Starting phenix.real_space_refine on Fri Aug 7 06:28:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pzc_72061/08_2026/9pzc_72061.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pzc_72061/08_2026/9pzc_72061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pzc_72061/08_2026/9pzc_72061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pzc_72061/08_2026/9pzc_72061.map" model { file = "/net/cci-nas-00/data/ceres_data/9pzc_72061/08_2026/9pzc_72061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pzc_72061/08_2026/9pzc_72061.cif" } resolution = 3.2 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= 0.018 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 83 5.16 5 C 12269 2.51 5 N 3326 2.21 5 O 3718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19396 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5256 Classifications: {'peptide': 655} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 624} Chain breaks: 2 Chain: "B" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1819 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 210} Chain breaks: 1 Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 812 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 969 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "E" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "F" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 814 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "I" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "J" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 795 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "N" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "O" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "P" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.26, per 1000 atoms: 0.17 Number of scatterers: 19396 At special positions: 0 Unit cell: (124.08, 142.88, 175.78, 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 83 16.00 O 3718 8.00 N 3326 7.00 C 12269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS B 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 55 " " NAG A 802 " - " ASN A 700 " " NAG B 301 " - " ASN B 74 " Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 552.9 milliseconds 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4568 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 49 sheets defined 17.8% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 95 through 98 removed outlier: 3.694A pdb=" N ALA A 98 " --> pdb=" O CYS A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 99 through 107 removed outlier: 4.056A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.546A pdb=" N LEU A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.547A pdb=" N ALA A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 363 through 384 Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.603A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.703A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 442 " --> pdb=" O TRP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 474 removed outlier: 3.580A pdb=" N GLN A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'A' and resid 480 through 494 removed outlier: 3.509A pdb=" N GLU A 486 " --> pdb=" O THR A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 removed outlier: 3.695A pdb=" N HIS A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 540 through 544 removed outlier: 4.159A pdb=" N VAL A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.574A pdb=" N GLN A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 680 removed outlier: 3.609A pdb=" N VAL A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'A' and resid 707 through 710 Processing helix chain 'B' and resid 46 through 57 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.504A pdb=" N ILE B 86 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 87 " --> pdb=" O GLN B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 87' Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.614A pdb=" N THR B 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 4.211A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 3.526A pdb=" N HIS B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.637A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU C 83 " --> pdb=" O THR C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 83' Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.582A pdb=" N ARG D 64 " --> pdb=" O GLN D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.677A pdb=" N THR D 87 " --> pdb=" O TYR D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.527A pdb=" N ASN E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.649A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.579A pdb=" N ASP G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.513A pdb=" N ASP G 86 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 99 Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.606A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N SER H 65 " --> pdb=" O SER H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.834A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.518A pdb=" N THR K 87 " --> pdb=" O ALA K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.726A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.982A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.124A pdb=" N ARG A 50 " --> pdb=" O VAL A 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.948A pdb=" N GLN A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA A 75 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE B 181 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL B 191 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 193 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG B 207 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE B 195 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA B 205 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN B 197 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN B 203 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.587A pdb=" N GLN A 271 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AA5, first strand: chain 'A' and resid 195 through 197 Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 581 removed outlier: 3.501A pdb=" N ILE A 615 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 638 removed outlier: 6.787A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER A 652 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TYR A 668 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 654 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A 666 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU A 656 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 642 through 643 removed outlier: 7.101A pdb=" N ILE A 642 " --> pdb=" O SER H 100C" (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 155 Processing sheet with id=AB1, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.610A pdb=" N LEU C 11 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 84 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.610A pdb=" N LEU C 11 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 84 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.526A pdb=" N THR C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.539A pdb=" N LEU D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.491A pdb=" N VAL E 89 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU E 34 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.645A pdb=" N SER E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.850A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.979A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.348A pdb=" N GLY G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP G 36 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.348A pdb=" N GLY G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.232A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AD1, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.549A pdb=" N LEU I 33 " --> pdb=" O PHE I 49 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.561A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.520A pdb=" N ALA J 84 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU J 46 " --> pdb=" O ARG J 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.528A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER K 40 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU K 45 " --> pdb=" O SER K 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.553A pdb=" N CYS K 92 " --> pdb=" O TRP K 103 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TRP K 103 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG K 94 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.540A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.540A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR L 95A" --> pdb=" O ALA L 92 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE2, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.551A pdb=" N GLU M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.915A pdb=" N LEU M 33 " --> pdb=" O LYS M 50 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS M 50 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE M 48 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS M 50 " --> pdb=" O ASN M 53 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.887A pdb=" N SER M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.793A pdb=" N GLU N 10 " --> pdb=" O THR N 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'N' and resid 57 through 59 removed outlier: 6.528A pdb=" N TRP N 36 " --> pdb=" O MET N 48 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE N 34 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR N 33 " --> pdb=" O GLY N 95 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP N 102 " --> pdb=" O ARG N 94 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.617A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.488A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET O 34 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL O 102 " --> pdb=" O LYS O 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.488A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET O 34 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.783A pdb=" N SER P 7 " --> pdb=" O SER P 22 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER P 22 " --> pdb=" O SER P 7 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA P 19 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR P 69 " --> pdb=" O ALA P 25 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N GLN P 27 " --> pdb=" O SER P 67 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N SER P 67 " --> pdb=" O GLN P 27 " (cutoff:3.500A) removed outlier: 11.162A pdb=" N VAL P 29 " --> pdb=" O GLY P 65 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N GLY P 65 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.524A pdb=" N ALA P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA P 50 " --> pdb=" O LYS P 53 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.524A pdb=" N ALA P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) 773 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6257 1.34 - 1.46: 4818 1.46 - 1.58: 8654 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 19849 Sorted by residual: bond pdb=" N ILE A 196 " pdb=" CA ILE A 196 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.27e-02 6.20e+03 8.00e+00 bond pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.76e+00 bond pdb=" N ASN A 700 " pdb=" CA ASN A 700 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.14e-02 7.69e+03 7.60e+00 bond pdb=" N ARG A 66 " pdb=" CA ARG A 66 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.18e-02 7.18e+03 7.47e+00 bond pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.03e+00 ... (remaining 19844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 26638 2.28 - 4.57: 334 4.57 - 6.85: 27 6.85 - 9.14: 1 9.14 - 11.42: 1 Bond angle restraints: 27001 Sorted by residual: angle pdb=" CB MET O 34 " pdb=" CG MET O 34 " pdb=" SD MET O 34 " ideal model delta sigma weight residual 112.70 101.28 11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 113.90 120.67 -6.77 1.80e+00 3.09e-01 1.41e+01 angle pdb=" CA THR A 56 " pdb=" C THR A 56 " pdb=" O THR A 56 " ideal model delta sigma weight residual 121.87 118.15 3.72 1.16e+00 7.43e-01 1.03e+01 angle pdb=" CA THR A 209 " pdb=" CB THR A 209 " pdb=" OG1 THR A 209 " ideal model delta sigma weight residual 109.60 104.92 4.68 1.50e+00 4.44e-01 9.74e+00 angle pdb=" CA ASN A 85 " pdb=" C ASN A 85 " pdb=" O ASN A 85 " ideal model delta sigma weight residual 121.54 117.92 3.62 1.16e+00 7.43e-01 9.74e+00 ... (remaining 26996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10860 17.98 - 35.95: 734 35.95 - 53.93: 158 53.93 - 71.91: 33 71.91 - 89.88: 29 Dihedral angle restraints: 11814 sinusoidal: 4657 harmonic: 7157 Sorted by residual: dihedral pdb=" CB CYS A 571 " pdb=" SG CYS A 571 " pdb=" SG CYS A 624 " pdb=" CB CYS A 624 " ideal model delta sinusoidal sigma weight residual -86.00 -165.26 79.26 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS M 23 " pdb=" SG CYS M 23 " pdb=" SG CYS M 88 " pdb=" CB CYS M 88 " ideal model delta sinusoidal sigma weight residual -86.00 -164.86 78.86 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 92 " pdb=" CB CYS K 92 " ideal model delta sinusoidal sigma weight residual 93.00 49.92 43.08 1 1.00e+01 1.00e-02 2.59e+01 ... (remaining 11811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2666 0.068 - 0.136: 339 0.136 - 0.203: 27 0.203 - 0.271: 2 0.271 - 0.339: 1 Chirality restraints: 3035 Sorted by residual: chirality pdb=" CG LEU N 29 " pdb=" CB LEU N 29 " pdb=" CD1 LEU N 29 " pdb=" CD2 LEU N 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 55 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CG LEU A 434 " pdb=" CB LEU A 434 " pdb=" CD1 LEU A 434 " pdb=" CD2 LEU A 434 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3032 not shown) Planarity restraints: 3447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 66 " -0.293 9.50e-02 1.11e+02 1.31e-01 1.06e+01 pdb=" NE ARG A 66 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 66 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 66 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 66 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 228 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C ALA B 228 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA B 228 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL B 229 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " 0.029 2.00e-02 2.50e+03 2.45e-02 7.52e+00 pdb=" C7 NAG A 802 " -0.007 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " -0.007 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " -0.038 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.024 2.00e-02 2.50e+03 ... (remaining 3444 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 278 2.66 - 3.22: 17294 3.22 - 3.78: 28295 3.78 - 4.34: 41649 4.34 - 4.90: 70444 Nonbonded interactions: 157960 Sorted by model distance: nonbonded pdb=" O SER K 32 " pdb=" OH TYR K 52 " model vdw 2.098 3.040 nonbonded pdb=" OE2 GLU A 491 " pdb=" OH TYR A 519 " model vdw 2.137 3.040 nonbonded pdb=" O VAL A 256 " pdb=" NH2 ARG A 264 " model vdw 2.201 3.120 nonbonded pdb=" O GLN E 43 " pdb=" OH TYR F 87 " model vdw 2.202 3.040 nonbonded pdb=" O GLY A 328 " pdb=" ND2 ASN D 54 " model vdw 2.216 3.120 ... (remaining 157955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.190 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: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.590 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19872 Z= 0.190 Angle : 0.643 11.421 27050 Z= 0.349 Chirality : 0.047 0.339 3035 Planarity : 0.006 0.131 3444 Dihedral : 13.458 89.882 7186 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.19 % Allowed : 1.41 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2445 helix: -1.30 (0.28), residues: 277 sheet: 0.38 (0.18), residues: 826 loop : -0.10 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG P 95A TYR 0.043 0.002 TYR L 49 PHE 0.031 0.002 PHE D 33 TRP 0.010 0.001 TRP N 36 HIS 0.009 0.001 HIS N 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (19849) covalent geometry : angle 0.64213 / 0.35 (27001) SS BOND : bond 0.00241 / 0.15 ( 20) SS BOND : angle 0.81048 / 0.48 ( 40) hydrogen bonds : bond 0.21731 / 14.40 ( 721) hydrogen bonds : angle 8.51835 / 5.92 ( 1917) link_NAG-ASN : bond 0.00468 / 0.24 ( 3) link_NAG-ASN : angle 1.55464 / 0.71 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 396 time to evaluate : 0.679 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: A 82 GLN cc_start: 0.9300 (tp40) cc_final: 0.9016 (tp40) REVERT: B 64 LYS cc_start: 0.9102 (tttp) cc_final: 0.8873 (tttp) REVERT: B 118 GLN cc_start: 0.8212 (tt0) cc_final: 0.7689 (tt0) REVERT: D 112 SER cc_start: 0.7843 (t) cc_final: 0.7449 (t) REVERT: H 77 GLN cc_start: 0.9030 (mt0) cc_final: 0.8779 (mt0) REVERT: I 17 GLU cc_start: 0.8552 (tp30) cc_final: 0.8245 (tp30) REVERT: J 17 ASP cc_start: 0.8571 (m-30) cc_final: 0.8309 (m-30) REVERT: K 13 LYS cc_start: 0.9182 (mmtp) cc_final: 0.8972 (mmmt) REVERT: M 5 THR cc_start: 0.8945 (m) cc_final: 0.8733 (p) REVERT: M 83 PHE cc_start: 0.8167 (m-80) cc_final: 0.7521 (m-80) REVERT: M 89 GLN cc_start: 0.8541 (pp30) cc_final: 0.7865 (pp30) REVERT: N 10 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8460 (tp30) REVERT: N 71 ARG cc_start: 0.9004 (pmt-80) cc_final: 0.8757 (ppt170) REVERT: N 80 MET cc_start: 0.7753 (tmm) cc_final: 0.7390 (tmm) REVERT: O 72 ASP cc_start: 0.8277 (t0) cc_final: 0.7551 (t0) REVERT: O 75 LYS cc_start: 0.8987 (mttt) cc_final: 0.8724 (mtpt) REVERT: O 78 LEU cc_start: 0.8852 (tp) cc_final: 0.8086 (tp) REVERT: O 79 TYR cc_start: 0.8183 (m-80) cc_final: 0.7654 (m-80) REVERT: O 81 HIS cc_start: 0.8223 (m-70) cc_final: 0.7824 (m170) REVERT: O 101 ASP cc_start: 0.8323 (t0) cc_final: 0.7938 (m-30) REVERT: P 24 ARG cc_start: 0.9052 (ttp-110) cc_final: 0.8812 (ttm-80) REVERT: P 45 ARG cc_start: 0.9134 (ttm170) cc_final: 0.8912 (ttt180) REVERT: P 61 ARG cc_start: 0.8302 (mtp-110) cc_final: 0.7223 (ptm160) outliers start: 4 outliers final: 3 residues processed: 399 average time/residue: 0.1605 time to fit residues: 91.0512 Evaluate side-chains 319 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 316 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain P residue 82 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 GLN A 475 HIS ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN A 693 HIS C 27BASN ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN J 3 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 HIS P 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.071642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.045194 restraints weight = 55041.690| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 3.26 r_work: 0.2493 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 19872 Z= 0.325 Angle : 0.693 8.697 27050 Z= 0.361 Chirality : 0.047 0.189 3035 Planarity : 0.005 0.066 3444 Dihedral : 5.627 77.252 2811 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.22 % Allowed : 9.42 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2445 helix: 0.11 (0.31), residues: 278 sheet: 0.33 (0.18), residues: 841 loop : -0.17 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 24 TYR 0.039 0.002 TYR L 49 PHE 0.027 0.002 PHE H 78 TRP 0.013 0.002 TRP E 47 HIS 0.005 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.32 (19849) covalent geometry : angle 0.69301 / 0.36 (27001) SS BOND : bond 0.00333 / 0.20 ( 20) SS BOND : angle 0.85745 / 0.54 ( 40) hydrogen bonds : bond 0.04572 / 2.98 ( 721) hydrogen bonds : angle 6.20912 / 4.31 ( 1917) link_NAG-ASN : bond 0.00371 / 0.19 ( 3) link_NAG-ASN : angle 1.16296 / 0.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 333 time to evaluate : 0.768 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: A 82 GLN cc_start: 0.9287 (tp40) cc_final: 0.8813 (tp40) REVERT: A 120 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8880 (pp30) REVERT: B 42 LYS cc_start: 0.8379 (mtpp) cc_final: 0.8169 (mmtm) REVERT: B 64 LYS cc_start: 0.9011 (tttp) cc_final: 0.8729 (tttp) REVERT: B 118 GLN cc_start: 0.7452 (tt0) cc_final: 0.6908 (tt0) REVERT: B 135 MET cc_start: 0.9087 (ttm) cc_final: 0.8693 (mtp) REVERT: B 166 ARG cc_start: 0.9414 (mtp180) cc_final: 0.9171 (ptt90) REVERT: C 79 GLN cc_start: 0.8722 (mt0) cc_final: 0.8083 (mt0) REVERT: D 13 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8611 (mmmt) REVERT: D 48 MET cc_start: 0.9134 (mtp) cc_final: 0.8837 (mtp) REVERT: D 64 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7368 (mtm-85) REVERT: D 81 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8057 (tm-30) REVERT: E 52 ASP cc_start: 0.8554 (t0) cc_final: 0.8236 (t0) REVERT: E 83 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7473 (ttp-110) REVERT: F 17 GLU cc_start: 0.8051 (mp0) cc_final: 0.7827 (mp0) REVERT: F 79 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8465 (mp0) REVERT: F 103 LYS cc_start: 0.9018 (tptp) cc_final: 0.8752 (tptp) REVERT: G 64 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8748 (ttmt) REVERT: H 77 GLN cc_start: 0.9001 (mt0) cc_final: 0.8785 (mt0) REVERT: H 109 VAL cc_start: 0.9246 (t) cc_final: 0.8904 (m) REVERT: I 17 GLU cc_start: 0.8735 (tp30) cc_final: 0.8405 (tp30) REVERT: I 70 GLU cc_start: 0.8787 (mp0) cc_final: 0.8386 (mp0) REVERT: J 17 ASP cc_start: 0.8861 (m-30) cc_final: 0.8484 (m-30) REVERT: J 105 GLU cc_start: 0.6889 (tp30) cc_final: 0.6666 (tp30) REVERT: K 13 LYS cc_start: 0.9285 (mmtp) cc_final: 0.8471 (mmtt) REVERT: K 16 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8297 (mt-10) REVERT: L 17 GLN cc_start: 0.8657 (mt0) cc_final: 0.8224 (mt0) REVERT: L 83 GLU cc_start: 0.8592 (tp30) cc_final: 0.8385 (tp30) REVERT: M 3 GLN cc_start: 0.8514 (tp40) cc_final: 0.8232 (tm-30) REVERT: M 7 TYR cc_start: 0.8389 (m-80) cc_final: 0.8143 (m-80) REVERT: M 89 GLN cc_start: 0.8474 (pp30) cc_final: 0.7838 (pp30) REVERT: N 10 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8524 (tp30) REVERT: N 71 ARG cc_start: 0.8944 (pmt-80) cc_final: 0.8541 (ppt170) REVERT: N 79 TYR cc_start: 0.8557 (m-10) cc_final: 0.8336 (m-10) REVERT: O 30 GLU cc_start: 0.8644 (mp0) cc_final: 0.8270 (mp0) REVERT: O 68 ARG cc_start: 0.6714 (ttp80) cc_final: 0.6346 (ttp80) REVERT: O 72 ASP cc_start: 0.7377 (t0) cc_final: 0.6741 (t0) REVERT: O 75 LYS cc_start: 0.8978 (mttt) cc_final: 0.8657 (mtpt) REVERT: O 79 TYR cc_start: 0.7722 (m-80) cc_final: 0.7150 (m-80) REVERT: O 101 ASP cc_start: 0.8508 (t0) cc_final: 0.7653 (m-30) REVERT: P 45 ARG cc_start: 0.9103 (ttm170) cc_final: 0.8883 (ttt180) REVERT: P 46 LEU cc_start: 0.8321 (tp) cc_final: 0.8030 (tp) REVERT: P 53 LYS cc_start: 0.8881 (mttp) cc_final: 0.8589 (ttmm) REVERT: P 61 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7253 (ttp80) REVERT: P 70 ASP cc_start: 0.8659 (m-30) cc_final: 0.8450 (m-30) outliers start: 26 outliers final: 21 residues processed: 346 average time/residue: 0.1528 time to fit residues: 76.6741 Evaluate side-chains 318 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 297 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 82 ARG Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain P residue 49 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 176 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 142 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN M 6 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN P 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.047473 restraints weight = 54949.927| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.31 r_work: 0.2556 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19872 Z= 0.118 Angle : 0.587 8.851 27050 Z= 0.301 Chirality : 0.043 0.181 3035 Planarity : 0.004 0.062 3444 Dihedral : 5.240 82.076 2809 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.69 % Allowed : 11.02 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2445 helix: 0.78 (0.31), residues: 278 sheet: 0.45 (0.18), residues: 834 loop : -0.04 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 81 TYR 0.018 0.001 TYR L 49 PHE 0.021 0.001 PHE H 78 TRP 0.009 0.001 TRP O 100B HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (19849) covalent geometry : angle 0.58674 / 0.30 (27001) SS BOND : bond 0.00238 / 0.17 ( 20) SS BOND : angle 0.55379 / 0.34 ( 40) hydrogen bonds : bond 0.03377 / 2.20 ( 721) hydrogen bonds : angle 5.61870 / 3.90 ( 1917) link_NAG-ASN : bond 0.00080 / 0.04 ( 3) link_NAG-ASN : angle 1.00837 / 0.44 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 331 time to evaluate : 0.510 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: A 82 GLN cc_start: 0.9289 (tp40) cc_final: 0.8766 (tp40) REVERT: A 120 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8664 (pp30) REVERT: A 630 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8627 (tpp) REVERT: A 647 CYS cc_start: 0.7946 (p) cc_final: 0.7693 (p) REVERT: B 42 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8171 (mmtm) REVERT: B 64 LYS cc_start: 0.8953 (tttp) cc_final: 0.8711 (tttp) REVERT: B 135 MET cc_start: 0.8924 (ttm) cc_final: 0.8607 (mtp) REVERT: B 166 ARG cc_start: 0.9400 (mtp180) cc_final: 0.9121 (ptt90) REVERT: B 204 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8072 (mtp-110) REVERT: B 237 GLN cc_start: 0.9311 (mp10) cc_final: 0.8718 (mp10) REVERT: C 79 GLN cc_start: 0.8706 (mt0) cc_final: 0.8092 (mt0) REVERT: C 83 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8631 (mm-30) REVERT: D 13 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8466 (mmmt) REVERT: D 64 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7722 (ttm-80) REVERT: D 81 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8045 (tm-30) REVERT: E 52 ASP cc_start: 0.8487 (t0) cc_final: 0.8057 (t0) REVERT: F 17 GLU cc_start: 0.8241 (mp0) cc_final: 0.8025 (mp0) REVERT: F 103 LYS cc_start: 0.9040 (tptp) cc_final: 0.8764 (tptp) REVERT: G 75 LYS cc_start: 0.9315 (mtmm) cc_final: 0.9099 (mtmm) REVERT: H 20 LEU cc_start: 0.8179 (mt) cc_final: 0.7978 (mt) REVERT: H 72 ASP cc_start: 0.8049 (t0) cc_final: 0.7839 (t0) REVERT: H 77 GLN cc_start: 0.8845 (mt0) cc_final: 0.8604 (mt0) REVERT: H 109 VAL cc_start: 0.9267 (t) cc_final: 0.9047 (m) REVERT: I 17 GLU cc_start: 0.8593 (tp30) cc_final: 0.8293 (tp30) REVERT: I 70 GLU cc_start: 0.8823 (mp0) cc_final: 0.8341 (mp0) REVERT: J 17 ASP cc_start: 0.8842 (m-30) cc_final: 0.8473 (m-30) REVERT: K 13 LYS cc_start: 0.9280 (mmtp) cc_final: 0.8453 (mmtt) REVERT: K 16 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8381 (mt-10) REVERT: L 17 GLN cc_start: 0.8719 (mt0) cc_final: 0.8280 (mt0) REVERT: L 42 LYS cc_start: 0.9173 (mtmm) cc_final: 0.8407 (mtmm) REVERT: M 3 GLN cc_start: 0.8411 (tp40) cc_final: 0.8094 (tm-30) REVERT: M 15 VAL cc_start: 0.8818 (m) cc_final: 0.8546 (t) REVERT: M 26 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.7968 (ptp-110) REVERT: M 83 PHE cc_start: 0.8190 (m-80) cc_final: 0.7696 (m-80) REVERT: M 89 GLN cc_start: 0.8425 (pp30) cc_final: 0.7655 (pp30) REVERT: M 106 MET cc_start: 0.7867 (mmm) cc_final: 0.6838 (mmm) REVERT: N 61 GLN cc_start: 0.9265 (tp-100) cc_final: 0.9006 (pm20) REVERT: N 71 ARG cc_start: 0.8898 (pmt-80) cc_final: 0.8574 (ppt170) REVERT: N 80 MET cc_start: 0.7526 (tmm) cc_final: 0.7023 (ttp) REVERT: O 28 ASN cc_start: 0.8886 (t0) cc_final: 0.8568 (t0) REVERT: O 68 ARG cc_start: 0.6905 (ttp80) cc_final: 0.6521 (ttp80) REVERT: O 72 ASP cc_start: 0.7282 (t0) cc_final: 0.6570 (t0) REVERT: O 75 LYS cc_start: 0.9022 (mttt) cc_final: 0.8692 (mtpt) REVERT: O 79 TYR cc_start: 0.7642 (m-80) cc_final: 0.6946 (m-80) REVERT: O 101 ASP cc_start: 0.8516 (t0) cc_final: 0.7743 (m-30) REVERT: P 46 LEU cc_start: 0.8320 (tp) cc_final: 0.8048 (tp) REVERT: P 53 LYS cc_start: 0.8885 (mttp) cc_final: 0.8479 (ttmm) outliers start: 36 outliers final: 17 residues processed: 355 average time/residue: 0.1511 time to fit residues: 78.2009 Evaluate side-chains 310 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 291 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 164 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 203 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.071856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.045541 restraints weight = 55271.588| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 3.24 r_work: 0.2502 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 19872 Z= 0.269 Angle : 0.634 9.205 27050 Z= 0.326 Chirality : 0.045 0.170 3035 Planarity : 0.005 0.073 3444 Dihedral : 5.361 77.768 2808 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.20 % Allowed : 12.61 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2445 helix: 1.00 (0.32), residues: 277 sheet: 0.34 (0.18), residues: 847 loop : -0.09 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.037 0.002 TYR L 49 PHE 0.021 0.002 PHE H 78 TRP 0.013 0.001 TRP E 47 HIS 0.004 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.27 (19849) covalent geometry : angle 0.63333 / 0.33 (27001) SS BOND : bond 0.00237 / 0.14 ( 20) SS BOND : angle 0.71027 / 0.44 ( 40) hydrogen bonds : bond 0.03604 / 2.35 ( 721) hydrogen bonds : angle 5.52336 / 3.84 ( 1917) link_NAG-ASN : bond 0.00273 / 0.14 ( 3) link_NAG-ASN : angle 1.21716 / 0.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 300 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9286 (tp40) cc_final: 0.8801 (tp40) REVERT: A 120 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8588 (pp30) REVERT: A 633 THR cc_start: 0.9447 (OUTLIER) cc_final: 0.9187 (m) REVERT: B 42 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8142 (mmtm) REVERT: B 64 LYS cc_start: 0.8924 (tttp) cc_final: 0.8661 (tttp) REVERT: B 135 MET cc_start: 0.8970 (ttm) cc_final: 0.8625 (mtp) REVERT: B 166 ARG cc_start: 0.9400 (mtp180) cc_final: 0.9145 (ptt90) REVERT: B 237 GLN cc_start: 0.9356 (mp10) cc_final: 0.8754 (mp10) REVERT: C 79 GLN cc_start: 0.8752 (mt0) cc_final: 0.8140 (mt0) REVERT: C 83 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8605 (tp30) REVERT: D 13 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8523 (mmmt) REVERT: D 64 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7712 (ttm-80) REVERT: D 81 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8198 (tm-30) REVERT: E 52 ASP cc_start: 0.8636 (t0) cc_final: 0.7992 (t0) REVERT: F 17 GLU cc_start: 0.8417 (mp0) cc_final: 0.8144 (mp0) REVERT: F 103 LYS cc_start: 0.9079 (tptp) cc_final: 0.8799 (tptp) REVERT: H 72 ASP cc_start: 0.8154 (t0) cc_final: 0.7919 (t0) REVERT: I 17 GLU cc_start: 0.8670 (tp30) cc_final: 0.8363 (tp30) REVERT: J 17 ASP cc_start: 0.8935 (m-30) cc_final: 0.8546 (m-30) REVERT: J 105 GLU cc_start: 0.6982 (tp30) cc_final: 0.6680 (tp30) REVERT: K 13 LYS cc_start: 0.9275 (mmtp) cc_final: 0.8712 (mmtt) REVERT: K 101 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8717 (m-30) REVERT: L 17 GLN cc_start: 0.8731 (mt0) cc_final: 0.8195 (mt0) REVERT: M 3 GLN cc_start: 0.8435 (tp40) cc_final: 0.8075 (tm-30) REVERT: M 15 VAL cc_start: 0.8852 (m) cc_final: 0.8631 (t) REVERT: M 26 ARG cc_start: 0.8488 (mtp-110) cc_final: 0.8004 (ptp-110) REVERT: M 83 PHE cc_start: 0.8092 (m-80) cc_final: 0.7679 (m-80) REVERT: M 89 GLN cc_start: 0.8506 (pp30) cc_final: 0.7865 (pp30) REVERT: M 106 MET cc_start: 0.7335 (mmm) cc_final: 0.6943 (mmm) REVERT: N 3 GLN cc_start: 0.7561 (tp-100) cc_final: 0.6474 (mp10) REVERT: N 10 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8724 (tm-30) REVERT: N 61 GLN cc_start: 0.9299 (tp-100) cc_final: 0.9065 (pm20) REVERT: N 71 ARG cc_start: 0.8915 (pmt-80) cc_final: 0.8601 (ppt170) REVERT: N 94 ARG cc_start: 0.7292 (ttp80) cc_final: 0.6870 (ttp-170) REVERT: O 30 GLU cc_start: 0.8763 (mp0) cc_final: 0.8497 (mp0) REVERT: O 68 ARG cc_start: 0.7097 (ttp80) cc_final: 0.6272 (ttp80) REVERT: O 72 ASP cc_start: 0.7167 (t0) cc_final: 0.6485 (t0) REVERT: O 79 TYR cc_start: 0.7719 (m-80) cc_final: 0.7324 (m-10) REVERT: O 101 ASP cc_start: 0.8619 (t0) cc_final: 0.7888 (m-30) REVERT: P 42 GLN cc_start: 0.7909 (mp10) cc_final: 0.6473 (pt0) REVERT: P 45 ARG cc_start: 0.9025 (ttt180) cc_final: 0.8724 (ttt180) REVERT: P 53 LYS cc_start: 0.8913 (mttp) cc_final: 0.8536 (ttmm) outliers start: 47 outliers final: 32 residues processed: 329 average time/residue: 0.1531 time to fit residues: 73.1516 Evaluate side-chains 323 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 289 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain P residue 49 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 228 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN L 53 ASN M 6 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.073511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.047230 restraints weight = 54581.292| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.26 r_work: 0.2549 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19872 Z= 0.120 Angle : 0.578 9.474 27050 Z= 0.295 Chirality : 0.043 0.179 3035 Planarity : 0.004 0.078 3444 Dihedral : 5.201 80.632 2808 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.78 % Allowed : 13.92 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2445 helix: 1.23 (0.31), residues: 277 sheet: 0.44 (0.18), residues: 842 loop : -0.03 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 81 TYR 0.021 0.001 TYR L 49 PHE 0.019 0.001 PHE A 317 TRP 0.013 0.001 TRP K 103 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (19849) covalent geometry : angle 0.57801 / 0.30 (27001) SS BOND : bond 0.00190 / 0.12 ( 20) SS BOND : angle 0.59565 / 0.37 ( 40) hydrogen bonds : bond 0.03067 / 1.99 ( 721) hydrogen bonds : angle 5.28387 / 3.67 ( 1917) link_NAG-ASN : bond 0.00079 / 0.04 ( 3) link_NAG-ASN : angle 1.06706 / 0.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 311 time to evaluate : 0.595 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: A 57 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 82 GLN cc_start: 0.9254 (tp40) cc_final: 0.8842 (tp40) REVERT: A 120 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8650 (pp30) REVERT: A 647 CYS cc_start: 0.8248 (t) cc_final: 0.7833 (p) REVERT: B 42 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8142 (mmmt) REVERT: B 64 LYS cc_start: 0.8933 (tttp) cc_final: 0.8609 (tttp) REVERT: B 135 MET cc_start: 0.8907 (ttm) cc_final: 0.8593 (mtp) REVERT: B 166 ARG cc_start: 0.9390 (mtp180) cc_final: 0.9127 (ptt90) REVERT: B 237 GLN cc_start: 0.9359 (mp10) cc_final: 0.8743 (mp10) REVERT: C 79 GLN cc_start: 0.8770 (mt0) cc_final: 0.8161 (mt0) REVERT: C 83 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8700 (mm-30) REVERT: D 13 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8556 (mmmt) REVERT: D 64 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7647 (ttm-80) REVERT: D 81 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8322 (tm-30) REVERT: E 46 GLU cc_start: 0.8752 (tt0) cc_final: 0.8432 (tt0) REVERT: E 52 ASP cc_start: 0.8565 (t0) cc_final: 0.8116 (t0) REVERT: F 17 GLU cc_start: 0.8483 (mp0) cc_final: 0.8039 (mp0) REVERT: F 103 LYS cc_start: 0.9101 (tptp) cc_final: 0.8808 (tptp) REVERT: G 75 LYS cc_start: 0.9311 (mtmm) cc_final: 0.9111 (mtmm) REVERT: H 72 ASP cc_start: 0.8155 (t0) cc_final: 0.7946 (t0) REVERT: H 77 GLN cc_start: 0.8765 (mt0) cc_final: 0.8382 (mt0) REVERT: I 17 GLU cc_start: 0.8575 (tp30) cc_final: 0.8266 (tp30) REVERT: I 70 GLU cc_start: 0.8901 (mp0) cc_final: 0.8429 (mp0) REVERT: J 17 ASP cc_start: 0.8918 (m-30) cc_final: 0.8523 (m-30) REVERT: J 105 GLU cc_start: 0.7075 (tp30) cc_final: 0.6795 (tp30) REVERT: K 13 LYS cc_start: 0.9289 (mmtp) cc_final: 0.8726 (mmtt) REVERT: L 17 GLN cc_start: 0.8783 (mt0) cc_final: 0.8284 (mt0) REVERT: L 42 LYS cc_start: 0.9095 (mtmm) cc_final: 0.8263 (mtmm) REVERT: M 3 GLN cc_start: 0.8417 (tp40) cc_final: 0.8072 (tm-30) REVERT: M 26 ARG cc_start: 0.8424 (mtp-110) cc_final: 0.8018 (ptp-110) REVERT: M 61 ARG cc_start: 0.8301 (mtm110) cc_final: 0.7748 (mtm110) REVERT: M 79 GLN cc_start: 0.8352 (mm110) cc_final: 0.7976 (mm110) REVERT: M 83 PHE cc_start: 0.8059 (m-80) cc_final: 0.7700 (m-80) REVERT: M 89 GLN cc_start: 0.8412 (pp30) cc_final: 0.7747 (pp30) REVERT: N 3 GLN cc_start: 0.7721 (tp-100) cc_final: 0.6696 (mp10) REVERT: N 10 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8583 (mm-30) REVERT: N 12 LYS cc_start: 0.8257 (mmmm) cc_final: 0.7517 (mmmm) REVERT: N 61 GLN cc_start: 0.9279 (tp-100) cc_final: 0.9042 (pm20) REVERT: N 71 ARG cc_start: 0.8884 (pmt-80) cc_final: 0.8601 (ppt170) REVERT: N 94 ARG cc_start: 0.7275 (ttp80) cc_final: 0.6917 (ttp-170) REVERT: O 67 PHE cc_start: 0.8625 (m-10) cc_final: 0.8326 (m-10) REVERT: O 68 ARG cc_start: 0.7316 (ttp80) cc_final: 0.7114 (ttp80) REVERT: O 72 ASP cc_start: 0.7213 (t0) cc_final: 0.6401 (t0) REVERT: O 75 LYS cc_start: 0.9006 (mttt) cc_final: 0.8655 (mtmt) REVERT: O 79 TYR cc_start: 0.7750 (m-80) cc_final: 0.7046 (m-80) REVERT: O 101 ASP cc_start: 0.8612 (t0) cc_final: 0.7905 (m-30) REVERT: P 45 ARG cc_start: 0.9011 (ttt180) cc_final: 0.8685 (ttt180) REVERT: P 53 LYS cc_start: 0.8898 (mttp) cc_final: 0.8493 (ttmm) outliers start: 38 outliers final: 29 residues processed: 332 average time/residue: 0.1533 time to fit residues: 73.7199 Evaluate side-chains 321 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain P residue 49 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 217 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.071050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.044680 restraints weight = 55336.671| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 3.26 r_work: 0.2480 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 19872 Z= 0.340 Angle : 0.673 8.884 27050 Z= 0.346 Chirality : 0.046 0.196 3035 Planarity : 0.005 0.078 3444 Dihedral : 5.459 74.163 2808 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.72 % Allowed : 13.92 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2445 helix: 1.09 (0.31), residues: 277 sheet: 0.35 (0.18), residues: 845 loop : -0.14 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 54 TYR 0.043 0.002 TYR L 49 PHE 0.030 0.002 PHE A 317 TRP 0.013 0.001 TRP E 47 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.34 (19849) covalent geometry : angle 0.67237 / 0.35 (27001) SS BOND : bond 0.00277 / 0.17 ( 20) SS BOND : angle 0.80087 / 0.51 ( 40) hydrogen bonds : bond 0.03704 / 2.41 ( 721) hydrogen bonds : angle 5.35754 / 3.73 ( 1917) link_NAG-ASN : bond 0.00371 / 0.19 ( 3) link_NAG-ASN : angle 1.35614 / 0.54 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.9269 (tp40) cc_final: 0.8802 (tp40) REVERT: B 42 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8186 (mmtm) REVERT: B 64 LYS cc_start: 0.8930 (tttp) cc_final: 0.8576 (tttp) REVERT: B 135 MET cc_start: 0.8988 (ttm) cc_final: 0.8632 (mtp) REVERT: B 166 ARG cc_start: 0.9403 (mtp180) cc_final: 0.9137 (ptt90) REVERT: C 79 GLN cc_start: 0.8779 (mt0) cc_final: 0.8131 (mt0) REVERT: D 64 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7738 (ttm-80) REVERT: D 72 ASP cc_start: 0.8066 (t0) cc_final: 0.7858 (t0) REVERT: D 81 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8192 (tm-30) REVERT: E 46 GLU cc_start: 0.8750 (tt0) cc_final: 0.8393 (tt0) REVERT: E 52 ASP cc_start: 0.8697 (t0) cc_final: 0.8286 (t0) REVERT: F 17 GLU cc_start: 0.8551 (mp0) cc_final: 0.8199 (mp0) REVERT: F 60 ASP cc_start: 0.9105 (m-30) cc_final: 0.8855 (t0) REVERT: F 103 LYS cc_start: 0.9063 (tptp) cc_final: 0.8762 (tptp) REVERT: G 82 MET cc_start: 0.9350 (mtm) cc_final: 0.9066 (mtt) REVERT: G 101 ASP cc_start: 0.9268 (t0) cc_final: 0.8829 (t0) REVERT: H 72 ASP cc_start: 0.8271 (t0) cc_final: 0.7960 (t0) REVERT: H 77 GLN cc_start: 0.8865 (mt0) cc_final: 0.8528 (mt0) REVERT: I 17 GLU cc_start: 0.8637 (tp30) cc_final: 0.8359 (tp30) REVERT: J 17 ASP cc_start: 0.8954 (m-30) cc_final: 0.8498 (m-30) REVERT: K 13 LYS cc_start: 0.9285 (mmtp) cc_final: 0.8485 (mmtt) REVERT: K 16 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8167 (mt-10) REVERT: L 17 GLN cc_start: 0.8767 (mt0) cc_final: 0.8243 (mt0) REVERT: L 83 GLU cc_start: 0.8583 (tp30) cc_final: 0.8352 (tp30) REVERT: M 83 PHE cc_start: 0.8148 (m-80) cc_final: 0.7901 (m-80) REVERT: M 89 GLN cc_start: 0.8555 (pp30) cc_final: 0.7911 (pp30) REVERT: M 103 LYS cc_start: 0.7773 (tppt) cc_final: 0.7497 (tppt) REVERT: N 3 GLN cc_start: 0.7829 (tp-100) cc_final: 0.6693 (mp10) REVERT: N 10 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8705 (tp30) REVERT: N 12 LYS cc_start: 0.8350 (mmmm) cc_final: 0.7680 (mmmm) REVERT: N 43 GLN cc_start: 0.7454 (mt0) cc_final: 0.6604 (mp10) REVERT: N 61 GLN cc_start: 0.9329 (tp-100) cc_final: 0.9094 (pm20) REVERT: N 71 ARG cc_start: 0.8924 (pmt-80) cc_final: 0.8619 (ppt170) REVERT: N 80 MET cc_start: 0.7443 (tmm) cc_final: 0.7200 (ttp) REVERT: N 94 ARG cc_start: 0.7383 (ttp80) cc_final: 0.7035 (ttp-170) REVERT: O 68 ARG cc_start: 0.7485 (ttp80) cc_final: 0.6970 (ttp80) REVERT: O 72 ASP cc_start: 0.7227 (t0) cc_final: 0.6464 (t0) REVERT: O 75 LYS cc_start: 0.9009 (mttt) cc_final: 0.8621 (mtmt) REVERT: O 79 TYR cc_start: 0.7825 (m-80) cc_final: 0.7024 (m-80) REVERT: O 101 ASP cc_start: 0.8618 (t0) cc_final: 0.7891 (m-30) REVERT: P 45 ARG cc_start: 0.9021 (ttt180) cc_final: 0.8653 (ttt180) REVERT: P 53 LYS cc_start: 0.8975 (mttp) cc_final: 0.8561 (ttmm) outliers start: 58 outliers final: 42 residues processed: 333 average time/residue: 0.1477 time to fit residues: 71.1781 Evaluate side-chains 325 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 283 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain P residue 49 TYR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 204 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN L 53 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.074143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.047828 restraints weight = 54258.805| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.33 r_work: 0.2567 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19872 Z= 0.143 Angle : 0.593 9.752 27050 Z= 0.303 Chirality : 0.043 0.170 3035 Planarity : 0.004 0.077 3444 Dihedral : 5.233 77.381 2808 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.88 % Allowed : 15.42 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2445 helix: 1.32 (0.31), residues: 277 sheet: 0.49 (0.18), residues: 843 loop : -0.06 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 54 TYR 0.024 0.001 TYR L 49 PHE 0.024 0.001 PHE A 317 TRP 0.016 0.001 TRP K 103 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (19849) covalent geometry : angle 0.59236 / 0.30 (27001) SS BOND : bond 0.00191 / 0.12 ( 20) SS BOND : angle 0.61442 / 0.38 ( 40) hydrogen bonds : bond 0.03083 / 1.98 ( 721) hydrogen bonds : angle 5.13037 / 3.59 ( 1917) link_NAG-ASN : bond 0.00074 / 0.04 ( 3) link_NAG-ASN : angle 1.13059 / 0.47 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8269 (p) REVERT: A 65 LEU cc_start: 0.9035 (mt) cc_final: 0.8775 (mm) REVERT: A 82 GLN cc_start: 0.9214 (tp40) cc_final: 0.8750 (tp40) REVERT: A 120 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8796 (pp30) REVERT: B 42 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8068 (mmmt) REVERT: B 64 LYS cc_start: 0.8920 (tttp) cc_final: 0.8602 (tttp) REVERT: B 135 MET cc_start: 0.8908 (ttm) cc_final: 0.8624 (mtp) REVERT: B 166 ARG cc_start: 0.9406 (mtp180) cc_final: 0.9114 (ptt90) REVERT: B 237 GLN cc_start: 0.9338 (mp10) cc_final: 0.8707 (mp10) REVERT: C 79 GLN cc_start: 0.8633 (mt0) cc_final: 0.7983 (mt0) REVERT: C 83 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8713 (mm-30) REVERT: D 13 LYS cc_start: 0.9330 (mmtm) cc_final: 0.8955 (mmmt) REVERT: D 64 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7639 (ttm-80) REVERT: D 72 ASP cc_start: 0.7911 (t0) cc_final: 0.7648 (t0) REVERT: D 81 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8338 (tm-30) REVERT: E 52 ASP cc_start: 0.8556 (t0) cc_final: 0.8136 (t0) REVERT: F 17 GLU cc_start: 0.8489 (mp0) cc_final: 0.7963 (mp0) REVERT: F 18 ARG cc_start: 0.9089 (ttm-80) cc_final: 0.8845 (ttm-80) REVERT: F 60 ASP cc_start: 0.9111 (m-30) cc_final: 0.8826 (t0) REVERT: F 103 LYS cc_start: 0.8971 (tptp) cc_final: 0.8669 (tptp) REVERT: G 75 LYS cc_start: 0.9239 (mtmm) cc_final: 0.8924 (mtmm) REVERT: G 101 ASP cc_start: 0.9210 (t0) cc_final: 0.8781 (t0) REVERT: H 72 ASP cc_start: 0.8201 (t0) cc_final: 0.7918 (t0) REVERT: H 77 GLN cc_start: 0.8692 (mt0) cc_final: 0.8434 (mt0) REVERT: H 105 GLN cc_start: 0.7961 (pm20) cc_final: 0.7649 (pm20) REVERT: I 17 GLU cc_start: 0.8549 (tp30) cc_final: 0.8227 (tp30) REVERT: J 17 ASP cc_start: 0.8883 (m-30) cc_final: 0.8446 (m-30) REVERT: J 79 GLN cc_start: 0.8562 (mm110) cc_final: 0.8359 (mm110) REVERT: J 105 GLU cc_start: 0.7065 (tp30) cc_final: 0.6783 (tp30) REVERT: K 13 LYS cc_start: 0.9232 (mmtp) cc_final: 0.8469 (mmtt) REVERT: K 16 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8171 (mt-10) REVERT: L 17 GLN cc_start: 0.8741 (mt0) cc_final: 0.8222 (mt0) REVERT: L 42 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8117 (mtmm) REVERT: M 3 GLN cc_start: 0.8392 (tp40) cc_final: 0.8033 (tm-30) REVERT: M 61 ARG cc_start: 0.8201 (mtm110) cc_final: 0.7612 (mtm110) REVERT: M 79 GLN cc_start: 0.8183 (mm110) cc_final: 0.7838 (mm-40) REVERT: M 89 GLN cc_start: 0.8434 (pp30) cc_final: 0.7755 (pp30) REVERT: M 103 LYS cc_start: 0.7684 (tppt) cc_final: 0.7460 (tppt) REVERT: N 3 GLN cc_start: 0.7710 (tp-100) cc_final: 0.6650 (mp10) REVERT: N 10 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8596 (mm-30) REVERT: N 12 LYS cc_start: 0.8369 (mmmm) cc_final: 0.7670 (mmmm) REVERT: N 43 GLN cc_start: 0.7322 (mt0) cc_final: 0.6522 (mp10) REVERT: N 61 GLN cc_start: 0.9306 (tp-100) cc_final: 0.9027 (pm20) REVERT: N 71 ARG cc_start: 0.8820 (pmt-80) cc_final: 0.8430 (ppt170) REVERT: N 79 TYR cc_start: 0.8654 (m-80) cc_final: 0.8270 (m-80) REVERT: N 80 MET cc_start: 0.7381 (tmm) cc_final: 0.7111 (ttp) REVERT: N 94 ARG cc_start: 0.7104 (ttp80) cc_final: 0.6526 (ttp80) REVERT: O 67 PHE cc_start: 0.8556 (m-10) cc_final: 0.8293 (m-10) REVERT: O 68 ARG cc_start: 0.7325 (ttp80) cc_final: 0.7001 (ttp80) REVERT: O 72 ASP cc_start: 0.7048 (t0) cc_final: 0.6311 (t0) REVERT: O 75 LYS cc_start: 0.8973 (mttt) cc_final: 0.8588 (mtmt) REVERT: O 79 TYR cc_start: 0.7703 (m-80) cc_final: 0.7059 (m-80) REVERT: O 101 ASP cc_start: 0.8588 (t0) cc_final: 0.7813 (m-30) REVERT: P 45 ARG cc_start: 0.9024 (ttt180) cc_final: 0.8676 (ttt180) REVERT: P 53 LYS cc_start: 0.8923 (mttp) cc_final: 0.8505 (ttmm) outliers start: 40 outliers final: 34 residues processed: 331 average time/residue: 0.1383 time to fit residues: 66.3424 Evaluate side-chains 326 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 291 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 104 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 63 optimal weight: 0.0770 chunk 157 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.047861 restraints weight = 54489.577| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.34 r_work: 0.2569 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 19872 Z= 0.154 Angle : 0.606 9.766 27050 Z= 0.306 Chirality : 0.043 0.188 3035 Planarity : 0.004 0.081 3444 Dihedral : 5.123 76.777 2808 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.06 % Allowed : 15.19 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2445 helix: 1.40 (0.32), residues: 277 sheet: 0.49 (0.18), residues: 856 loop : 0.01 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 83 TYR 0.023 0.001 TYR L 49 PHE 0.026 0.001 PHE A 317 TRP 0.012 0.001 TRP K 103 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (19849) covalent geometry : angle 0.60583 / 0.31 (27001) SS BOND : bond 0.00209 / 0.14 ( 20) SS BOND : angle 0.63922 / 0.40 ( 40) hydrogen bonds : bond 0.03072 / 1.97 ( 721) hydrogen bonds : angle 5.03707 / 3.53 ( 1917) link_NAG-ASN : bond 0.00089 / 0.05 ( 3) link_NAG-ASN : angle 1.15532 / 0.48 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 299 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8252 (p) REVERT: A 65 LEU cc_start: 0.9069 (mt) cc_final: 0.8814 (mm) REVERT: A 82 GLN cc_start: 0.9175 (tp40) cc_final: 0.8683 (tp40) REVERT: A 120 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8605 (pp30) REVERT: A 434 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8992 (mp) REVERT: B 42 LYS cc_start: 0.8430 (mtpp) cc_final: 0.8058 (mmtm) REVERT: B 64 LYS cc_start: 0.8926 (tttp) cc_final: 0.8609 (tttp) REVERT: B 135 MET cc_start: 0.8898 (ttm) cc_final: 0.8577 (mtp) REVERT: B 166 ARG cc_start: 0.9402 (mtp180) cc_final: 0.9076 (ptt90) REVERT: B 237 GLN cc_start: 0.9345 (mp10) cc_final: 0.8709 (mp10) REVERT: C 79 GLN cc_start: 0.8660 (mt0) cc_final: 0.7999 (mt0) REVERT: C 83 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8703 (mm-30) REVERT: D 64 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7660 (ttm-80) REVERT: D 72 ASP cc_start: 0.7919 (t0) cc_final: 0.7643 (t0) REVERT: D 81 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8324 (tm-30) REVERT: E 52 ASP cc_start: 0.8558 (t0) cc_final: 0.7857 (t0) REVERT: F 17 GLU cc_start: 0.8530 (mp0) cc_final: 0.7985 (mp0) REVERT: F 18 ARG cc_start: 0.9106 (ttm-80) cc_final: 0.8893 (ttm-80) REVERT: F 60 ASP cc_start: 0.8999 (m-30) cc_final: 0.8762 (t0) REVERT: F 103 LYS cc_start: 0.8976 (tptp) cc_final: 0.8675 (tptp) REVERT: G 75 LYS cc_start: 0.9273 (mtmm) cc_final: 0.8953 (mtmm) REVERT: G 101 ASP cc_start: 0.9210 (t0) cc_final: 0.8781 (t0) REVERT: H 72 ASP cc_start: 0.8192 (t0) cc_final: 0.7944 (t0) REVERT: H 77 GLN cc_start: 0.8694 (mt0) cc_final: 0.8421 (mt0) REVERT: H 105 GLN cc_start: 0.7914 (pm20) cc_final: 0.7647 (pm20) REVERT: I 70 GLU cc_start: 0.8957 (mp0) cc_final: 0.8540 (mp0) REVERT: J 17 ASP cc_start: 0.8900 (m-30) cc_final: 0.8480 (m-30) REVERT: J 79 GLN cc_start: 0.8559 (mm110) cc_final: 0.8348 (mm110) REVERT: J 105 GLU cc_start: 0.7058 (tp30) cc_final: 0.6772 (tp30) REVERT: K 13 LYS cc_start: 0.9241 (mmtp) cc_final: 0.8467 (mmtt) REVERT: K 16 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8187 (mt-10) REVERT: L 17 GLN cc_start: 0.8765 (mt0) cc_final: 0.8206 (mt0) REVERT: L 42 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8049 (mtmm) REVERT: M 3 GLN cc_start: 0.8265 (tp40) cc_final: 0.7972 (tm-30) REVERT: M 61 ARG cc_start: 0.8245 (mtm110) cc_final: 0.7706 (mtm110) REVERT: M 83 PHE cc_start: 0.8010 (m-80) cc_final: 0.7685 (m-80) REVERT: M 89 GLN cc_start: 0.8432 (pp30) cc_final: 0.7695 (pp30) REVERT: M 103 LYS cc_start: 0.7735 (tppt) cc_final: 0.7524 (tppt) REVERT: N 3 GLN cc_start: 0.7724 (tp-100) cc_final: 0.6690 (mp10) REVERT: N 10 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8580 (mm-30) REVERT: N 12 LYS cc_start: 0.8465 (mmmm) cc_final: 0.7885 (mmmm) REVERT: N 43 GLN cc_start: 0.7508 (mt0) cc_final: 0.6744 (mp10) REVERT: N 61 GLN cc_start: 0.9291 (tp-100) cc_final: 0.9021 (pm20) REVERT: N 71 ARG cc_start: 0.8820 (pmt-80) cc_final: 0.8454 (ppt170) REVERT: N 80 MET cc_start: 0.7364 (tmm) cc_final: 0.7121 (ttp) REVERT: O 13 ARG cc_start: 0.8539 (mmp-170) cc_final: 0.8063 (ttm-80) REVERT: O 30 GLU cc_start: 0.8509 (mp0) cc_final: 0.8043 (mp0) REVERT: O 68 ARG cc_start: 0.7435 (ttp80) cc_final: 0.7083 (ttp80) REVERT: O 72 ASP cc_start: 0.7068 (t0) cc_final: 0.6363 (t0) REVERT: O 75 LYS cc_start: 0.8969 (mttt) cc_final: 0.8595 (mtmt) REVERT: O 79 TYR cc_start: 0.7714 (m-80) cc_final: 0.7004 (m-80) REVERT: O 101 ASP cc_start: 0.8587 (t0) cc_final: 0.7839 (m-30) REVERT: P 45 ARG cc_start: 0.9022 (ttt180) cc_final: 0.8690 (ttt180) REVERT: P 53 LYS cc_start: 0.8869 (mttp) cc_final: 0.8439 (ttmm) outliers start: 44 outliers final: 33 residues processed: 329 average time/residue: 0.1551 time to fit residues: 73.4844 Evaluate side-chains 324 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 289 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 188 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 208 optimal weight: 20.0000 chunk 220 optimal weight: 0.0670 chunk 70 optimal weight: 8.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.073741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.047383 restraints weight = 54390.564| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.34 r_work: 0.2550 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19872 Z= 0.188 Angle : 0.622 10.668 27050 Z= 0.315 Chirality : 0.044 0.171 3035 Planarity : 0.004 0.079 3444 Dihedral : 5.120 74.679 2808 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.92 % Allowed : 15.28 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2445 helix: 1.38 (0.32), residues: 277 sheet: 0.49 (0.18), residues: 853 loop : 0.01 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 83 TYR 0.028 0.001 TYR L 49 PHE 0.025 0.001 PHE A 317 TRP 0.014 0.001 TRP E 47 HIS 0.003 0.001 HIS H 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (19849) covalent geometry : angle 0.62125 / 0.31 (27001) SS BOND : bond 0.00201 / 0.13 ( 20) SS BOND : angle 0.66477 / 0.41 ( 40) hydrogen bonds : bond 0.03155 / 2.03 ( 721) hydrogen bonds : angle 5.02093 / 3.52 ( 1917) link_NAG-ASN : bond 0.00157 / 0.08 ( 3) link_NAG-ASN : angle 1.21302 / 0.50 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 292 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8243 (p) REVERT: A 65 LEU cc_start: 0.9080 (mt) cc_final: 0.8831 (mm) REVERT: A 82 GLN cc_start: 0.9176 (tp40) cc_final: 0.8677 (tp40) REVERT: A 120 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8612 (pp30) REVERT: B 64 LYS cc_start: 0.8901 (tttp) cc_final: 0.8570 (tttp) REVERT: B 135 MET cc_start: 0.8924 (ttm) cc_final: 0.8630 (mtp) REVERT: B 166 ARG cc_start: 0.9402 (mtp180) cc_final: 0.9076 (ptt90) REVERT: B 237 GLN cc_start: 0.9353 (mp10) cc_final: 0.8719 (mp10) REVERT: C 79 GLN cc_start: 0.8663 (mt0) cc_final: 0.7995 (mt0) REVERT: C 83 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8713 (mm-30) REVERT: D 64 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7663 (ttm-80) REVERT: D 72 ASP cc_start: 0.7979 (t0) cc_final: 0.7693 (t0) REVERT: D 81 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8353 (tm-30) REVERT: E 52 ASP cc_start: 0.8575 (t0) cc_final: 0.7887 (t0) REVERT: F 17 GLU cc_start: 0.8502 (mp0) cc_final: 0.7980 (mp0) REVERT: F 42 GLN cc_start: 0.8314 (mp10) cc_final: 0.7916 (mp10) REVERT: F 60 ASP cc_start: 0.8996 (m-30) cc_final: 0.8759 (t0) REVERT: F 103 LYS cc_start: 0.8976 (tptp) cc_final: 0.8677 (tptp) REVERT: G 75 LYS cc_start: 0.9290 (mtmm) cc_final: 0.8955 (mtmm) REVERT: G 101 ASP cc_start: 0.9235 (t0) cc_final: 0.8804 (t0) REVERT: H 72 ASP cc_start: 0.8222 (t0) cc_final: 0.7956 (t0) REVERT: H 77 GLN cc_start: 0.8685 (mt0) cc_final: 0.8435 (mt0) REVERT: H 105 GLN cc_start: 0.8030 (pm20) cc_final: 0.7804 (pm20) REVERT: I 17 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7985 (mp0) REVERT: J 17 ASP cc_start: 0.8919 (m-30) cc_final: 0.8497 (m-30) REVERT: J 79 GLN cc_start: 0.8560 (mm110) cc_final: 0.8348 (mm110) REVERT: J 105 GLU cc_start: 0.7073 (tp30) cc_final: 0.6785 (tp30) REVERT: K 13 LYS cc_start: 0.9216 (mmtp) cc_final: 0.8435 (mmtt) REVERT: K 16 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8126 (mt-10) REVERT: L 17 GLN cc_start: 0.8770 (mt0) cc_final: 0.8168 (mt0) REVERT: L 42 LYS cc_start: 0.8870 (mtmm) cc_final: 0.8117 (mtmm) REVERT: M 3 GLN cc_start: 0.8380 (tp40) cc_final: 0.8061 (tm-30) REVERT: M 61 ARG cc_start: 0.8242 (mtm110) cc_final: 0.7660 (mtm110) REVERT: M 79 GLN cc_start: 0.8262 (mm110) cc_final: 0.7971 (mm-40) REVERT: M 89 GLN cc_start: 0.8420 (pp30) cc_final: 0.7661 (pp30) REVERT: M 103 LYS cc_start: 0.7748 (tppt) cc_final: 0.7544 (tppt) REVERT: N 3 GLN cc_start: 0.7632 (tp-100) cc_final: 0.6540 (mp10) REVERT: N 10 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8589 (mm-30) REVERT: N 12 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8022 (mmmm) REVERT: N 43 GLN cc_start: 0.7615 (mt0) cc_final: 0.6862 (mp10) REVERT: N 61 GLN cc_start: 0.9313 (tp-100) cc_final: 0.9050 (pm20) REVERT: N 71 ARG cc_start: 0.8796 (pmt-80) cc_final: 0.8433 (ppt170) REVERT: N 80 MET cc_start: 0.7264 (tmm) cc_final: 0.7061 (ttp) REVERT: O 13 ARG cc_start: 0.8534 (mmp-170) cc_final: 0.8087 (ttm-80) REVERT: O 16 ARG cc_start: 0.8305 (mpp-170) cc_final: 0.8012 (mpp-170) REVERT: O 30 GLU cc_start: 0.8502 (mp0) cc_final: 0.8052 (mp0) REVERT: O 68 ARG cc_start: 0.7485 (ttp80) cc_final: 0.7006 (ttp80) REVERT: O 72 ASP cc_start: 0.7098 (t0) cc_final: 0.6408 (t0) REVERT: O 75 LYS cc_start: 0.8967 (mttt) cc_final: 0.8589 (mtmt) REVERT: O 79 TYR cc_start: 0.7735 (m-80) cc_final: 0.6980 (m-80) REVERT: O 101 ASP cc_start: 0.8616 (t0) cc_final: 0.7870 (m-30) REVERT: P 11 LEU cc_start: 0.6517 (mp) cc_final: 0.6248 (pp) REVERT: P 45 ARG cc_start: 0.9037 (ttt180) cc_final: 0.8702 (ttt180) REVERT: P 53 LYS cc_start: 0.8890 (mttp) cc_final: 0.8447 (ttmm) outliers start: 41 outliers final: 33 residues processed: 319 average time/residue: 0.1525 time to fit residues: 70.5908 Evaluate side-chains 322 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 288 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 79 ARG Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 139 optimal weight: 0.2980 chunk 107 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 99 optimal weight: 0.0980 chunk 188 optimal weight: 5.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 HIS ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 HIS ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.075597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.049439 restraints weight = 54144.630| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.33 r_work: 0.2612 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19872 Z= 0.105 Angle : 0.602 11.852 27050 Z= 0.301 Chirality : 0.042 0.217 3035 Planarity : 0.004 0.080 3444 Dihedral : 4.909 78.241 2808 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.41 % Allowed : 15.99 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.17), residues: 2445 helix: 1.48 (0.31), residues: 277 sheet: 0.63 (0.18), residues: 858 loop : 0.06 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 83 TYR 0.018 0.001 TYR F 49 PHE 0.019 0.001 PHE A 317 TRP 0.014 0.001 TRP K 103 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 (19849) covalent geometry : angle 0.60173 / 0.30 (27001) SS BOND : bond 0.00215 / 0.14 ( 20) SS BOND : angle 0.60795 / 0.37 ( 40) hydrogen bonds : bond 0.02771 / 1.76 ( 721) hydrogen bonds : angle 4.86478 / 3.41 ( 1917) link_NAG-ASN : bond 0.00152 / 0.08 ( 3) link_NAG-ASN : angle 1.05993 / 0.47 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 308 time to evaluate : 0.584 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: A 65 LEU cc_start: 0.9111 (mt) cc_final: 0.8898 (mm) REVERT: A 82 GLN cc_start: 0.9148 (tp40) cc_final: 0.8689 (tp40) REVERT: A 117 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8528 (ttp80) REVERT: A 120 GLN cc_start: 0.9015 (tm-30) cc_final: 0.8631 (pp30) REVERT: A 630 MET cc_start: 0.8773 (tpp) cc_final: 0.8564 (tpp) REVERT: B 42 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8298 (mmmt) REVERT: B 64 LYS cc_start: 0.8930 (tttp) cc_final: 0.8596 (tttp) REVERT: B 118 GLN cc_start: 0.7366 (tt0) cc_final: 0.6992 (mm110) REVERT: B 135 MET cc_start: 0.8882 (ttm) cc_final: 0.8586 (mtp) REVERT: B 166 ARG cc_start: 0.9376 (mtp180) cc_final: 0.9070 (ptt90) REVERT: B 237 GLN cc_start: 0.9360 (mp10) cc_final: 0.8722 (mp10) REVERT: C 79 GLN cc_start: 0.8698 (mt0) cc_final: 0.8041 (mt0) REVERT: C 83 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8695 (mm-30) REVERT: D 64 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7725 (ttm-80) REVERT: D 72 ASP cc_start: 0.7868 (t0) cc_final: 0.7592 (t0) REVERT: D 81 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8362 (tm-30) REVERT: E 52 ASP cc_start: 0.8515 (t0) cc_final: 0.7768 (t0) REVERT: F 17 GLU cc_start: 0.8507 (mp0) cc_final: 0.7934 (mp0) REVERT: F 60 ASP cc_start: 0.8954 (m-30) cc_final: 0.8719 (t0) REVERT: F 77 ARG cc_start: 0.8780 (tpp80) cc_final: 0.8324 (tpp80) REVERT: F 79 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7957 (mm-30) REVERT: F 103 LYS cc_start: 0.8987 (tptp) cc_final: 0.8674 (tptp) REVERT: G 32 TYR cc_start: 0.9368 (m-80) cc_final: 0.8878 (m-80) REVERT: H 77 GLN cc_start: 0.8570 (mt0) cc_final: 0.8339 (mt0) REVERT: H 105 GLN cc_start: 0.7952 (pm20) cc_final: 0.7680 (pm20) REVERT: I 70 GLU cc_start: 0.8966 (mp0) cc_final: 0.8523 (mp0) REVERT: J 17 ASP cc_start: 0.8886 (m-30) cc_final: 0.8474 (m-30) REVERT: J 79 GLN cc_start: 0.8583 (mm110) cc_final: 0.8343 (mm110) REVERT: J 105 GLU cc_start: 0.7060 (tp30) cc_final: 0.6752 (tp30) REVERT: K 13 LYS cc_start: 0.9240 (mmtp) cc_final: 0.8474 (mmtt) REVERT: K 16 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8228 (mt-10) REVERT: K 105 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8278 (pm20) REVERT: L 17 GLN cc_start: 0.8776 (mt0) cc_final: 0.8215 (mt0) REVERT: L 42 LYS cc_start: 0.8895 (mtmm) cc_final: 0.8202 (mtmm) REVERT: M 3 GLN cc_start: 0.8238 (tp40) cc_final: 0.7951 (tm-30) REVERT: M 61 ARG cc_start: 0.8207 (mtm110) cc_final: 0.7632 (mtm110) REVERT: M 79 GLN cc_start: 0.8278 (mm110) cc_final: 0.7900 (mm-40) REVERT: M 89 GLN cc_start: 0.8330 (pp30) cc_final: 0.7592 (pp30) REVERT: N 3 GLN cc_start: 0.7553 (tp-100) cc_final: 0.6573 (mp10) REVERT: N 10 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8612 (mm-30) REVERT: N 12 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8115 (mmmm) REVERT: N 23 LYS cc_start: 0.8866 (mmmt) cc_final: 0.8167 (tppt) REVERT: N 43 GLN cc_start: 0.7736 (mt0) cc_final: 0.6957 (mp10) REVERT: N 61 GLN cc_start: 0.9260 (tp-100) cc_final: 0.9024 (pm20) REVERT: N 71 ARG cc_start: 0.8776 (pmt-80) cc_final: 0.8442 (ppt170) REVERT: N 79 TYR cc_start: 0.8666 (m-80) cc_final: 0.8439 (m-80) REVERT: N 80 MET cc_start: 0.7328 (tmm) cc_final: 0.7104 (ttp) REVERT: O 13 ARG cc_start: 0.8493 (mmp-170) cc_final: 0.8078 (ttm-80) REVERT: O 30 GLU cc_start: 0.8568 (mp0) cc_final: 0.8116 (mp0) REVERT: O 68 ARG cc_start: 0.7551 (ttp80) cc_final: 0.7217 (ttp80) REVERT: O 72 ASP cc_start: 0.7077 (t0) cc_final: 0.6563 (t0) REVERT: O 75 LYS cc_start: 0.8975 (mttt) cc_final: 0.8680 (mtpt) REVERT: O 79 TYR cc_start: 0.7776 (m-80) cc_final: 0.7389 (m-10) REVERT: O 101 ASP cc_start: 0.8577 (t0) cc_final: 0.7826 (m-30) REVERT: P 11 LEU cc_start: 0.6580 (mp) cc_final: 0.6357 (pp) REVERT: P 31 ASP cc_start: 0.8463 (t0) cc_final: 0.8158 (m-30) REVERT: P 45 ARG cc_start: 0.9047 (ttt180) cc_final: 0.8698 (ttt180) REVERT: P 53 LYS cc_start: 0.8821 (mttp) cc_final: 0.8340 (ttmm) outliers start: 30 outliers final: 25 residues processed: 326 average time/residue: 0.1490 time to fit residues: 69.8686 Evaluate side-chains 317 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 291 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 79 ARG Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 239 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 3 GLN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.073905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.047554 restraints weight = 54422.604| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.32 r_work: 0.2558 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19872 Z= 0.198 Angle : 0.632 11.744 27050 Z= 0.318 Chirality : 0.044 0.171 3035 Planarity : 0.005 0.081 3444 Dihedral : 5.003 74.407 2808 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.41 % Allowed : 16.17 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.17), residues: 2445 helix: 1.46 (0.31), residues: 277 sheet: 0.61 (0.18), residues: 849 loop : 0.08 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 83 TYR 0.029 0.001 TYR L 49 PHE 0.020 0.001 PHE A 317 TRP 0.010 0.001 TRP O 100B HIS 0.004 0.001 HIS A 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (19849) covalent geometry : angle 0.63150 / 0.32 (27001) SS BOND : bond 0.00213 / 0.13 ( 20) SS BOND : angle 0.68112 / 0.42 ( 40) hydrogen bonds : bond 0.03160 / 2.04 ( 721) hydrogen bonds : angle 4.92631 / 3.46 ( 1917) link_NAG-ASN : bond 0.00146 / 0.08 ( 3) link_NAG-ASN : angle 1.20186 / 0.50 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4088.95 seconds wall clock time: 70 minutes 48.82 seconds (4248.82 seconds total)