier: 3.798A pdb=" N LEU a 813 " --> pdb=" O VAL a 809 " (cutoff:3.500A) Processing helix chain 'a' and resid 816 through 825 Processing helix chain 'a' and resid 832 through 845 removed outlier: 3.592A pdb=" N VAL a 836 " --> pdb=" O ARG a 832 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS a 845 " --> pdb=" O ILE a 841 " (cutoff:3.500A) Processing helix chain 'a' and resid 850 through 877 removed outlier: 3.677A pdb=" N GLU a 866 " --> pdb=" O ASN a 862 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN a 867 " --> pdb=" O LYS a 863 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP a 871 " --> pdb=" O GLN a 867 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU a 872 " --> pdb=" O ARG a 868 " (cutoff:3.500A) Processing helix chain 'a' and resid 909 through 919 removed outlier: 3.875A pdb=" N SER a 918 " --> pdb=" O ALA a 914 " (cutoff:3.500A) Processing helix chain 'a' and resid 937 through 955 removed outlier: 3.551A pdb=" N ARG a 941 " --> pdb=" O ASN a 937 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 17 removed outlier: 3.617A pdb=" N ALA b 8 " --> pdb=" O SER b 4 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS b 9 " --> pdb=" O LYS b 5 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU b 14 " --> pdb=" O GLU b 10 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU b 15 " --> pdb=" O LEU b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 92 removed outlier: 4.316A pdb=" N LYS b 91 " --> pdb=" O LEU b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 109 Processing helix chain 'b' and resid 121 through 131 Processing helix chain 'b' and resid 131 through 146 Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.906A pdb=" N ARG D 42 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 13 through 16 removed outlier: 9.229A pdb=" N LEU E 67 " --> pdb=" O GLN E 2 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE E 4 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU E 69 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS E 6 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 44 " --> pdb=" O HIS E 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 12 through 16 removed outlier: 9.280A pdb=" N LEU F 67 " --> pdb=" O GLN F 2 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE F 4 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU F 69 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS F 6 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU F 71 " --> pdb=" O LYS F 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 2 through 3 Processing sheet with id=AA6, first strand: chain 'd' and resid 48 through 49 removed outlier: 3.936A pdb=" N ARG d 42 " --> pdb=" O VAL d 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 13 through 16 removed outlier: 3.594A pdb=" N ILE e 13 " --> pdb=" O VAL e 5 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL e 5 " --> pdb=" O ILE e 13 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N LEU e 67 " --> pdb=" O GLN e 2 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE e 4 " --> pdb=" O LEU e 67 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU e 69 " --> pdb=" O PHE e 4 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS e 6 " --> pdb=" O LEU e 69 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE e 44 " --> pdb=" O HIS e 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 12 through 16 removed outlier: 9.185A pdb=" N LEU f 67 " --> pdb=" O GLN f 2 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE f 4 " --> pdb=" O LEU f 67 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU f 69 " --> pdb=" O PHE f 4 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS f 6 " --> pdb=" O LEU f 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 15 removed outlier: 4.055A pdb=" N VAL C 5 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU C 15 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE C 4 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU C 69 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS C 6 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS C 68 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 43 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 50 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE C 45 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 12 through 16 removed outlier: 4.003A pdb=" N VAL c 5 " --> pdb=" O ILE c 13 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU c 15 " --> pdb=" O ILE c 3 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N LEU c 67 " --> pdb=" O GLN c 2 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE c 4 " --> pdb=" O LEU c 67 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU c 69 " --> pdb=" O PHE c 4 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LYS c 6 " --> pdb=" O LEU c 69 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS c 68 " --> pdb=" O ILE c 44 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU c 43 " --> pdb=" O LEU c 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU c 50 " --> pdb=" O LEU c 43 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE c 45 " --> pdb=" O LYS c 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.944A pdb=" N THR A 11 " --> pdb=" O SER A 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 906 through 908 Processing sheet with id=AB4, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.689A pdb=" N HIS B 56 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS B 67 " --> pdb=" O HIS B 56 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 10 through 11 removed outlier: 3.966A pdb=" N THR a 11 " --> pdb=" O SER a 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'a' and resid 906 through 908 Processing sheet with id=AB7, first strand: chain 'b' and resid 22 through 23 removed outlier: 3.841A pdb=" N SER b 23 " --> pdb=" O SER b 37 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE b 38 " --> pdb=" O PHE b 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 22 through 23 removed outlier: 3.841A pdb=" N SER b 23 " --> pdb=" O SER b 37 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE b 38 " --> pdb=" O PHE b 51 " (cutoff:3.500A) 1025 hydrogen bonds defined for protein. 2875 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: 3.43 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6050 1.33 - 1.45: 2741 1.45 - 1.57: 11452 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 20323 Sorted by residual: bond pdb=" N ASP B 118 " pdb=" CA ASP B 118 " ideal model delta sigma weight residual 1.463 1.432 0.031 1.11e-02 8.12e+03 7.60e+00 bond pdb=" CA ASP B 118 " pdb=" CB ASP B 118 " ideal model delta sigma weight residual 1.529 1.501 0.028 1.13e-02 7.83e+03 6.06e+00 bond pdb=" CA PRO C 37 " pdb=" C PRO C 37 " ideal model delta sigma weight residual 1.517 1.531 -0.014 6.70e-03 2.23e+04 4.15e+00 bond pdb=" C VAL A 28 " pdb=" N PRO A 29 " ideal model delta sigma weight residual 1.334 1.379 -0.046 2.34e-02 1.83e+03 3.79e+00 bond pdb=" CA ASP B 118 " pdb=" C ASP B 118 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.24e-02 6.50e+03 3.45e+00 ... (remaining 20318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 26610 1.37 - 2.75: 883 2.75 - 4.12: 123 4.12 - 5.49: 29 5.49 - 6.87: 11 Bond angle restraints: 27656 Sorted by residual: angle pdb=" N GLU a 405 " pdb=" CA GLU a 405 " pdb=" C GLU a 405 " ideal model delta sigma weight residual 111.28 105.54 5.74 1.09e+00 8.42e-01 2.77e+01 angle pdb=" C LYS a 24 " pdb=" N SER a 25 " pdb=" CA SER a 25 " ideal model delta sigma weight residual 121.70 128.57 -6.87 1.80e+00 3.09e-01 1.46e+01 angle pdb=" C LYS A 24 " pdb=" N SER A 25 " pdb=" CA SER A 25 " ideal model delta sigma weight residual 121.70 128.42 -6.72 1.80e+00 3.09e-01 1.39e+01 angle pdb=" N LEU a 93 " pdb=" CA LEU a 93 " pdb=" C LEU a 93 " ideal model delta sigma weight residual 111.36 114.95 -3.59 1.09e+00 8.42e-01 1.08e+01 angle pdb=" C ASP B 131 " pdb=" N ARG B 132 " pdb=" CA ARG B 132 " ideal model delta sigma weight residual 120.58 124.81 -4.23 1.32e+00 5.74e-01 1.03e+01 ... (remaining 27651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 11567 17.69 - 35.38: 614 35.38 - 53.07: 91 53.07 - 70.76: 14 70.76 - 88.45: 3 Dihedral angle restraints: 12289 sinusoidal: 4269 harmonic: 8020 Sorted by residual: dihedral pdb=" CA ASP A 13 " pdb=" C ASP A 13 " pdb=" N PRO A 14 " pdb=" CA PRO A 14 " ideal model delta harmonic sigma weight residual 0.00 -19.84 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA SER B 2 " pdb=" C SER B 2 " pdb=" N SER B 3 " pdb=" CA SER B 3 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ASN a 798 " pdb=" C ASN a 798 " pdb=" N PRO a 799 " pdb=" CA PRO a 799 " ideal model delta harmonic sigma weight residual 180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 12286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1899 0.031 - 0.061: 926 0.061 - 0.092: 287 0.092 - 0.122: 125 0.122 - 0.153: 9 Chirality restraints: 3246 Sorted by residual: chirality pdb=" CA VAL a 521 " pdb=" N VAL a 521 " pdb=" C VAL a 521 " pdb=" CB VAL a 521 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA VAL A 521 " pdb=" N VAL A 521 " pdb=" C VAL A 521 " pdb=" CB VAL A 521 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA GLN A 324 " pdb=" N GLN A 324 " pdb=" C GLN A 324 " pdb=" CB GLN A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 3243 not shown) Planarity restraints: 3641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO b 116 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C PRO b 116 " -0.040 2.00e-02 2.50e+03 pdb=" O PRO b 116 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP b 117 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 13 " 0.038 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 14 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP a 13 " 0.038 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO a 14 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO a 14 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO a 14 " 0.028 5.00e-02 4.00e+02 ... (remaining 3638 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1768 2.74 - 3.28: 22295 3.28 - 3.82: 32418 3.82 - 4.36: 37289 4.36 - 4.90: 59757 Nonbonded interactions: 153527 Sorted by model distance: nonbonded pdb=" NH2 ARG B 6 " pdb=" O PRO B 96 " model vdw 2.197 3.120 nonbonded pdb=" OD2 ASP a 328 " pdb=" OG SER a 330 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU A 404 " pdb=" OH TYR A 540 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP a 40 " pdb=" OH TYR a 97 " model vdw 2.205 3.040 nonbonded pdb=" O PHE A 286 " pdb=" OH TYR A 392 " model vdw 2.208 3.040 ... (remaining 153522 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 (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 151 or resid 153 or resid 155 throu \ gh 162 or resid 165 through 247 or resid 249 through 257 or resid 259 through 34 \ 5 or (resid 346 through 347 and (name N or name CA or name C or name O or name C \ B )) or resid 348 through 403 or (resid 404 through 407 and (name N or name CA o \ r name C or name O or name CB )) or resid 408 through 420 or (resid 421 through \ 423 and (name N or name CA or name C or name O or name CB )) or resid 424 throug \ h 429 or (resid 430 through 435 and (name N or name CA or name C or name O or na \ me CB )) or resid 436 through 437 or resid 439 through 442 or (resid 443 through \ 450 and (name N or name CA or name C or name O or name CB )) or resid 451 throu \ gh 554 or (resid 555 and (name N or name CA or name C or name O or name CB )) or \ resid 556 through 613 or (resid 614 and (name N or name CA or name C or name O \ or name CB )) or resid 615 through 645 or (resid 646 and (name N or name CA or n \ ame C or name O or name CB )) or resid 647 or (resid 648 through 649 and (name N \ or name CA or name C or name O or name CB )) or resid 650 through 661 or resid \ 663 through 673 or resid 675 through 681 or resid 683 through 747 or (resid 748 \ and (name N or name CA or name C or name O or name CB )) or resid 749 through 84 \ 9 or resid 851 through 933 or (resid 934 and (name N or name CA or name C or nam \ e O or name CB )) or resid 935 through 955)) selection = (chain 'a' and (resid 1 through 22 or (resid 23 and (name N or name CA or name C \ or name O or name CB )) or resid 24 through 49 or resid 54 through 96 or (resid \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 through \ 114 or (resid 115 and (name N or name CA or name C or name O or name CB )) or r \ esid 116 through 203 or resid 205 through 225 or (resid 226 and (name N or name \ CA or name C or name O or name CB )) or resid 227 through 238 or (resid 239 thro \ ugh 241 and (name N or name CA or name C or name O or name CB )) or resid 242 th \ rough 247 or resid 249 through 257 or resid 259 through 320 or (resid 321 and (n \ ame N or name CA or name C or name O or name CB )) or resid 322 through 428 or ( \ resid 429 through 435 and (name N or name CA or name C or name O or name CB )) o \ r resid 436 through 437 or resid 439 through 447 or (resid 448 through 450 and ( \ name N or name CA or name C or name O or name CB )) or resid 451 through 464 or \ (resid 465 through 467 and (name N or name CA or name C or name O or name CB )) \ or resid 468 through 477 or (resid 478 and (name N or name CA or name C or name \ O or name CB )) or resid 479 through 558 or (resid 559 and (name N or name CA or \ name C or name O or name CB )) or resid 560 through 571 or (resid 572 and (name \ N or name CA or name C or name O or name CB )) or resid 573 or (resid 574 and ( \ name N or name CA or name C or name O or name CB )) or resid 575 through 661 or \ resid 663 through 673 or resid 675 through 679 or (resid 680 and (name N or name \ CA or name C or name O or name CB )) or resid 681 or resid 683 through 832 or ( \ resid 833 and (name N or name CA or name C or name O or name CB )) or resid 834 \ through 849 or resid 851 through 891 or (resid 892 and (name N or name CA or nam \ e C or name O or name CB )) or resid 893 through 914 or (resid 915 and (name N o \ r name CA or name C or name O or name CB )) or resid 916 through 919 or (resid 9 \ 25 through 926 and (name N or name CA or name C or name O or name CB )) or resid \ 927 through 955)) } ncs_group { reference = (chain 'B' and (resid 1 through 14 or (resid 15 through 17 and (name N or name C \ A or name C or name O or name CB )) or resid 18 through 26 or resid 28 through 5 \ 8 or (resid 59 through 61 and (name N or name CA or name C or name O or name CB \ )) or resid 62 or (resid 63 through 64 and (name N or name CA or name C or name \ O or name CB )) or resid 65 through 130 or (resid 131 and (name N or name CA or \ name C or name O or name CB )) or resid 132 through 139 or (resid 140 and (name \ N or name CA or name C or name O or name CB )) or resid 141 through 148)) selection = (chain 'b' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 20 or (resid 21 and (name N or name CA \ or name C or name O or name CB )) or resid 22 through 33 or (resid 34 through 3 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 39 through 9 \ 2 or (resid 93 through 94 and (name N or name CA or name C or name O or name CB \ )) or resid 95 through 116 or (resid 117 and (name N or name CA or name C or nam \ e O or name CB )) or resid 118 through 135 or (resid 136 through 137 and (name N \ or name CA or name C or name O or name CB )) or resid 138 through 148)) } ncs_group { reference = (chain 'C' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 11 or (resid 12 through 17 and (name N \ or name CA or name C or name O or name CB )) or resid 18 through 26 or (resid 2 \ 7 through 28 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 9 through 32 or (resid 33 through 34 and (name N or name CA or name C or name O \ or name CB )) or resid 35 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 47 or resid 49 or (resid 50 thr \ ough 51 and (name N or name CA or name C or name O or name CB )) or resid 52 thr \ ough 53 or (resid 54 through 55 and (name N or name CA or name C or name O or na \ me CB )) or resid 56 or (resid 57 through 61 and (name N or name CA or name C or \ name O or name CB )) or resid 62 through 63 or (resid 64 and (name N or name CA \ or name C or name O or name CB )) or resid 65 through 68 or (resid 69 through 7 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 75 through 7 \ 6)) selection = (chain 'D' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or resid 7 through 14 or (resid 15 through 17 and (name N \ or name CA or name C or name O or name CB )) or resid 18 through 19 or (resid 20 \ and (name N or name CA or name C or name O or name CB )) or resid 21 through 29 \ or (resid 30 and (name N or name CA or name C or name O or name CB )) or resid \ 31 through 35 or (resid 36 and (name N or name CA or name C or name O or name CB \ )) or resid 37 through 38 or (resid 39 through 42 and (name N or name CA or nam \ e C or name O or name CB )) or resid 43 or (resid 44 and (name N or name CA or n \ ame C or name O or name CB )) or resid 45 through 47 or resid 49 or (resid 50 th \ rough 51 and (name N or name CA or name C or name O or name CB )) or resid 52 th \ rough 58 or (resid 59 through 61 and (name N or name CA or name C or name O or n \ ame CB )) or resid 62 through 63 or (resid 64 and (name N or name CA or name C o \ r name O or name CB )) or resid 65 through 66 or (resid 67 and (name N or name C \ A or name C or name O or name CB )) or resid 68 or (resid 69 through 74 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 75 through 76 and (na \ me N or name CA or name C or name O )))) selection = (chain 'E' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 11 or (resid 12 through 17 and (name N or name CA \ or name C or name O or name CB )) or resid 18 through 19 or (resid 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 23 or (resid \ 24 and (name N or name CA or name C or name O or name CB )) or resid 25 through \ 26 or (resid 27 through 28 and (name N or name CA or name C or name O or name C \ B )) or resid 29 or (resid 30 and (name N or name CA or name C or name O or name \ CB )) or resid 31 through 32 or (resid 33 through 34 and (name N or name CA or \ name C or name O or name CB )) or resid 35 or (resid 36 and (name N or name CA o \ r name C or name O or name CB )) or resid 37 through 38 or (resid 39 through 42 \ and (name N or name CA or name C or name O or name CB )) or resid 43 or (resid 4 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 45 through 4 \ 7 or resid 49 through 50 or (resid 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 53 or (resid 54 through 55 and (name N or nam \ e CA or name C or name O or name CB )) or resid 56 or (resid 57 through 61 and ( \ name N or name CA or name C or name O or name CB )) or resid 62 or (resid 63 thr \ ough 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thr \ ough 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or \ resid 68 through 69 or (resid 70 through 74 and (name N or name CA or name C or \ name O or name CB )) or resid 75 through 76)) selection = (chain 'F' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or resid 7 through 11 or (resid 12 through 17 and (name N \ or name CA or name C or name O or name CB )) or resid 18 through 19 or (resid 20 \ and (name N or name CA or name C or name O or name CB )) or resid 21 through 23 \ or (resid 24 and (name N or name CA or name C or name O or name CB )) or resid \ 25 through 26 or (resid 27 through 28 and (name N or name CA or name C or name O \ or name CB )) or resid 29 or (resid 30 and (name N or name CA or name C or name \ O or name CB )) or resid 31 through 32 or (resid 33 through 34 and (name N or n \ ame CA or name C or name O or name CB )) or resid 35 or (resid 36 and (name N or \ name CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 t \ hrough 42 and (name N or name CA or name C or name O or name CB )) or resid 43 t \ hrough 47 or resid 49 or (resid 50 through 51 and (name N or name CA or name C o \ r name O or name CB )) or resid 52 through 53 or (resid 54 through 55 and (name \ N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 through \ 61 and (name N or name CA or name C or name O or name CB )) or resid 62 or (resi \ d 63 through 64 and (name N or name CA or name C or name O or name CB )) or resi \ d 65 through 66 or (resid 67 and (name N or name CA or name C or name O or name \ CB )) or resid 68 or (resid 69 through 74 and (name N or name CA or name C or na \ me O or name CB )) or resid 75 through 76)) selection = (chain 'c' and (resid 1 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 11 or (resid 12 through 17 and (name N \ or name CA or name C or name O or name CB )) or resid 18 through 26 or (resid 2 \ 7 through 28 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 9 through 32 or (resid 33 through 34 and (name N or name CA or name C or name O \ or name CB )) or resid 35 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 or (resid 44 and (name N or name CA or na \ me C or name O or name CB )) or resid 45 through 47 or resid 49 or (resid 50 thr \ ough 51 and (name N or name CA or name C or name O or name CB )) or resid 52 thr \ ough 53 or (resid 54 through 55 and (name N or name CA or name C or name O or na \ me CB )) or resid 56 or (resid 57 through 61 and (name N or name CA or name C or \ name O or name CB )) or resid 62 through 63 or (resid 64 and (name N or name CA \ or name C or name O or name CB )) or resid 65 through 68 or (resid 69 through 7 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 75 through 7 \ 6)) selection = (chain 'd' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or resid 7 through 13 or (resid 14 through 17 and (name N \ or name CA or name C or name O or name CB )) or resid 18 through 19 or (resid 20 \ and (name N or name CA or name C or name O or name CB )) or resid 21 through 29 \ or (resid 30 and (name N or name CA or name C or name O or name CB )) or resid \ 31 through 32 or (resid 33 through 34 and (name N or name CA or name C or name O \ or name CB )) or resid 35 or (resid 36 and (name N or name CA or name C or name \ O or name CB )) or resid 37 through 38 or (resid 39 through 42 and (name N or n \ ame CA or name C or name O or name CB )) or resid 43 or (resid 44 and (name N or \ name CA or name C or name O or name CB )) or resid 45 through 47 or resid 49 or \ (resid 50 through 51 and (name N or name CA or name C or name O or name CB )) o \ r resid 52 through 53 or (resid 54 through 55 and (name N or name CA or name C o \ r name O or name CB )) or resid 56 or (resid 57 through 61 and (name N or name C \ A or name C or name O or name CB )) or resid 62 through 66 or (resid 67 and (nam \ e N or name CA or name C or name O or name CB )) or resid 68 through 69 or (resi \ d 70 through 74 and (name N or name CA or name C or name O or name CB )) or (res \ id 75 through 76 and (name N or name CA or name C or name O )))) selection = (chain 'e' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 11 or (resid 12 through 17 and (name N or name CA \ or name C or name O or name CB )) or resid 18 through 19 or (resid 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 23 or (resid \ 24 and (name N or name CA or name C or name O or name CB )) or resid 25 through \ 26 or (resid 27 through 28 and (name N or name CA or name C or name O or name C \ B )) or resid 29 or (resid 30 and (name N or name CA or name C or name O or name \ CB )) or resid 31 through 32 or (resid 33 through 34 and (name N or name CA or \ name C or name O or name CB )) or resid 35 or (resid 36 and (name N or name CA o \ r name C or name O or name CB )) or resid 37 through 38 or (resid 39 through 42 \ and (name N or name CA or name C or name O or name CB )) or resid 43 or (resid 4 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 45 through 4 \ 7 or resid 49 through 50 or (resid 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 53 or (resid 54 through 55 and (name N or nam \ e CA or name C or name O or name CB )) or resid 56 or (resid 57 through 61 and ( \ name N or name CA or name C or name O or name CB )) or resid 62 or (resid 63 thr \ ough 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thr \ ough 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or \ resid 68 through 69 or (resid 70 through 74 and (name N or name CA or name C or \ name O or name CB )) or resid 75 through 76)) selection = (chain 'f' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or resid 7 through 11 or (resid 12 through 17 and (name N \ or name CA or name C or name O or name CB )) or resid 18 through 19 or (resid 20 \ and (name N or name CA or name C or name O or name CB )) or resid 21 through 23 \ or (resid 24 and (name N or name CA or name C or name O or name CB )) or resid \ 25 through 26 or (resid 27 through 28 and (name N or name CA or name C or name O \ or name CB )) or resid 29 or (resid 30 and (name N or name CA or name C or name \ O or name CB )) or resid 31 through 32 or (resid 33 through 34 and (name N or n \ ame CA or name C or name O or name CB )) or resid 35 or (resid 36 and (name N or \ name CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 t \ hrough 42 and (name N or name CA or name C or name O or name CB )) or resid 43 t \ hrough 47 or resid 49 or (resid 50 through 51 and (name N or name CA or name C o \ r name O or name CB )) or resid 52 through 53 or (resid 54 through 55 and (name \ N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 through \ 61 and (name N or name CA or name C or name O or name CB )) or resid 62 or (resi \ d 63 through 64 and (name N or name CA or name C or name O or name CB )) or resi \ d 65 through 66 or (resid 67 and (name N or name CA or name C or name O or name \ CB )) or resid 68 through 69 or (resid 70 through 74 and (name N or name CA or n \ ame C or name O or name CB )) or resid 75 through 76)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.140 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: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.500 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 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 : 0.003 0.046 20323 Z= 0.191 Angle : 0.621 6.867 27656 Z= 0.370 Chirality : 0.041 0.153 3246 Planarity : 0.004 0.057 3641 Dihedral : 11.148 88.451 7043 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.12 % 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: -0.71 (0.17), residues: 2671 helix: 0.12 (0.14), residues: 1302 sheet: -1.74 (0.35), residues: 198 loop : -0.79 (0.19), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 641 TYR 0.013 0.002 TYR A 766 PHE 0.017 0.002 PHE a 403 TRP 0.009 0.001 TRP b 34 HIS 0.003 0.001 HIS b 76 Details of bonding type rmsd covalent geometry : bond 0.00343 (20323) covalent geometry : angle 0.62099 (27656) hydrogen bonds : bond 0.19832 ( 1023) hydrogen bonds : angle 7.04598 ( 2875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 PHE cc_start: 0.7825 (m-10) cc_final: 0.7590 (m-10) REVERT: D 22 THR cc_start: 0.8096 (p) cc_final: 0.7890 (t) REVERT: D 42 ARG cc_start: 0.6145 (tpt170) cc_final: 0.5751 (tpp80) REVERT: D 49 GLN cc_start: 0.5022 (mt0) cc_final: 0.4390 (mp10) REVERT: D 64 GLU cc_start: 0.7591 (mp0) cc_final: 0.7362 (mp0) REVERT: E 14 THR cc_start: 0.6568 (p) cc_final: 0.6332 (m) REVERT: F 29 LYS cc_start: 0.7881 (mttm) cc_final: 0.7536 (tttt) REVERT: d 22 THR cc_start: 0.7878 (p) cc_final: 0.7640 (t) REVERT: d 42 ARG cc_start: 0.5706 (tpt170) cc_final: 0.5487 (tpp80) REVERT: e 3 ILE cc_start: 0.5404 (pt) cc_final: 0.5178 (mt) REVERT: e 44 ILE cc_start: 0.8489 (mm) cc_final: 0.7843 (mm) REVERT: f 29 LYS cc_start: 0.7825 (mttm) cc_final: 0.7581 (tttt) REVERT: A 109 MET cc_start: 0.3003 (mmt) cc_final: 0.2678 (ttt) REVERT: A 146 ASP cc_start: 0.8937 (m-30) cc_final: 0.8492 (p0) REVERT: A 178 LEU cc_start: 0.9203 (mp) cc_final: 0.8975 (mp) REVERT: A 213 ARG cc_start: 0.7506 (mtp-110) cc_final: 0.6854 (mmt180) REVERT: A 338 ASP cc_start: 0.8317 (t0) cc_final: 0.8015 (t70) REVERT: A 524 LYS cc_start: 0.8194 (ptmt) cc_final: 0.7942 (ptpp) REVERT: A 526 TYR cc_start: 0.7824 (m-10) cc_final: 0.7605 (m-10) REVERT: A 540 TYR cc_start: 0.8559 (t80) cc_final: 0.7857 (t80) REVERT: A 544 TYR cc_start: 0.7092 (m-80) cc_final: 0.6386 (m-10) REVERT: A 555 LEU cc_start: 0.6803 (mm) cc_final: 0.6473 (mm) REVERT: A 683 ASP cc_start: 0.9138 (m-30) cc_final: 0.8553 (m-30) REVERT: A 687 LEU cc_start: 0.9038 (mt) cc_final: 0.8238 (tp) REVERT: A 699 HIS cc_start: 0.6532 (m90) cc_final: 0.6263 (m90) REVERT: A 732 ARG cc_start: 0.8550 (mtm180) cc_final: 0.8055 (ptt-90) REVERT: A 737 SER cc_start: 0.8481 (m) cc_final: 0.7976 (p) REVERT: A 745 MET cc_start: 0.8589 (tpp) cc_final: 0.8359 (tpp) REVERT: A 771 MET cc_start: 0.9550 (tmm) cc_final: 0.9268 (tmm) REVERT: A 773 ASN cc_start: 0.9116 (m-40) cc_final: 0.8868 (m-40) REVERT: A 809 VAL cc_start: 0.8518 (t) cc_final: 0.8307 (t) REVERT: A 828 ARG cc_start: 0.8244 (ttt-90) cc_final: 0.7942 (ttt90) REVERT: A 890 MET cc_start: 0.8172 (tpp) cc_final: 0.7773 (ttp) REVERT: B 14 LEU cc_start: 0.5191 (mp) cc_final: 0.4960 (mt) REVERT: B 60 ASP cc_start: 0.8691 (p0) cc_final: 0.8484 (t0) REVERT: B 84 ASN cc_start: 0.9049 (m-40) cc_final: 0.8718 (t0) REVERT: B 85 ILE cc_start: 0.7397 (mm) cc_final: 0.6631 (mm) REVERT: B 135 TYR cc_start: 0.7210 (t80) cc_final: 0.6970 (t80) REVERT: B 141 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7360 (tm-30) REVERT: a 38 PHE cc_start: 0.8299 (m-10) cc_final: 0.8006 (m-10) REVERT: a 109 MET cc_start: 0.4246 (mmt) cc_final: 0.3746 (ttt) REVERT: a 133 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7832 (mt0) REVERT: a 146 ASP cc_start: 0.8870 (m-30) cc_final: 0.8584 (p0) REVERT: a 213 ARG cc_start: 0.7411 (mtp-110) cc_final: 0.6730 (mmt180) REVERT: a 299 ASP cc_start: 0.7399 (m-30) cc_final: 0.6960 (p0) REVERT: a 326 PHE cc_start: 0.8343 (m-80) cc_final: 0.8130 (m-80) REVERT: a 333 LYS cc_start: 0.7717 (mttt) cc_final: 0.7468 (mmtt) REVERT: a 336 LYS cc_start: 0.6364 (mmtp) cc_final: 0.6107 (mtpt) REVERT: a 338 ASP cc_start: 0.8266 (t0) cc_final: 0.8055 (t70) REVERT: a 388 LEU cc_start: 0.9257 (tp) cc_final: 0.9031 (tp) REVERT: a 524 LYS cc_start: 0.8441 (ptmt) cc_final: 0.8004 (ptpp) REVERT: a 525 TYR cc_start: 0.8214 (m-80) cc_final: 0.7470 (m-10) REVERT: a 526 TYR cc_start: 0.7764 (m-10) cc_final: 0.7538 (m-10) REVERT: a 544 TYR cc_start: 0.6578 (m-80) cc_final: 0.5971 (m-10) REVERT: a 665 GLN cc_start: 0.9129 (mm110) cc_final: 0.8863 (tp40) REVERT: a 680 MET cc_start: 0.8360 (ptm) cc_final: 0.8059 (tpp) REVERT: a 687 LEU cc_start: 0.9066 (mt) cc_final: 0.8264 (tp) REVERT: a 693 SER cc_start: 0.9292 (t) cc_final: 0.8979 (p) REVERT: a 697 GLU cc_start: 0.7334 (tp30) cc_final: 0.7016 (mt-10) REVERT: a 699 HIS cc_start: 0.6291 (m90) cc_final: 0.6020 (m90) REVERT: a 732 ARG cc_start: 0.8710 (mtm180) cc_final: 0.8350 (mtm110) REVERT: a 737 SER cc_start: 0.8603 (m) cc_final: 0.8176 (p) REVERT: a 771 MET cc_start: 0.9543 (tmm) cc_final: 0.9295 (tmm) REVERT: a 825 LYS cc_start: 0.8153 (mttp) cc_final: 0.7937 (mtmt) REVERT: b 72 THR cc_start: 0.5942 (m) cc_final: 0.5649 (p) REVERT: b 141 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7388 (tm-30) outliers start: 0 outliers final: 0 residues processed: 600 average time/residue: 0.1526 time to fit residues: 139.8940 Evaluate side-chains 411 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN E 25 ASN F 40 GLN F 49 GLN ** d 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 49 GLN f 40 GLN A 46 GLN A 68 GLN A 162 HIS A 234 ASN A 245 GLN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 HIS A 394 HIS A 694 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 46 GLN a 68 GLN a 115 ASN a 234 ASN ** a 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 84 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.162116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111648 restraints weight = 106533.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114695 restraints weight = 61364.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116800 restraints weight = 39657.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119102 restraints weight = 31663.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119167 restraints weight = 27762.272| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20323 Z= 0.203 Angle : 0.673 9.865 27656 Z= 0.361 Chirality : 0.045 0.244 3246 Planarity : 0.005 0.059 3641 Dihedral : 4.996 23.470 2856 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.12 % 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: -0.76 (0.16), residues: 2671 helix: 0.11 (0.14), residues: 1353 sheet: -1.65 (0.36), residues: 192 loop : -0.92 (0.20), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 92 TYR 0.018 0.002 TYR A 540 PHE 0.024 0.002 PHE A 748 TRP 0.007 0.001 TRP A 664 HIS 0.014 0.002 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00424 (20323) covalent geometry : angle 0.67265 (27656) hydrogen bonds : bond 0.05071 ( 1023) hydrogen bonds : angle 5.83103 ( 2875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 486 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 ILE cc_start: 0.7584 (mm) cc_final: 0.7348 (tp) REVERT: D 22 THR cc_start: 0.8253 (p) cc_final: 0.7987 (t) REVERT: D 42 ARG cc_start: 0.6856 (tpt170) cc_final: 0.6227 (tpp80) REVERT: D 49 GLN cc_start: 0.5615 (mt0) cc_final: 0.4691 (mp10) REVERT: D 64 GLU cc_start: 0.7956 (mp0) cc_final: 0.7687 (mp0) REVERT: d 22 THR cc_start: 0.7992 (p) cc_final: 0.7733 (t) REVERT: d 42 ARG cc_start: 0.6687 (tpt170) cc_final: 0.6238 (tpp80) REVERT: e 14 THR cc_start: 0.6703 (p) cc_final: 0.6501 (t) REVERT: e 18 GLU cc_start: 0.8428 (tp30) cc_final: 0.8213 (tp30) REVERT: e 25 ASN cc_start: 0.8929 (t0) cc_final: 0.8718 (t0) REVERT: f 59 TYR cc_start: 0.5082 (m-80) cc_final: 0.4817 (m-10) REVERT: C 69 LEU cc_start: 0.5689 (tt) cc_final: 0.5423 (pp) REVERT: c 69 LEU cc_start: 0.5942 (tt) cc_final: 0.5656 (pp) REVERT: A 38 PHE cc_start: 0.7580 (m-10) cc_final: 0.7113 (m-10) REVERT: A 109 MET cc_start: 0.2487 (mmt) cc_final: 0.2139 (ttt) REVERT: A 127 TYR cc_start: 0.7755 (m-80) cc_final: 0.7306 (m-80) REVERT: A 133 GLN cc_start: 0.8303 (mp-120) cc_final: 0.7817 (mp10) REVERT: A 146 ASP cc_start: 0.9043 (m-30) cc_final: 0.8603 (p0) REVERT: A 336 LYS cc_start: 0.8408 (mmtm) cc_final: 0.8142 (mmmt) REVERT: A 524 LYS cc_start: 0.8594 (ptmt) cc_final: 0.8314 (ptpp) REVERT: A 526 TYR cc_start: 0.8028 (m-10) cc_final: 0.7681 (m-10) REVERT: A 540 TYR cc_start: 0.8296 (t80) cc_final: 0.7700 (t80) REVERT: A 544 TYR cc_start: 0.6844 (m-80) cc_final: 0.6541 (m-10) REVERT: A 590 MET cc_start: 0.8914 (ttt) cc_final: 0.8705 (tmm) REVERT: A 683 ASP cc_start: 0.8919 (m-30) cc_final: 0.8316 (m-30) REVERT: A 687 LEU cc_start: 0.9067 (mt) cc_final: 0.8546 (tp) REVERT: A 695 LEU cc_start: 0.8829 (mt) cc_final: 0.8607 (tp) REVERT: A 699 HIS cc_start: 0.6593 (m90) cc_final: 0.6205 (m90) REVERT: A 732 ARG cc_start: 0.8688 (mtm180) cc_final: 0.8130 (ptt90) REVERT: A 737 SER cc_start: 0.8948 (m) cc_final: 0.8697 (p) REVERT: A 771 MET cc_start: 0.8943 (tmm) cc_final: 0.8680 (tmm) REVERT: A 828 ARG cc_start: 0.8593 (ttt-90) cc_final: 0.8113 (ttt90) REVERT: A 890 MET cc_start: 0.7728 (tpp) cc_final: 0.7447 (ttp) REVERT: B 60 ASP cc_start: 0.8953 (p0) cc_final: 0.8577 (t0) REVERT: B 84 ASN cc_start: 0.8536 (m-40) cc_final: 0.8306 (t0) REVERT: B 91 LYS cc_start: 0.7741 (mttt) cc_final: 0.7445 (ttmt) REVERT: B 121 VAL cc_start: 0.0995 (m) cc_final: 0.0750 (m) REVERT: a 38 PHE cc_start: 0.7808 (m-10) cc_final: 0.7047 (m-10) REVERT: a 109 MET cc_start: 0.3615 (mmt) cc_final: 0.2731 (ttt) REVERT: a 299 ASP cc_start: 0.6728 (m-30) cc_final: 0.6432 (p0) REVERT: a 372 ARG cc_start: 0.5738 (tpm170) cc_final: 0.5532 (tpm170) REVERT: a 474 CYS cc_start: 0.9251 (m) cc_final: 0.8983 (m) REVERT: a 525 TYR cc_start: 0.8047 (m-80) cc_final: 0.7104 (m-10) REVERT: a 526 TYR cc_start: 0.8078 (m-10) cc_final: 0.7761 (m-10) REVERT: a 632 SER cc_start: 0.6051 (t) cc_final: 0.5698 (t) REVERT: a 665 GLN cc_start: 0.8736 (mm110) cc_final: 0.8375 (tp40) REVERT: a 680 MET cc_start: 0.8205 (ptm) cc_final: 0.7751 (tpp) REVERT: a 687 LEU cc_start: 0.9058 (mt) cc_final: 0.8292 (tp) REVERT: a 693 SER cc_start: 0.9372 (t) cc_final: 0.8968 (p) REVERT: a 695 LEU cc_start: 0.8255 (tp) cc_final: 0.7974 (tp) REVERT: a 697 GLU cc_start: 0.7269 (tp30) cc_final: 0.6980 (mt-10) REVERT: a 699 HIS cc_start: 0.6769 (m90) cc_final: 0.6465 (m90) REVERT: a 732 ARG cc_start: 0.8807 (mtm180) cc_final: 0.8348 (mtm110) REVERT: a 771 MET cc_start: 0.9272 (tmm) cc_final: 0.8909 (tmm) REVERT: a 833 ASN cc_start: 0.8327 (m110) cc_final: 0.8001 (t0) REVERT: b 6 ARG cc_start: 0.6640 (tpt-90) cc_final: 0.6353 (ttp-170) REVERT: b 82 ASN cc_start: 0.7566 (m110) cc_final: 0.6912 (t0) REVERT: b 121 VAL cc_start: 0.1736 (m) cc_final: 0.1512 (m) REVERT: b 138 THR cc_start: 0.4257 (m) cc_final: 0.3652 (m) REVERT: b 141 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7386 (tm-30) outliers start: 2 outliers final: 0 residues processed: 488 average time/residue: 0.1375 time to fit residues: 104.6112 Evaluate side-chains 390 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 205 optimal weight: 8.9990 chunk 193 optimal weight: 0.5980 chunk 50 optimal weight: 30.0000 chunk 58 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 265 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 41 optimal weight: 20.0000 chunk 182 optimal weight: 0.0010 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 HIS e 49 GLN A 488 HIS A 665 GLN B 84 ASN ** a 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.164726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.112987 restraints weight = 110274.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.118056 restraints weight = 58205.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121011 restraints weight = 34610.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.121300 restraints weight = 27075.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.122124 restraints weight = 25800.033| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20323 Z= 0.123 Angle : 0.579 10.619 27656 Z= 0.302 Chirality : 0.043 0.258 3246 Planarity : 0.004 0.053 3641 Dihedral : 4.596 23.373 2856 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.12 % 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 (0.17), residues: 2671 helix: 0.57 (0.14), residues: 1355 sheet: -1.45 (0.38), residues: 182 loop : -0.76 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 42 TYR 0.023 0.001 TYR A 540 PHE 0.023 0.002 PHE a 459 TRP 0.012 0.002 TRP A 664 HIS 0.011 0.001 HIS a 250 Details of bonding type rmsd covalent geometry : bond 0.00254 (20323) covalent geometry : angle 0.57890 (27656) hydrogen bonds : bond 0.04387 ( 1023) hydrogen bonds : angle 5.26697 ( 2875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 477 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 ILE cc_start: 0.8077 (mm) cc_final: 0.7658 (tp) REVERT: D 22 THR cc_start: 0.8131 (p) cc_final: 0.7868 (t) REVERT: D 49 GLN cc_start: 0.6151 (mt0) cc_final: 0.5707 (mp10) REVERT: D 64 GLU cc_start: 0.7958 (mp0) cc_final: 0.7753 (mp0) REVERT: E 25 ASN cc_start: 0.9078 (m-40) cc_final: 0.8576 (m-40) REVERT: d 22 THR cc_start: 0.7905 (p) cc_final: 0.7621 (t) REVERT: e 18 GLU cc_start: 0.8425 (tp30) cc_final: 0.8170 (tp30) REVERT: C 69 LEU cc_start: 0.5671 (tt) cc_final: 0.5426 (pp) REVERT: c 69 LEU cc_start: 0.5906 (tt) cc_final: 0.5613 (pp) REVERT: A 109 MET cc_start: 0.2584 (mmt) cc_final: 0.2317 (ttt) REVERT: A 127 TYR cc_start: 0.7605 (m-80) cc_final: 0.7156 (m-80) REVERT: A 133 GLN cc_start: 0.8361 (mp-120) cc_final: 0.7785 (mp-120) REVERT: A 146 ASP cc_start: 0.9044 (m-30) cc_final: 0.8563 (p0) REVERT: A 178 LEU cc_start: 0.9357 (mt) cc_final: 0.9101 (mt) REVERT: A 471 ASP cc_start: 0.8757 (m-30) cc_final: 0.8510 (m-30) REVERT: A 474 CYS cc_start: 0.9079 (m) cc_final: 0.8850 (m) REVERT: A 536 ASN cc_start: 0.9483 (m-40) cc_final: 0.8997 (t0) REVERT: A 537 TYR cc_start: 0.8751 (t80) cc_final: 0.8357 (t80) REVERT: A 540 TYR cc_start: 0.8401 (t80) cc_final: 0.7668 (t80) REVERT: A 543 LYS cc_start: 0.7723 (ptmm) cc_final: 0.7337 (tmtt) REVERT: A 544 TYR cc_start: 0.6658 (m-80) cc_final: 0.6164 (m-80) REVERT: A 590 MET cc_start: 0.8946 (ttt) cc_final: 0.8635 (tmm) REVERT: A 683 ASP cc_start: 0.9023 (m-30) cc_final: 0.8532 (m-30) REVERT: A 687 LEU cc_start: 0.9072 (mt) cc_final: 0.8731 (tp) REVERT: A 695 LEU cc_start: 0.8752 (mt) cc_final: 0.8443 (tp) REVERT: A 697 GLU cc_start: 0.7415 (pt0) cc_final: 0.7082 (tm-30) REVERT: A 699 HIS cc_start: 0.6763 (m90) cc_final: 0.6470 (m90) REVERT: A 732 ARG cc_start: 0.8643 (mtm180) cc_final: 0.8209 (mtm110) REVERT: A 737 SER cc_start: 0.8948 (m) cc_final: 0.8667 (p) REVERT: A 747 LEU cc_start: 0.9464 (tt) cc_final: 0.9245 (tt) REVERT: A 751 TYR cc_start: 0.8443 (m-10) cc_final: 0.7859 (m-80) REVERT: A 771 MET cc_start: 0.8967 (tmm) cc_final: 0.8617 (tmm) REVERT: A 828 ARG cc_start: 0.8472 (ttt-90) cc_final: 0.7938 (ttt90) REVERT: B 60 ASP cc_start: 0.8950 (p0) cc_final: 0.8576 (t0) REVERT: B 91 LYS cc_start: 0.7829 (mttt) cc_final: 0.7605 (ttmt) REVERT: a 38 PHE cc_start: 0.7833 (m-10) cc_final: 0.7050 (m-10) REVERT: a 109 MET cc_start: 0.3627 (mmt) cc_final: 0.2776 (ttt) REVERT: a 133 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8072 (mp10) REVERT: a 146 ASP cc_start: 0.8027 (p0) cc_final: 0.7826 (p0) REVERT: a 182 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8390 (mt-10) REVERT: a 250 HIS cc_start: 0.7324 (m-70) cc_final: 0.7044 (m90) REVERT: a 299 ASP cc_start: 0.6717 (m-30) cc_final: 0.6451 (p0) REVERT: a 471 ASP cc_start: 0.8815 (m-30) cc_final: 0.8556 (m-30) REVERT: a 474 CYS cc_start: 0.9249 (m) cc_final: 0.8971 (m) REVERT: a 525 TYR cc_start: 0.8002 (m-80) cc_final: 0.7103 (m-10) REVERT: a 650 GLU cc_start: 0.8283 (pp20) cc_final: 0.7927 (pp20) REVERT: a 680 MET cc_start: 0.8378 (ptm) cc_final: 0.7947 (tpp) REVERT: a 693 SER cc_start: 0.9353 (t) cc_final: 0.8939 (p) REVERT: a 697 GLU cc_start: 0.7241 (tp30) cc_final: 0.7020 (mt-10) REVERT: a 699 HIS cc_start: 0.6565 (m90) cc_final: 0.6309 (m90) REVERT: a 732 ARG cc_start: 0.8745 (mtm180) cc_final: 0.8311 (mtm110) REVERT: a 771 MET cc_start: 0.9328 (tmm) cc_final: 0.9047 (tmm) REVERT: a 833 ASN cc_start: 0.8370 (m110) cc_final: 0.8045 (t0) REVERT: b 6 ARG cc_start: 0.6483 (tpt-90) cc_final: 0.6216 (ttp-170) REVERT: b 138 THR cc_start: 0.4166 (m) cc_final: 0.3289 (p) outliers start: 1 outliers final: 0 residues processed: 478 average time/residue: 0.1342 time to fit residues: 102.0442 Evaluate side-chains 388 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 190 optimal weight: 0.9980 chunk 195 optimal weight: 0.0670 chunk 103 optimal weight: 5.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 40 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 488 HIS ** a 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 773 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.162951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.111945 restraints weight = 96618.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116845 restraints weight = 57308.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119309 restraints weight = 33710.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119788 restraints weight = 30711.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121296 restraints weight = 26503.682| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20323 Z= 0.130 Angle : 0.573 9.698 27656 Z= 0.301 Chirality : 0.043 0.268 3246 Planarity : 0.004 0.054 3641 Dihedral : 4.515 20.181 2856 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.12 % 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: -0.11 (0.17), residues: 2671 helix: 0.73 (0.14), residues: 1351 sheet: -1.46 (0.38), residues: 182 loop : -0.72 (0.20), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 42 TYR 0.026 0.002 TYR A 285 PHE 0.024 0.002 PHE A 459 TRP 0.011 0.001 TRP A 664 HIS 0.007 0.001 HIS a 250 Details of bonding type rmsd covalent geometry : bond 0.00278 (20323) covalent geometry : angle 0.57258 (27656) hydrogen bonds : bond 0.04084 ( 1023) hydrogen bonds : angle 5.20241 ( 2875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 ILE cc_start: 0.8027 (mm) cc_final: 0.7704 (tp) REVERT: D 22 THR cc_start: 0.8205 (p) cc_final: 0.7961 (t) REVERT: D 49 GLN cc_start: 0.6173 (mt0) cc_final: 0.5622 (mp10) REVERT: E 25 ASN cc_start: 0.9041 (m-40) cc_final: 0.8696 (m110) REVERT: E 27 LYS cc_start: 0.8453 (pttt) cc_final: 0.8200 (ptmt) REVERT: F 59 TYR cc_start: 0.4557 (m-10) cc_final: 0.4334 (m-10) REVERT: d 22 THR cc_start: 0.7946 (p) cc_final: 0.7645 (t) REVERT: e 18 GLU cc_start: 0.8360 (tp30) cc_final: 0.8086 (tp30) REVERT: f 55 THR cc_start: 0.5803 (p) cc_final: 0.5602 (p) REVERT: f 59 TYR cc_start: 0.4974 (m-80) cc_final: 0.4709 (m-10) REVERT: c 69 LEU cc_start: 0.5803 (tt) cc_final: 0.5568 (pp) REVERT: A 109 MET cc_start: 0.2653 (mmt) cc_final: 0.2354 (ttt) REVERT: A 127 TYR cc_start: 0.7730 (m-80) cc_final: 0.7278 (m-80) REVERT: A 133 GLN cc_start: 0.8381 (mp-120) cc_final: 0.7814 (mp-120) REVERT: A 146 ASP cc_start: 0.9064 (m-30) cc_final: 0.8527 (p0) REVERT: A 178 LEU cc_start: 0.9344 (mt) cc_final: 0.9117 (mt) REVERT: A 182 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8301 (mt-10) REVERT: A 336 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7261 (mmmt) REVERT: A 471 ASP cc_start: 0.8795 (m-30) cc_final: 0.8526 (m-30) REVERT: A 474 CYS cc_start: 0.9096 (m) cc_final: 0.8864 (m) REVERT: A 526 TYR cc_start: 0.8384 (m-80) cc_final: 0.8081 (m-80) REVERT: A 536 ASN cc_start: 0.9390 (m-40) cc_final: 0.9037 (t0) REVERT: A 540 TYR cc_start: 0.8350 (t80) cc_final: 0.7945 (t80) REVERT: A 590 MET cc_start: 0.8980 (ttt) cc_final: 0.8640 (tmm) REVERT: A 624 ILE cc_start: 0.8588 (mm) cc_final: 0.8124 (mt) REVERT: A 683 ASP cc_start: 0.8922 (m-30) cc_final: 0.8537 (m-30) REVERT: A 687 LEU cc_start: 0.9101 (mt) cc_final: 0.8790 (tp) REVERT: A 695 LEU cc_start: 0.8782 (mt) cc_final: 0.8448 (tp) REVERT: A 699 HIS cc_start: 0.6756 (m90) cc_final: 0.6430 (m90) REVERT: A 732 ARG cc_start: 0.8692 (mtm180) cc_final: 0.8297 (mtm110) REVERT: A 742 ASP cc_start: 0.8018 (m-30) cc_final: 0.7761 (m-30) REVERT: A 751 TYR cc_start: 0.8431 (m-10) cc_final: 0.7803 (m-80) REVERT: A 768 LEU cc_start: 0.9488 (tp) cc_final: 0.9255 (tp) REVERT: A 771 MET cc_start: 0.8969 (tmm) cc_final: 0.8615 (tmm) REVERT: A 797 PHE cc_start: 0.6605 (t80) cc_final: 0.6226 (t80) REVERT: A 894 MET cc_start: 0.4600 (mpp) cc_final: 0.4259 (mpp) REVERT: B 60 ASP cc_start: 0.8992 (p0) cc_final: 0.8591 (t0) REVERT: B 82 ASN cc_start: 0.7707 (t0) cc_final: 0.7368 (t0) REVERT: B 91 LYS cc_start: 0.7868 (mttt) cc_final: 0.7658 (ttmt) REVERT: a 109 MET cc_start: 0.3668 (mmt) cc_final: 0.2736 (ttt) REVERT: a 133 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8046 (mp10) REVERT: a 178 LEU cc_start: 0.9436 (mt) cc_final: 0.9228 (mt) REVERT: a 250 HIS cc_start: 0.7376 (m-70) cc_final: 0.7038 (m90) REVERT: a 299 ASP cc_start: 0.6746 (m-30) cc_final: 0.6455 (p0) REVERT: a 471 ASP cc_start: 0.8879 (m-30) cc_final: 0.8631 (m-30) REVERT: a 474 CYS cc_start: 0.9188 (m) cc_final: 0.8904 (m) REVERT: a 525 TYR cc_start: 0.8264 (m-80) cc_final: 0.7573 (m-10) REVERT: a 526 TYR cc_start: 0.8497 (m-80) cc_final: 0.8135 (m-80) REVERT: a 536 ASN cc_start: 0.9342 (m110) cc_final: 0.8956 (t0) REVERT: a 537 TYR cc_start: 0.8865 (t80) cc_final: 0.8662 (t80) REVERT: a 650 GLU cc_start: 0.8376 (pp20) cc_final: 0.8110 (pp20) REVERT: a 652 TYR cc_start: 0.6881 (t80) cc_final: 0.6302 (t80) REVERT: a 664 TRP cc_start: 0.7933 (t60) cc_final: 0.7715 (t60) REVERT: a 665 GLN cc_start: 0.8690 (mm110) cc_final: 0.8480 (mm110) REVERT: a 680 MET cc_start: 0.8279 (ptm) cc_final: 0.7929 (tpp) REVERT: a 683 ASP cc_start: 0.8917 (m-30) cc_final: 0.8232 (m-30) REVERT: a 687 LEU cc_start: 0.9196 (mt) cc_final: 0.8695 (tp) REVERT: a 693 SER cc_start: 0.9359 (t) cc_final: 0.9050 (p) REVERT: a 695 LEU cc_start: 0.8162 (tp) cc_final: 0.7862 (tp) REVERT: a 697 GLU cc_start: 0.7255 (tp30) cc_final: 0.6991 (mt-10) REVERT: a 699 HIS cc_start: 0.6420 (m90) cc_final: 0.6061 (m90) REVERT: a 732 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8360 (mtm110) REVERT: a 768 LEU cc_start: 0.9566 (tp) cc_final: 0.9329 (tp) REVERT: a 771 MET cc_start: 0.9271 (tmm) cc_final: 0.8931 (tmm) REVERT: a 833 ASN cc_start: 0.8342 (m110) cc_final: 0.8012 (t0) REVERT: b 6 ARG cc_start: 0.6422 (tpt-90) cc_final: 0.6193 (ttp-170) REVERT: b 121 VAL cc_start: 0.2000 (m) cc_final: 0.1786 (m) REVERT: b 138 THR cc_start: 0.3603 (m) cc_final: 0.3291 (p) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.1350 time to fit residues: 98.7954 Evaluate side-chains 383 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 242 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 254 optimal weight: 8.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN A 724 GLN a 103 GLN ** a 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 394 HIS ** a 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 700 ASN a 724 GLN ** b 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.160395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111295 restraints weight = 118583.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115247 restraints weight = 66952.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.117370 restraints weight = 44411.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117199 restraints weight = 35806.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.118099 restraints weight = 32920.913| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20323 Z= 0.187 Angle : 0.635 8.454 27656 Z= 0.338 Chirality : 0.045 0.292 3246 Planarity : 0.005 0.055 3641 Dihedral : 4.887 20.010 2856 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.12 % 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: -0.41 (0.16), residues: 2671 helix: 0.45 (0.14), residues: 1358 sheet: -1.40 (0.38), residues: 168 loop : -0.89 (0.19), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 42 TYR 0.029 0.002 TYR a 652 PHE 0.035 0.002 PHE a 403 TRP 0.007 0.001 TRP A 664 HIS 0.007 0.001 HIS a 488 Details of bonding type rmsd covalent geometry : bond 0.00394 (20323) covalent geometry : angle 0.63541 (27656) hydrogen bonds : bond 0.04186 ( 1023) hydrogen bonds : angle 5.44540 ( 2875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 ILE cc_start: 0.8160 (mm) cc_final: 0.7778 (tp) REVERT: D 49 GLN cc_start: 0.6167 (mt0) cc_final: 0.5436 (mp10) REVERT: D 64 GLU cc_start: 0.8168 (mp0) cc_final: 0.7814 (mp0) REVERT: E 25 ASN cc_start: 0.9140 (m-40) cc_final: 0.8690 (m110) REVERT: E 27 LYS cc_start: 0.8340 (pttt) cc_final: 0.7852 (pttt) REVERT: F 21 ASP cc_start: 0.5635 (m-30) cc_final: 0.5246 (m-30) REVERT: F 55 THR cc_start: 0.6020 (p) cc_final: 0.5780 (p) REVERT: d 22 THR cc_start: 0.8331 (p) cc_final: 0.8003 (t) REVERT: d 54 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7734 (ttm-80) REVERT: f 59 TYR cc_start: 0.4917 (m-80) cc_final: 0.4700 (m-10) REVERT: c 69 LEU cc_start: 0.5921 (tt) cc_final: 0.5659 (pp) REVERT: A 64 PHE cc_start: 0.7613 (t80) cc_final: 0.7395 (t80) REVERT: A 127 TYR cc_start: 0.7796 (m-80) cc_final: 0.7391 (m-80) REVERT: A 129 ASP cc_start: 0.8342 (m-30) cc_final: 0.7838 (p0) REVERT: A 133 GLN cc_start: 0.8409 (mp-120) cc_final: 0.7781 (mp-120) REVERT: A 146 ASP cc_start: 0.9082 (m-30) cc_final: 0.8614 (p0) REVERT: A 178 LEU cc_start: 0.9422 (mt) cc_final: 0.9149 (mt) REVERT: A 282 MET cc_start: 0.9478 (tpt) cc_final: 0.9026 (tpp) REVERT: A 348 PHE cc_start: 0.8791 (m-80) cc_final: 0.8377 (m-10) REVERT: A 388 LEU cc_start: 0.8991 (tp) cc_final: 0.8786 (tp) REVERT: A 480 LEU cc_start: 0.9275 (pp) cc_final: 0.9055 (pp) REVERT: A 536 ASN cc_start: 0.9459 (m-40) cc_final: 0.9094 (t0) REVERT: A 540 TYR cc_start: 0.8328 (t80) cc_final: 0.7891 (t80) REVERT: A 683 ASP cc_start: 0.8803 (m-30) cc_final: 0.8456 (m-30) REVERT: A 687 LEU cc_start: 0.9078 (mt) cc_final: 0.8735 (tp) REVERT: A 695 LEU cc_start: 0.8889 (mt) cc_final: 0.8447 (tp) REVERT: A 697 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7827 (tm-30) REVERT: A 699 HIS cc_start: 0.6842 (m90) cc_final: 0.6364 (m90) REVERT: A 732 ARG cc_start: 0.8715 (mtm180) cc_final: 0.8246 (ptt90) REVERT: A 768 LEU cc_start: 0.9468 (tp) cc_final: 0.9214 (tp) REVERT: A 771 MET cc_start: 0.9024 (tmm) cc_final: 0.8593 (tmm) REVERT: A 797 PHE cc_start: 0.6605 (t80) cc_final: 0.6214 (t80) REVERT: B 60 ASP cc_start: 0.8903 (p0) cc_final: 0.8575 (t0) REVERT: B 82 ASN cc_start: 0.7924 (t0) cc_final: 0.7523 (t0) REVERT: B 91 LYS cc_start: 0.7872 (mttt) cc_final: 0.7082 (ttmm) REVERT: B 121 VAL cc_start: 0.1489 (m) cc_final: 0.1279 (m) REVERT: a 109 MET cc_start: 0.3472 (mmt) cc_final: 0.2531 (ttt) REVERT: a 133 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8170 (mp10) REVERT: a 178 LEU cc_start: 0.9453 (mt) cc_final: 0.9226 (mt) REVERT: a 250 HIS cc_start: 0.7441 (m-70) cc_final: 0.7108 (m90) REVERT: a 282 MET cc_start: 0.9412 (tpt) cc_final: 0.9046 (tpp) REVERT: a 471 ASP cc_start: 0.8916 (m-30) cc_final: 0.8624 (m-30) REVERT: a 474 CYS cc_start: 0.9192 (m) cc_final: 0.8953 (m) REVERT: a 525 TYR cc_start: 0.8350 (m-80) cc_final: 0.7501 (m-10) REVERT: a 536 ASN cc_start: 0.9439 (m110) cc_final: 0.9030 (t0) REVERT: a 564 MET cc_start: 0.9022 (tpt) cc_final: 0.8743 (tpt) REVERT: a 665 GLN cc_start: 0.8760 (mm110) cc_final: 0.8551 (mm110) REVERT: a 680 MET cc_start: 0.8201 (ptm) cc_final: 0.7952 (tpp) REVERT: a 687 LEU cc_start: 0.9147 (mt) cc_final: 0.8729 (tp) REVERT: a 693 SER cc_start: 0.9387 (t) cc_final: 0.9045 (p) REVERT: a 695 LEU cc_start: 0.8408 (tp) cc_final: 0.8006 (tp) REVERT: a 697 GLU cc_start: 0.7112 (tp30) cc_final: 0.6905 (mt-10) REVERT: a 699 HIS cc_start: 0.6354 (m90) cc_final: 0.5882 (m90) REVERT: a 721 LYS cc_start: 0.6475 (mttt) cc_final: 0.6072 (ttmt) REVERT: a 732 ARG cc_start: 0.8708 (mtm180) cc_final: 0.8320 (mtm110) REVERT: a 771 MET cc_start: 0.9206 (tmm) cc_final: 0.8801 (tmm) REVERT: a 797 PHE cc_start: 0.7003 (t80) cc_final: 0.6645 (t80) REVERT: a 833 ASN cc_start: 0.8374 (m110) cc_final: 0.7997 (t0) REVERT: b 6 ARG cc_start: 0.6458 (tpt-90) cc_final: 0.6218 (ttp-170) REVERT: b 82 ASN cc_start: 0.7567 (m110) cc_final: 0.7275 (t0) REVERT: b 121 VAL cc_start: 0.2350 (m) cc_final: 0.2150 (m) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.1299 time to fit residues: 90.5176 Evaluate side-chains 359 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 62 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 223 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 255 optimal weight: 30.0000 chunk 218 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 25 ASN A 165 HIS ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 613 ASN a 700 ASN a 937 ASN ** b 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.159743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111909 restraints weight = 101975.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113887 restraints weight = 61392.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116275 restraints weight = 42115.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116072 restraints weight = 35703.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116768 restraints weight = 31794.219| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20323 Z= 0.204 Angle : 0.651 8.730 27656 Z= 0.348 Chirality : 0.045 0.289 3246 Planarity : 0.005 0.053 3641 Dihedral : 5.015 19.890 2856 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.12 % 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: -0.55 (0.16), residues: 2671 helix: 0.38 (0.14), residues: 1352 sheet: -1.43 (0.37), residues: 179 loop : -1.00 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 6 TYR 0.021 0.002 TYR a 751 PHE 0.032 0.002 PHE a 459 TRP 0.008 0.001 TRP a 664 HIS 0.006 0.001 HIS a 576 Details of bonding type rmsd covalent geometry : bond 0.00431 (20323) covalent geometry : angle 0.65092 (27656) hydrogen bonds : bond 0.04232 ( 1023) hydrogen bonds : angle 5.53071 ( 2875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 ILE cc_start: 0.8217 (mm) cc_final: 0.7815 (tp) REVERT: D 15 LEU cc_start: 0.6333 (pp) cc_final: 0.6037 (pp) REVERT: D 49 GLN cc_start: 0.6170 (mt0) cc_final: 0.5349 (mp10) REVERT: D 64 GLU cc_start: 0.8101 (mp0) cc_final: 0.7890 (mp0) REVERT: E 25 ASN cc_start: 0.9124 (m-40) cc_final: 0.8785 (m110) REVERT: E 27 LYS cc_start: 0.8472 (pttt) cc_final: 0.8015 (pttt) REVERT: F 21 ASP cc_start: 0.5950 (m-30) cc_final: 0.5650 (m-30) REVERT: F 33 LYS cc_start: 0.3931 (pttt) cc_final: 0.3530 (pttp) REVERT: F 59 TYR cc_start: 0.4372 (m-10) cc_final: 0.4034 (m-10) REVERT: d 11 LYS cc_start: 0.8281 (mmtm) cc_final: 0.7734 (mmtm) REVERT: d 22 THR cc_start: 0.8289 (p) cc_final: 0.7931 (t) REVERT: d 54 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7667 (ttm-80) REVERT: e 25 ASN cc_start: 0.9112 (m110) cc_final: 0.8747 (m110) REVERT: f 59 TYR cc_start: 0.4564 (m-80) cc_final: 0.4236 (m-80) REVERT: c 69 LEU cc_start: 0.5883 (tt) cc_final: 0.5569 (pp) REVERT: A 133 GLN cc_start: 0.8522 (mp-120) cc_final: 0.7905 (mp-120) REVERT: A 146 ASP cc_start: 0.9041 (m-30) cc_final: 0.8483 (p0) REVERT: A 178 LEU cc_start: 0.9446 (mt) cc_final: 0.9246 (mt) REVERT: A 182 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8430 (mt-10) REVERT: A 282 MET cc_start: 0.9419 (tpt) cc_final: 0.9056 (tpp) REVERT: A 348 PHE cc_start: 0.8529 (m-80) cc_final: 0.8102 (m-80) REVERT: A 683 ASP cc_start: 0.8789 (m-30) cc_final: 0.8478 (m-30) REVERT: A 687 LEU cc_start: 0.9140 (mt) cc_final: 0.8816 (tp) REVERT: A 695 LEU cc_start: 0.8900 (mt) cc_final: 0.8494 (tp) REVERT: A 697 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7592 (tm-30) REVERT: A 699 HIS cc_start: 0.6927 (m90) cc_final: 0.6433 (m90) REVERT: A 732 ARG cc_start: 0.8733 (mtm180) cc_final: 0.8243 (ptt90) REVERT: A 737 SER cc_start: 0.9081 (m) cc_final: 0.8784 (p) REVERT: A 742 ASP cc_start: 0.7800 (m-30) cc_final: 0.7581 (m-30) REVERT: A 768 LEU cc_start: 0.9465 (tp) cc_final: 0.9255 (tp) REVERT: A 771 MET cc_start: 0.8980 (tmm) cc_final: 0.8584 (tmm) REVERT: A 797 PHE cc_start: 0.7013 (t80) cc_final: 0.6669 (t80) REVERT: B 60 ASP cc_start: 0.8902 (p0) cc_final: 0.8607 (t70) REVERT: B 91 LYS cc_start: 0.7875 (mttt) cc_final: 0.7112 (ttmm) REVERT: a 109 MET cc_start: 0.3076 (mmt) cc_final: 0.2111 (ttt) REVERT: a 127 TYR cc_start: 0.8024 (m-80) cc_final: 0.7473 (m-80) REVERT: a 133 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8176 (mp10) REVERT: a 178 LEU cc_start: 0.9447 (mt) cc_final: 0.9217 (mt) REVERT: a 250 HIS cc_start: 0.7409 (m-70) cc_final: 0.7060 (m90) REVERT: a 282 MET cc_start: 0.9428 (tpt) cc_final: 0.9059 (tpp) REVERT: a 348 PHE cc_start: 0.8549 (m-80) cc_final: 0.8206 (m-80) REVERT: a 471 ASP cc_start: 0.8892 (m-30) cc_final: 0.8583 (m-30) REVERT: a 474 CYS cc_start: 0.9206 (m) cc_final: 0.8956 (m) REVERT: a 536 ASN cc_start: 0.9494 (m110) cc_final: 0.8987 (t0) REVERT: a 680 MET cc_start: 0.8114 (ptm) cc_final: 0.7828 (tpp) REVERT: a 687 LEU cc_start: 0.9113 (mt) cc_final: 0.8679 (mt) REVERT: a 693 SER cc_start: 0.9372 (t) cc_final: 0.9054 (p) REVERT: a 695 LEU cc_start: 0.8434 (tp) cc_final: 0.7966 (tp) REVERT: a 697 GLU cc_start: 0.7189 (tp30) cc_final: 0.6959 (mt-10) REVERT: a 699 HIS cc_start: 0.6350 (m90) cc_final: 0.5863 (m90) REVERT: a 732 ARG cc_start: 0.8717 (mtm180) cc_final: 0.8355 (mtm110) REVERT: a 771 MET cc_start: 0.9102 (tmm) cc_final: 0.8716 (tmm) REVERT: a 833 ASN cc_start: 0.8336 (m110) cc_final: 0.7962 (t0) REVERT: b 6 ARG cc_start: 0.6459 (tpt-90) cc_final: 0.6253 (ttp-170) REVERT: b 121 VAL cc_start: 0.2498 (m) cc_final: 0.2294 (m) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.1320 time to fit residues: 89.9007 Evaluate side-chains 367 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 107 optimal weight: 0.5980 chunk 204 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 163 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 GLN A 700 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 660 ASN a 700 ASN ** b 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.162930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111627 restraints weight = 83193.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116095 restraints weight = 55524.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117353 restraints weight = 37318.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.117686 restraints weight = 34173.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118171 restraints weight = 31422.480| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20323 Z= 0.116 Angle : 0.572 9.774 27656 Z= 0.297 Chirality : 0.043 0.290 3246 Planarity : 0.004 0.051 3641 Dihedral : 4.597 20.281 2856 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.12 % 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: -0.11 (0.17), residues: 2671 helix: 0.80 (0.14), residues: 1364 sheet: -1.33 (0.38), residues: 175 loop : -0.87 (0.20), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 42 TYR 0.021 0.002 TYR A 537 PHE 0.025 0.001 PHE a 459 TRP 0.016 0.002 TRP a 664 HIS 0.005 0.001 HIS a 250 Details of bonding type rmsd covalent geometry : bond 0.00248 (20323) covalent geometry : angle 0.57218 (27656) hydrogen bonds : bond 0.03753 ( 1023) hydrogen bonds : angle 5.06096 ( 2875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 ILE cc_start: 0.8349 (mm) cc_final: 0.7934 (tp) REVERT: D 15 LEU cc_start: 0.6322 (pp) cc_final: 0.6050 (pp) REVERT: D 49 GLN cc_start: 0.6087 (mt0) cc_final: 0.5400 (mp10) REVERT: E 27 LYS cc_start: 0.8253 (pttt) cc_final: 0.7806 (pttt) REVERT: F 21 ASP cc_start: 0.6166 (m-30) cc_final: 0.5897 (m-30) REVERT: F 33 LYS cc_start: 0.4034 (pttt) cc_final: 0.3649 (pttp) REVERT: d 11 LYS cc_start: 0.8289 (mmtm) cc_final: 0.7911 (mmtm) REVERT: d 22 THR cc_start: 0.8089 (p) cc_final: 0.7753 (t) REVERT: d 54 ARG cc_start: 0.7821 (ttm-80) cc_final: 0.7548 (ttm-80) REVERT: e 18 GLU cc_start: 0.8206 (tp30) cc_final: 0.7962 (tp30) REVERT: e 25 ASN cc_start: 0.9079 (m110) cc_final: 0.8704 (m110) REVERT: f 59 TYR cc_start: 0.4497 (m-80) cc_final: 0.4266 (m-10) REVERT: c 69 LEU cc_start: 0.5717 (tt) cc_final: 0.5515 (pp) REVERT: A 1 MET cc_start: 0.5736 (mmm) cc_final: 0.5445 (tpp) REVERT: A 133 GLN cc_start: 0.8484 (mp-120) cc_final: 0.7989 (mp10) REVERT: A 146 ASP cc_start: 0.9008 (m-30) cc_final: 0.8436 (p0) REVERT: A 178 LEU cc_start: 0.9449 (mt) cc_final: 0.9235 (mt) REVERT: A 348 PHE cc_start: 0.8489 (m-80) cc_final: 0.8085 (m-80) REVERT: A 471 ASP cc_start: 0.8811 (m-30) cc_final: 0.8577 (m-30) REVERT: A 474 CYS cc_start: 0.9082 (m) cc_final: 0.8842 (m) REVERT: A 480 LEU cc_start: 0.9201 (pp) cc_final: 0.8985 (pp) REVERT: A 536 ASN cc_start: 0.9405 (m-40) cc_final: 0.8878 (t0) REVERT: A 543 LYS cc_start: 0.8079 (ptmm) cc_final: 0.7638 (tmtt) REVERT: A 608 GLU cc_start: 0.8019 (pp20) cc_final: 0.7817 (pp20) REVERT: A 665 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8134 (mm110) REVERT: A 687 LEU cc_start: 0.9065 (mt) cc_final: 0.8761 (tp) REVERT: A 690 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8867 (mt-10) REVERT: A 695 LEU cc_start: 0.8884 (mt) cc_final: 0.8528 (tp) REVERT: A 697 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7769 (tm-30) REVERT: A 699 HIS cc_start: 0.6864 (m90) cc_final: 0.6391 (m90) REVERT: A 732 ARG cc_start: 0.8751 (mtm180) cc_final: 0.8362 (mtm110) REVERT: A 797 PHE cc_start: 0.6955 (t80) cc_final: 0.6520 (t80) REVERT: B 60 ASP cc_start: 0.8950 (p0) cc_final: 0.8700 (t70) REVERT: B 91 LYS cc_start: 0.7792 (mttt) cc_final: 0.7060 (ttmm) REVERT: a 109 MET cc_start: 0.3027 (mmt) cc_final: 0.2524 (ttt) REVERT: a 127 TYR cc_start: 0.8027 (m-80) cc_final: 0.7529 (m-80) REVERT: a 133 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8193 (mm-40) REVERT: a 250 HIS cc_start: 0.7384 (m-70) cc_final: 0.7112 (m90) REVERT: a 282 MET cc_start: 0.9376 (tpt) cc_final: 0.9087 (tpp) REVERT: a 348 PHE cc_start: 0.8545 (m-80) cc_final: 0.8179 (m-80) REVERT: a 474 CYS cc_start: 0.9111 (m) cc_final: 0.8883 (m) REVERT: a 526 TYR cc_start: 0.8456 (m-80) cc_final: 0.8210 (m-80) REVERT: a 536 ASN cc_start: 0.9390 (m110) cc_final: 0.8970 (t0) REVERT: a 651 LEU cc_start: 0.8334 (tp) cc_final: 0.8016 (tt) REVERT: a 680 MET cc_start: 0.8316 (ptm) cc_final: 0.7827 (tpp) REVERT: a 687 LEU cc_start: 0.9098 (mt) cc_final: 0.8736 (mt) REVERT: a 693 SER cc_start: 0.9335 (t) cc_final: 0.9043 (p) REVERT: a 695 LEU cc_start: 0.8411 (tp) cc_final: 0.7998 (tp) REVERT: a 699 HIS cc_start: 0.6353 (m90) cc_final: 0.5899 (m90) REVERT: a 732 ARG cc_start: 0.8691 (mtm180) cc_final: 0.8318 (mtm110) REVERT: a 771 MET cc_start: 0.9057 (tmm) cc_final: 0.8688 (tmm) REVERT: a 833 ASN cc_start: 0.8255 (m110) cc_final: 0.8005 (t0) REVERT: b 74 ILE cc_start: 0.7924 (tp) cc_final: 0.7688 (tp) REVERT: b 82 ASN cc_start: 0.8221 (t0) cc_final: 0.8005 (t0) REVERT: b 135 TYR cc_start: 0.6962 (t80) cc_final: 0.6681 (t80) REVERT: b 138 THR cc_start: 0.3574 (m) cc_final: 0.3234 (p) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.1342 time to fit residues: 95.8182 Evaluate side-chains 374 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 209 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 700 ASN ** a 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.159601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111013 restraints weight = 105726.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113437 restraints weight = 63443.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115735 restraints weight = 42254.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115563 restraints weight = 37185.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116339 restraints weight = 32861.364| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20323 Z= 0.192 Angle : 0.652 9.843 27656 Z= 0.347 Chirality : 0.045 0.301 3246 Planarity : 0.005 0.052 3641 Dihedral : 4.915 18.625 2856 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.12 % 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: -0.52 (0.16), residues: 2671 helix: 0.44 (0.14), residues: 1367 sheet: -1.49 (0.38), residues: 169 loop : -1.05 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 42 TYR 0.027 0.002 TYR A 285 PHE 0.037 0.002 PHE A 748 TRP 0.010 0.002 TRP A 664 HIS 0.007 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00408 (20323) covalent geometry : angle 0.65155 (27656) hydrogen bonds : bond 0.04118 ( 1023) hydrogen bonds : angle 5.43805 ( 2875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 ILE cc_start: 0.8223 (mm) cc_final: 0.7715 (tp) REVERT: D 15 LEU cc_start: 0.6126 (pp) cc_final: 0.5833 (pp) REVERT: D 49 GLN cc_start: 0.5980 (mt0) cc_final: 0.5193 (mp10) REVERT: E 44 ILE cc_start: 0.8276 (mp) cc_final: 0.8068 (mp) REVERT: F 21 ASP cc_start: 0.6249 (m-30) cc_final: 0.5967 (m-30) REVERT: F 33 LYS cc_start: 0.3966 (pttt) cc_final: 0.3256 (pttp) REVERT: d 11 LYS cc_start: 0.8154 (mmtm) cc_final: 0.7780 (mmtm) REVERT: d 22 THR cc_start: 0.8257 (p) cc_final: 0.7994 (t) REVERT: d 54 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7488 (ttm-80) REVERT: f 59 TYR cc_start: 0.4220 (m-80) cc_final: 0.4001 (m-80) REVERT: c 69 LEU cc_start: 0.5680 (tt) cc_final: 0.5422 (pp) REVERT: A 70 GLN cc_start: 0.7696 (mm110) cc_final: 0.7253 (tp40) REVERT: A 133 GLN cc_start: 0.8407 (mp10) cc_final: 0.8001 (mp10) REVERT: A 146 ASP cc_start: 0.9078 (m-30) cc_final: 0.8511 (p0) REVERT: A 348 PHE cc_start: 0.8623 (m-80) cc_final: 0.8095 (m-80) REVERT: A 687 LEU cc_start: 0.9051 (mt) cc_final: 0.8802 (tp) REVERT: A 695 LEU cc_start: 0.8878 (mt) cc_final: 0.8603 (tp) REVERT: A 699 HIS cc_start: 0.6822 (m90) cc_final: 0.6245 (m90) REVERT: A 732 ARG cc_start: 0.8780 (mtm180) cc_final: 0.8244 (ptt90) REVERT: A 737 SER cc_start: 0.9115 (m) cc_final: 0.8780 (p) REVERT: A 742 ASP cc_start: 0.8025 (m-30) cc_final: 0.7814 (m-30) REVERT: A 750 ILE cc_start: 0.9394 (mt) cc_final: 0.9097 (mm) REVERT: A 797 PHE cc_start: 0.7187 (t80) cc_final: 0.6847 (t80) REVERT: B 60 ASP cc_start: 0.8925 (p0) cc_final: 0.8618 (t70) REVERT: B 91 LYS cc_start: 0.7883 (mttt) cc_final: 0.7175 (ttmm) REVERT: a 109 MET cc_start: 0.3118 (mmt) cc_final: 0.2202 (ttt) REVERT: a 127 TYR cc_start: 0.8193 (m-80) cc_final: 0.7678 (m-80) REVERT: a 133 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8145 (mp10) REVERT: a 250 HIS cc_start: 0.7488 (m-70) cc_final: 0.7144 (m90) REVERT: a 282 MET cc_start: 0.9556 (tpt) cc_final: 0.9128 (tpp) REVERT: a 348 PHE cc_start: 0.8632 (m-80) cc_final: 0.8214 (m-80) REVERT: a 471 ASP cc_start: 0.8937 (m-30) cc_final: 0.8629 (m-30) REVERT: a 474 CYS cc_start: 0.9225 (m) cc_final: 0.8982 (m) REVERT: a 526 TYR cc_start: 0.8450 (m-80) cc_final: 0.8230 (m-80) REVERT: a 536 ASN cc_start: 0.9488 (m110) cc_final: 0.9006 (t0) REVERT: a 540 TYR cc_start: 0.8775 (t80) cc_final: 0.8565 (t80) REVERT: a 675 ARG cc_start: 0.8671 (ptp-170) cc_final: 0.8280 (ptt-90) REVERT: a 680 MET cc_start: 0.8324 (ptm) cc_final: 0.7997 (tpp) REVERT: a 687 LEU cc_start: 0.9171 (mt) cc_final: 0.8746 (mt) REVERT: a 695 LEU cc_start: 0.8451 (tp) cc_final: 0.8023 (tp) REVERT: a 699 HIS cc_start: 0.6295 (m90) cc_final: 0.5859 (m90) REVERT: a 732 ARG cc_start: 0.8733 (mtm180) cc_final: 0.8327 (mtm110) REVERT: a 771 MET cc_start: 0.9161 (tmm) cc_final: 0.8821 (tmm) REVERT: a 833 ASN cc_start: 0.8273 (m110) cc_final: 0.7996 (t0) outliers start: 0 outliers final: 0 residues processed: 427 average time/residue: 0.1322 time to fit residues: 91.7703 Evaluate side-chains 367 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 63 optimal weight: 0.0970 chunk 54 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 210 optimal weight: 0.0870 chunk 127 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 249 optimal weight: 0.0670 chunk 33 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 overall best weight: 1.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 25 ASN ** a 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 700 ASN ** b 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.162682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.110486 restraints weight = 86517.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115379 restraints weight = 55854.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118513 restraints weight = 35255.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119454 restraints weight = 26834.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119776 restraints weight = 25142.035| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20323 Z= 0.119 Angle : 0.583 10.568 27656 Z= 0.303 Chirality : 0.043 0.287 3246 Planarity : 0.004 0.051 3641 Dihedral : 4.563 18.084 2856 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.05 % Allowed : 0.57 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.12 % 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: -0.19 (0.17), residues: 2671 helix: 0.74 (0.14), residues: 1378 sheet: -1.35 (0.39), residues: 169 loop : -0.94 (0.20), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 42 TYR 0.024 0.002 TYR a 537 PHE 0.024 0.001 PHE a 459 TRP 0.017 0.002 TRP a 664 HIS 0.006 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00259 (20323) covalent geometry : angle 0.58265 (27656) hydrogen bonds : bond 0.03709 ( 1023) hydrogen bonds : angle 5.06005 ( 2875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 ILE cc_start: 0.8325 (mm) cc_final: 0.7843 (tp) REVERT: D 15 LEU cc_start: 0.6346 (pp) cc_final: 0.6040 (pp) REVERT: D 49 GLN cc_start: 0.5982 (mt0) cc_final: 0.5489 (mp10) REVERT: F 21 ASP cc_start: 0.5999 (m-30) cc_final: 0.5301 (p0) REVERT: F 33 LYS cc_start: 0.4012 (pttt) cc_final: 0.3325 (pttp) REVERT: d 11 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7755 (mmtm) REVERT: d 22 THR cc_start: 0.8099 (p) cc_final: 0.7846 (t) REVERT: d 51 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8098 (tm-30) REVERT: e 25 ASN cc_start: 0.9152 (m110) cc_final: 0.8825 (m110) REVERT: f 59 TYR cc_start: 0.3916 (m-80) cc_final: 0.3701 (m-10) REVERT: A 133 GLN cc_start: 0.8378 (mp10) cc_final: 0.7864 (mp10) REVERT: A 146 ASP cc_start: 0.9054 (m-30) cc_final: 0.8299 (p0) REVERT: A 348 PHE cc_start: 0.8582 (m-80) cc_final: 0.8108 (m-80) REVERT: A 471 ASP cc_start: 0.8829 (m-30) cc_final: 0.8562 (m-30) REVERT: A 474 CYS cc_start: 0.9067 (m) cc_final: 0.8852 (m) REVERT: A 536 ASN cc_start: 0.9252 (m110) cc_final: 0.8722 (t0) REVERT: A 540 TYR cc_start: 0.8079 (t80) cc_final: 0.7771 (t80) REVERT: A 543 LYS cc_start: 0.8066 (ptmm) cc_final: 0.7595 (tmtt) REVERT: A 683 ASP cc_start: 0.9356 (m-30) cc_final: 0.9043 (m-30) REVERT: A 695 LEU cc_start: 0.8882 (mt) cc_final: 0.8617 (tp) REVERT: A 699 HIS cc_start: 0.6724 (m90) cc_final: 0.6241 (m90) REVERT: A 732 ARG cc_start: 0.8765 (mtm180) cc_final: 0.8085 (ptt-90) REVERT: A 737 SER cc_start: 0.9096 (m) cc_final: 0.8830 (p) REVERT: A 797 PHE cc_start: 0.7096 (t80) cc_final: 0.6723 (t80) REVERT: B 1 MET cc_start: -0.2433 (ttp) cc_final: -0.2910 (ttp) REVERT: B 60 ASP cc_start: 0.8988 (p0) cc_final: 0.8675 (t70) REVERT: B 91 LYS cc_start: 0.7765 (mttt) cc_final: 0.7031 (ttmm) REVERT: a 109 MET cc_start: 0.2894 (mmt) cc_final: 0.2370 (ttt) REVERT: a 127 TYR cc_start: 0.8099 (m-80) cc_final: 0.7623 (m-80) REVERT: a 133 GLN cc_start: 0.8627 (mm-40) cc_final: 0.7936 (mp10) REVERT: a 250 HIS cc_start: 0.7351 (m-70) cc_final: 0.7068 (m90) REVERT: a 282 MET cc_start: 0.9420 (tpt) cc_final: 0.9145 (tpp) REVERT: a 348 PHE cc_start: 0.8631 (m-80) cc_final: 0.8237 (m-80) REVERT: a 536 ASN cc_start: 0.9497 (m110) cc_final: 0.8820 (t0) REVERT: a 540 TYR cc_start: 0.8655 (t80) cc_final: 0.8455 (t80) REVERT: a 651 LEU cc_start: 0.7845 (tp) cc_final: 0.7536 (tt) REVERT: a 675 ARG cc_start: 0.8579 (ptp-170) cc_final: 0.8233 (ptt-90) REVERT: a 680 MET cc_start: 0.8338 (ptm) cc_final: 0.7818 (tpp) REVERT: a 687 LEU cc_start: 0.9129 (mt) cc_final: 0.8737 (mt) REVERT: a 695 LEU cc_start: 0.8279 (tp) cc_final: 0.7873 (tp) REVERT: a 697 GLU cc_start: 0.7942 (pt0) cc_final: 0.7382 (tm-30) REVERT: a 699 HIS cc_start: 0.6248 (m90) cc_final: 0.5832 (m90) REVERT: a 732 ARG cc_start: 0.8685 (mtm180) cc_final: 0.8276 (mtm110) REVERT: a 771 MET cc_start: 0.9069 (tmm) cc_final: 0.8755 (tmm) REVERT: a 833 ASN cc_start: 0.8225 (m110) cc_final: 0.8013 (t0) REVERT: b 135 TYR cc_start: 0.7005 (t80) cc_final: 0.6760 (t80) REVERT: b 138 THR cc_start: 0.3549 (m) cc_final: 0.3212 (p) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.1357 time to fit residues: 94.9438 Evaluate side-chains 368 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 248 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 245 optimal weight: 0.0770 chunk 212 optimal weight: 0.9990 chunk 260 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 193 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 68 HIS A 68 GLN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 46 GLN ** a 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 694 ASN a 700 ASN ** b 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.164106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114066 restraints weight = 123749.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118316 restraints weight = 66998.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121858 restraints weight = 40803.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.121459 restraints weight = 33506.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122308 restraints weight = 32539.886| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3605 r_free = 0.3605 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20323 Z= 0.113 Angle : 0.590 10.649 27656 Z= 0.303 Chirality : 0.043 0.307 3246 Planarity : 0.004 0.050 3641 Dihedral : 4.422 18.665 2856 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.05 % Allowed : 0.62 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.12 % 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: -0.06 (0.17), residues: 2671 helix: 0.86 (0.14), residues: 1383 sheet: -1.32 (0.39), residues: 169 loop : -0.91 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 66 TYR 0.022 0.002 TYR a 285 PHE 0.034 0.001 PHE A 748 TRP 0.033 0.003 TRP B 142 HIS 0.016 0.001 HIS a 257 Details of bonding type rmsd covalent geometry : bond 0.00244 (20323) covalent geometry : angle 0.59033 (27656) hydrogen bonds : bond 0.03660 ( 1023) hydrogen bonds : angle 4.94007 ( 2875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 ILE cc_start: 0.8317 (mm) cc_final: 0.7871 (tp) REVERT: D 15 LEU cc_start: 0.6265 (pp) cc_final: 0.5970 (pp) REVERT: D 49 GLN cc_start: 0.6054 (mt0) cc_final: 0.5469 (mp10) REVERT: F 21 ASP cc_start: 0.6283 (m-30) cc_final: 0.5565 (p0) REVERT: F 33 LYS cc_start: 0.4162 (pttt) cc_final: 0.3422 (pttp) REVERT: d 11 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7816 (mmtm) REVERT: d 22 THR cc_start: 0.8102 (p) cc_final: 0.7824 (t) REVERT: A 133 GLN cc_start: 0.8274 (mp10) cc_final: 0.7898 (mp10) REVERT: A 146 ASP cc_start: 0.9050 (m-30) cc_final: 0.8368 (p0) REVERT: A 348 PHE cc_start: 0.8679 (m-80) cc_final: 0.8246 (m-10) REVERT: A 474 CYS cc_start: 0.9019 (m) cc_final: 0.8753 (m) REVERT: A 536 ASN cc_start: 0.9009 (m110) cc_final: 0.8642 (m110) REVERT: A 540 TYR cc_start: 0.8113 (t80) cc_final: 0.7898 (t80) REVERT: A 543 LYS cc_start: 0.8153 (ptmm) cc_final: 0.7621 (tmtt) REVERT: A 590 MET cc_start: 0.8596 (tmm) cc_final: 0.8296 (tmm) REVERT: A 695 LEU cc_start: 0.8921 (mt) cc_final: 0.8511 (tp) REVERT: A 699 HIS cc_start: 0.6747 (m90) cc_final: 0.6255 (m90) REVERT: A 732 ARG cc_start: 0.8701 (mtm180) cc_final: 0.8303 (mtm110) REVERT: A 747 LEU cc_start: 0.9596 (tt) cc_final: 0.9176 (tt) REVERT: A 751 TYR cc_start: 0.8236 (m-10) cc_final: 0.7533 (m-80) REVERT: A 797 PHE cc_start: 0.7153 (t80) cc_final: 0.6819 (t80) REVERT: B 1 MET cc_start: -0.2588 (ttp) cc_final: -0.3048 (ttp) REVERT: B 60 ASP cc_start: 0.8998 (p0) cc_final: 0.8628 (t70) REVERT: B 91 LYS cc_start: 0.7807 (mttt) cc_final: 0.7065 (ttmm) REVERT: a 109 MET cc_start: 0.2710 (mmt) cc_final: 0.2208 (ttt) REVERT: a 127 TYR cc_start: 0.8053 (m-80) cc_final: 0.7695 (m-80) REVERT: a 133 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8037 (mp10) REVERT: a 250 HIS cc_start: 0.7326 (m-70) cc_final: 0.7036 (m90) REVERT: a 259 VAL cc_start: 0.8586 (p) cc_final: 0.8359 (m) REVERT: a 282 MET cc_start: 0.9411 (tpt) cc_final: 0.9134 (tpp) REVERT: a 348 PHE cc_start: 0.8543 (m-80) cc_final: 0.8214 (m-80) REVERT: a 471 ASP cc_start: 0.8800 (m-30) cc_final: 0.8599 (m-30) REVERT: a 474 CYS cc_start: 0.9051 (m) cc_final: 0.8821 (m) REVERT: a 536 ASN cc_start: 0.9368 (m110) cc_final: 0.8814 (t0) REVERT: a 540 TYR cc_start: 0.8719 (t80) cc_final: 0.8487 (t80) REVERT: a 564 MET cc_start: 0.8757 (tpt) cc_final: 0.8436 (tpt) REVERT: a 651 LEU cc_start: 0.7823 (tp) cc_final: 0.7374 (tt) REVERT: a 660 ASN cc_start: 0.8990 (m-40) cc_final: 0.8234 (p0) REVERT: a 680 MET cc_start: 0.8295 (ptm) cc_final: 0.7555 (ttp) REVERT: a 687 LEU cc_start: 0.9143 (mt) cc_final: 0.8791 (mt) REVERT: a 695 LEU cc_start: 0.8242 (tp) cc_final: 0.7813 (tp) REVERT: a 699 HIS cc_start: 0.6240 (m90) cc_final: 0.5820 (m90) REVERT: a 732 ARG cc_start: 0.8642 (mtm180) cc_final: 0.8233 (mtm110) REVERT: a 742 ASP cc_start: 0.8007 (m-30) cc_final: 0.7795 (m-30) REVERT: a 771 MET cc_start: 0.9061 (tmm) cc_final: 0.8735 (tmm) REVERT: b 1 MET cc_start: -0.0566 (ttp) cc_final: -0.1009 (ttp) REVERT: b 135 TYR cc_start: 0.6998 (t80) cc_final: 0.6761 (t80) REVERT: b 138 THR cc_start: 0.3587 (m) cc_final: 0.3295 (p) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.1298 time to fit residues: 90.5489 Evaluate side-chains 371 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 199 optimal weight: 0.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 68 HIS ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 46 GLN ** a 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 694 ASN a 700 ASN ** b 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.160052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110731 restraints weight = 84497.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114052 restraints weight = 59587.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115135 restraints weight = 38635.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115815 restraints weight = 36261.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116970 restraints weight = 32404.567| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20323 Z= 0.175 Angle : 0.639 9.118 27656 Z= 0.337 Chirality : 0.045 0.302 3246 Planarity : 0.005 0.053 3641 Dihedral : 4.695 20.373 2856 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.05 % Allowed : 0.52 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.12 % 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: -0.30 (0.16), residues: 2671 helix: 0.69 (0.14), residues: 1362 sheet: -1.42 (0.40), residues: 157 loop : -1.04 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 42 TYR 0.018 0.002 TYR a 285 PHE 0.028 0.002 PHE a 459 TRP 0.024 0.002 TRP B 142 HIS 0.005 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00374 (20323) covalent geometry : angle 0.63911 (27656) hydrogen bonds : bond 0.03808 ( 1023) hydrogen bonds : angle 5.24406 ( 2875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3980.95 seconds wall clock time: 69 minutes 22.88 seconds (4162.88 seconds total)