Starting phenix.real_space_refine on Fri Aug 7 06:31:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pzb_72060/08_2026/9pzb_72060.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pzb_72060/08_2026/9pzb_72060.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 { model { file = "/net/cci-nas-00/data/ceres_data/9pzb_72060/08_2026/9pzb_72060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pzb_72060/08_2026/9pzb_72060.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pzb_72060/08_2026/9pzb_72060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pzb_72060/08_2026/9pzb_72060.map" } 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= 0.001 sd= 0.019 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 92 5.16 5 C 12289 2.51 5 N 3311 2.21 5 O 3727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s 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: 19419 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5179 Classifications: {'peptide': 645} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 612} Chain breaks: 3 Chain: "B" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1891 Classifications: {'peptide': 240} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 219} Chain breaks: 1 Chain: "D" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 937 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "G" 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': 4, 'TRANS': 100} Chain: "H" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 880 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "J" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "K" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 862 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 799 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "M" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 898 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "N" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 904 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "O" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "P" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 116} Chain: "Q" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.09, per 1000 atoms: 0.21 Number of scatterers: 19419 At special positions: 0 Unit cell: (108.1, 133.48, 152.28, 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 92 16.00 O 3727 8.00 N 3311 7.00 C 12289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, 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 A 647 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 149 " - pdb=" SG CYS I 220 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 21 " - pdb=" SG CYS Q 86 " distance=2.03 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 67 " " NAG A 802 " - " ASN A 55 " " NAG A 803 " - " ASN A 62 " Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 826.3 milliseconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4574 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 45 sheets defined 18.6% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 93 through 98 removed outlier: 3.555A pdb=" N LEU A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A 97 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 107 removed outlier: 4.025A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.627A pdb=" N LEU A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 266 removed outlier: 3.597A pdb=" N ASN A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 327 Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.779A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 358' Processing helix chain 'A' and resid 362 through 385 removed outlier: 3.509A pdb=" N PHE A 379 " --> pdb=" O GLN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 396 through 408 removed outlier: 3.593A pdb=" N ASP A 401 " --> pdb=" O PRO A 397 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.720A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.653A pdb=" N ILE A 435 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.960A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 474 removed outlier: 3.676A pdb=" N SER A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 494 removed outlier: 3.560A pdb=" N GLU A 486 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 506 Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' 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 536 Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.847A pdb=" N LEU A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 553 " --> pdb=" O PRO A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 648 removed outlier: 3.526A pdb=" N ALA A 648 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.886A pdb=" N LEU B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.600A pdb=" N ILE B 86 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 3.586A 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 removed outlier: 3.600A pdb=" N LEU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.510A pdb=" N THR B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 removed outlier: 3.507A pdb=" N ARG B 166 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 167 " --> pdb=" O LEU B 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 163 through 167' 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: 4.083A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 3.732A pdb=" N LYS B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.774A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.582A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.580A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.833A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.962A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.523A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.901A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 215 removed outlier: 3.598A pdb=" N VAL I 215 " --> pdb=" O VAL I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 67 No H-bonds generated for 'chain 'J' and resid 65 through 67' Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.987A pdb=" N THR J 92 " --> pdb=" O ALA J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.729A pdb=" N GLU K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.533A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.531A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.753A pdb=" N GLN N 65 " --> pdb=" O GLN N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.886A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.832A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 61 through 66 removed outlier: 4.553A pdb=" N ASP P 66 " --> pdb=" O GLN P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 removed outlier: 3.829A pdb=" N THR P 91 " --> pdb=" O SER P 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 81 removed outlier: 3.793A pdb=" N PHE Q 81 " --> pdb=" O SER Q 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.848A pdb=" N GLN A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.587A pdb=" N ARG A 136 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 271 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLN A 193 " --> pdb=" O CYS A 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA5, first strand: chain 'A' and resid 578 through 581 Processing sheet with id=AA6, first strand: chain 'A' and resid 637 through 638 removed outlier: 7.206A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER A 652 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TYR A 668 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 654 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE A 666 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU A 656 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 151 through 155 Processing sheet with id=AA8, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.586A pdb=" N TRP D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB1, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.554A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 12 removed outlier: 4.988A pdb=" N TYR E 33 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.159A pdb=" N ALA F 33 " --> pdb=" O GLU F 99 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.873A pdb=" N CYS F 96 " --> pdb=" O TRP F 107 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TRP F 107 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ARG F 98 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 5 through 7 removed outlier: 4.140A pdb=" N ALA G 70 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR G 67 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.563A pdb=" N THR G 85 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.593A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.700A pdb=" N ALA H 92 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.700A pdb=" N ALA H 92 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 130 through 133 removed outlier: 3.558A pdb=" N ASP I 202 " --> pdb=" O SER I 199 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 136 through 138 removed outlier: 6.787A pdb=" N TRP I 167 " --> pdb=" O LEU I 179 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 156 through 157 removed outlier: 3.605A pdb=" N LYS I 162 " --> pdb=" O PHE I 157 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.593A pdb=" N LEU J 82 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.593A pdb=" N LEU J 82 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.573A pdb=" N VAL J 98 " --> pdb=" O THR J 37B" (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP J 36A" --> pdb=" O TYR J 52 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR J 52 " --> pdb=" O TRP J 36A" (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP J 38 " --> pdb=" O ILE J 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.615A pdb=" N TYR J 108 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR J 101 " --> pdb=" O PHE J 106A" (cutoff:3.500A) removed outlier: 5.502A pdb=" N PHE J 106A" --> pdb=" O THR J 101 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AD3, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.573A pdb=" N LEU K 10 " --> pdb=" O THR K 113 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE K 35 " --> pdb=" O ARG K 51 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG K 51 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP K 57A" --> pdb=" O LYS K 53 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.573A pdb=" N LEU K 10 " --> pdb=" O THR K 113 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AD6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.112A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.529A pdb=" N ALA M 91 " --> pdb=" O VAL M 115 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.529A pdb=" N ALA M 91 " --> pdb=" O VAL M 115 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER M 108 " --> pdb=" O ARG M 97 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.964A pdb=" N ILE N 34 " --> pdb=" O ARG N 50 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.215A pdb=" N TYR N 107 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.869A pdb=" N ASP O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.774A pdb=" N LEU O 11 " --> pdb=" O ASP O 105 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AE7, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.575A pdb=" N ILE P 34 " --> pdb=" O TRP P 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TRP P 50 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 2 through 5 removed outlier: 5.833A pdb=" N THR Q 67 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLN Q 25 " --> pdb=" O SER Q 65 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N SER Q 65 " --> pdb=" O GLN Q 25 " (cutoff:3.500A) removed outlier: 11.952A pdb=" N ILE Q 27 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 12.529A pdb=" N ALA Q 63 " --> pdb=" O ILE Q 27 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 8 through 11 removed outlier: 6.596A pdb=" N VAL Q 31 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR Q 47 " --> pdb=" O VAL Q 31 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP Q 33 " --> pdb=" O LEU Q 45 " (cutoff:3.500A) 791 hydrogen bonds defined for protein. 1965 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: 4.90 Time building geometry restraints manager: 2.18 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: 6260 1.34 - 1.46: 5091 1.46 - 1.59: 8396 1.59 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 19883 Sorted by residual: bond pdb=" C PRO A 388 " pdb=" N PRO A 389 " ideal model delta sigma weight residual 1.335 1.374 -0.040 1.19e-02 7.06e+03 1.12e+01 bond pdb=" CA ASP B 79 " pdb=" CB ASP B 79 " ideal model delta sigma weight residual 1.526 1.557 -0.031 1.68e-02 3.54e+03 3.46e+00 bond pdb=" CB ASP A 296 " pdb=" CG ASP A 296 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.38e+00 bond pdb=" C LYS L 38 " pdb=" N PRO L 39 " ideal model delta sigma weight residual 1.332 1.348 -0.016 1.12e-02 7.97e+03 2.14e+00 bond pdb=" C ALA P 40 " pdb=" N PRO P 41 " ideal model delta sigma weight residual 1.332 1.346 -0.014 1.12e-02 7.97e+03 1.48e+00 ... (remaining 19878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 26395 1.77 - 3.55: 563 3.55 - 5.32: 67 5.32 - 7.10: 19 7.10 - 8.87: 3 Bond angle restraints: 27047 Sorted by residual: angle pdb=" C SER Q 29 " pdb=" CA SER Q 29 " pdb=" CB SER Q 29 " ideal model delta sigma weight residual 116.63 110.76 5.87 1.16e+00 7.43e-01 2.56e+01 angle pdb=" N VAL A 706 " pdb=" CA VAL A 706 " pdb=" CB VAL A 706 " ideal model delta sigma weight residual 111.23 104.25 6.98 1.65e+00 3.67e-01 1.79e+01 angle pdb=" CA SER Q 29 " pdb=" C SER Q 29 " pdb=" N TYR Q 30 " ideal model delta sigma weight residual 119.63 116.81 2.82 8.10e-01 1.52e+00 1.21e+01 angle pdb=" CA TYR I 181 " pdb=" CB TYR I 181 " pdb=" CG TYR I 181 " ideal model delta sigma weight residual 113.90 120.01 -6.11 1.80e+00 3.09e-01 1.15e+01 angle pdb=" C VAL A 706 " pdb=" CA VAL A 706 " pdb=" CB VAL A 706 " ideal model delta sigma weight residual 111.29 116.85 -5.56 1.64e+00 3.72e-01 1.15e+01 ... (remaining 27042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 10940 18.03 - 36.06: 666 36.06 - 54.09: 155 54.09 - 72.12: 38 72.12 - 90.15: 16 Dihedral angle restraints: 11815 sinusoidal: 4643 harmonic: 7172 Sorted by residual: dihedral pdb=" CB CYS A 330 " pdb=" SG CYS A 330 " pdb=" SG CYS A 383 " pdb=" CB CYS A 383 " ideal model delta sinusoidal sigma weight residual 93.00 179.25 -86.25 1 1.00e+01 1.00e-02 8.97e+01 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 -162.31 76.31 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 97 " pdb=" CB CYS J 97 " ideal model delta sinusoidal sigma weight residual 93.00 139.47 -46.47 1 1.00e+01 1.00e-02 2.99e+01 ... (remaining 11812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2641 0.067 - 0.133: 357 0.133 - 0.200: 9 0.200 - 0.267: 2 0.267 - 0.333: 1 Chirality restraints: 3010 Sorted by residual: chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 55 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ASP A 296 " pdb=" N ASP A 296 " pdb=" C ASP A 296 " pdb=" CB ASP A 296 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3007 not shown) Planarity restraints: 3466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 240 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO B 241 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 388 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO A 389 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 570 " -0.012 2.00e-02 2.50e+03 1.56e-02 4.27e+00 pdb=" CG PHE A 570 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 570 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 570 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 570 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 570 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 570 " -0.000 2.00e-02 2.50e+03 ... (remaining 3463 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3635 2.78 - 3.31: 17040 3.31 - 3.84: 31100 3.84 - 4.37: 38144 4.37 - 4.90: 68087 Nonbonded interactions: 158006 Sorted by model distance: nonbonded pdb=" NH2 ARG D 41 " pdb=" OE2 GLU D 83 " model vdw 2.244 3.120 nonbonded pdb=" OD2 ASP A 323 " pdb=" NH1 ARG H 102 " model vdw 2.248 3.120 nonbonded pdb=" NH2 ARG A 365 " pdb=" OD2 ASP A 368 " model vdw 2.257 3.120 nonbonded pdb=" O VAL A 256 " pdb=" NH2 ARG A 264 " model vdw 2.260 3.120 nonbonded pdb=" OE1 GLN B 118 " pdb=" OG1 THR B 153 " model vdw 2.264 3.040 ... (remaining 158001 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: 4.720 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: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.900 Find NCS groups from input model: 0.230 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19908 Z= 0.152 Angle : 0.658 12.253 27100 Z= 0.361 Chirality : 0.044 0.333 3010 Planarity : 0.005 0.058 3463 Dihedral : 13.063 90.149 7175 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -0.04 (0.17), residues: 2440 helix: -1.40 (0.28), residues: 254 sheet: 0.25 (0.17), residues: 967 loop : 0.23 (0.19), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 43 TYR 0.032 0.001 TYR I 181 PHE 0.036 0.002 PHE A 570 TRP 0.017 0.001 TRP H 50 HIS 0.004 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (19883) covalent geometry : angle 0.64647 / 0.36 (27047) SS BOND : bond 0.00242 / 0.14 ( 22) SS BOND : angle 1.18971 / 0.82 ( 44) hydrogen bonds : bond 0.22995 / 15.30 ( 739) hydrogen bonds : angle 8.91937 / 6.26 ( 1965) link_NAG-ASN : bond 0.01643 / 0.86 ( 3) link_NAG-ASN : angle 6.35811 / 2.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 0.742 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: B 115 ASN cc_start: 0.8529 (t0) cc_final: 0.8013 (t0) REVERT: E 62 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8696 (tp-100) REVERT: I 130 MET cc_start: 0.8206 (mmm) cc_final: 0.7980 (mmm) REVERT: I 141 LEU cc_start: 0.9275 (mp) cc_final: 0.9022 (tp) REVERT: I 210 LEU cc_start: 0.9436 (tp) cc_final: 0.9140 (tt) REVERT: J 1 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7581 (tm-30) REVERT: L 36 GLN cc_start: 0.7635 (tt0) cc_final: 0.6690 (tm-30) REVERT: L 46 VAL cc_start: 0.9325 (t) cc_final: 0.9105 (p) REVERT: L 48 TYR cc_start: 0.8674 (p90) cc_final: 0.8455 (p90) REVERT: L 60 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7118 (mtm110) REVERT: M 32 TYR cc_start: 0.8158 (m-80) cc_final: 0.7884 (m-10) REVERT: M 58 ASN cc_start: 0.8833 (t0) cc_final: 0.8617 (t0) REVERT: M 76 ASN cc_start: 0.8331 (m-40) cc_final: 0.7782 (m-40) REVERT: M 77 GLN cc_start: 0.8320 (mt0) cc_final: 0.7780 (mm-40) REVERT: P 10 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8252 (mm-30) REVERT: P 48 MET cc_start: 0.9159 (mmm) cc_final: 0.8795 (mmt) REVERT: P 90 ASP cc_start: 0.8145 (m-30) cc_final: 0.7937 (m-30) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.1363 time to fit residues: 81.9200 Evaluate side-chains 281 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN A 213 HIS A 641 ASN ** I 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 GLN M 101 ASN N 65 GLN ** P 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.070061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.050405 restraints weight = 59014.136| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.41 r_work: 0.2738 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 19908 Z= 0.203 Angle : 0.639 11.215 27100 Z= 0.331 Chirality : 0.045 0.240 3010 Planarity : 0.005 0.054 3463 Dihedral : 6.003 86.667 2808 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.27 % Allowed : 7.63 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.19 (0.17), residues: 2440 helix: -0.17 (0.31), residues: 276 sheet: 0.21 (0.16), residues: 966 loop : 0.32 (0.19), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 16 TYR 0.028 0.001 TYR I 181 PHE 0.031 0.002 PHE F 53A TRP 0.013 0.001 TRP H 50 HIS 0.006 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (19883) covalent geometry : angle 0.62842 / 0.33 (27047) SS BOND : bond 0.00287 / 0.16 ( 22) SS BOND : angle 1.48590 / 0.94 ( 44) hydrogen bonds : bond 0.04050 / 2.67 ( 739) hydrogen bonds : angle 6.12249 / 4.30 ( 1965) link_NAG-ASN : bond 0.01140 / 0.60 ( 3) link_NAG-ASN : angle 5.49206 / 2.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 303 time to evaluate : 0.747 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 108 GLN cc_start: 0.9259 (mt0) cc_final: 0.8957 (mt0) REVERT: B 118 GLN cc_start: 0.6803 (tt0) cc_final: 0.6210 (tt0) REVERT: F 60 TYR cc_start: 0.8873 (m-80) cc_final: 0.8364 (m-80) REVERT: F 73 ASP cc_start: 0.7398 (t0) cc_final: 0.7116 (t0) REVERT: F 111 THR cc_start: 0.8136 (p) cc_final: 0.7705 (t) REVERT: F 114 THR cc_start: 0.8872 (m) cc_final: 0.8260 (p) REVERT: G 19 VAL cc_start: 0.8873 (t) cc_final: 0.8575 (p) REVERT: G 61 ARG cc_start: 0.8556 (ptp90) cc_final: 0.8098 (mtm180) REVERT: I 141 LEU cc_start: 0.9401 (mp) cc_final: 0.8786 (tp) REVERT: I 143 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8748 (mp0) REVERT: I 174 GLN cc_start: 0.8746 (mp10) cc_final: 0.8239 (mp10) REVERT: I 210 LEU cc_start: 0.9269 (tp) cc_final: 0.9041 (tt) REVERT: I 211 GLN cc_start: 0.7886 (mt0) cc_final: 0.7550 (mt0) REVERT: J 1 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7683 (tm-30) REVERT: J 29 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8650 (tp) REVERT: J 74 ASP cc_start: 0.8508 (t0) cc_final: 0.8278 (t0) REVERT: K 73 ASP cc_start: 0.8074 (t0) cc_final: 0.7783 (t0) REVERT: L 33 CYS cc_start: 0.8787 (m) cc_final: 0.7389 (t) REVERT: L 35 TYR cc_start: 0.7834 (m-80) cc_final: 0.7406 (m-80) REVERT: L 36 GLN cc_start: 0.7255 (tt0) cc_final: 0.6861 (tt0) REVERT: L 78 GLN cc_start: 0.7597 (mp-120) cc_final: 0.7082 (mp-120) REVERT: L 85 TYR cc_start: 0.7973 (m-80) cc_final: 0.7749 (m-10) REVERT: M 5 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7651 (tm-30) REVERT: M 16 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8620 (tt0) REVERT: M 32 TYR cc_start: 0.8412 (m-80) cc_final: 0.8127 (m-10) REVERT: M 52 ASP cc_start: 0.8288 (t0) cc_final: 0.7925 (t0) REVERT: M 75 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8596 (mtmm) REVERT: M 105 VAL cc_start: 0.8602 (t) cc_final: 0.8362 (p) REVERT: M 111 GLN cc_start: 0.8175 (mp10) cc_final: 0.7476 (pm20) REVERT: N 43 GLN cc_start: 0.8769 (mp10) cc_final: 0.8268 (mp10) REVERT: N 62 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8861 (mm-40) REVERT: P 10 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8431 (mm-30) REVERT: P 43 GLN cc_start: 0.8603 (mp10) cc_final: 0.8073 (mp10) REVERT: P 54 TYR cc_start: 0.9476 (t80) cc_final: 0.8782 (t80) REVERT: P 82 GLU cc_start: 0.8950 (tt0) cc_final: 0.8661 (tp30) REVERT: P 90 ASP cc_start: 0.8749 (m-30) cc_final: 0.7953 (m-30) outliers start: 27 outliers final: 15 residues processed: 318 average time/residue: 0.1618 time to fit residues: 77.1432 Evaluate side-chains 289 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 272 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain P residue 75 PHE Chi-restraints excluded: chain Q residue 44 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 145 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS I 160 ASN ** I 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.070922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051302 restraints weight = 58738.942| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.45 r_work: 0.2765 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19908 Z= 0.115 Angle : 0.567 10.707 27100 Z= 0.292 Chirality : 0.043 0.213 3010 Planarity : 0.004 0.053 3463 Dihedral : 5.679 86.201 2808 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.13 % Allowed : 9.09 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.39 (0.18), residues: 2440 helix: 0.45 (0.32), residues: 276 sheet: 0.29 (0.16), residues: 968 loop : 0.36 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 87 TYR 0.029 0.001 TYR I 181 PHE 0.016 0.001 PHE F 53A TRP 0.011 0.001 TRP H 50 HIS 0.005 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (19883) covalent geometry : angle 0.55604 / 0.29 (27047) SS BOND : bond 0.00463 / 0.23 ( 22) SS BOND : angle 1.46677 / 0.94 ( 44) hydrogen bonds : bond 0.03365 / 2.24 ( 739) hydrogen bonds : angle 5.56885 / 3.91 ( 1965) link_NAG-ASN : bond 0.01006 / 0.53 ( 3) link_NAG-ASN : angle 5.29941 / 2.28 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 0.739 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: 0.8767 (tm-30) cc_final: 0.7734 (tm-30) REVERT: A 103 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8322 (mt-10) REVERT: A 104 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8809 (mm-40) REVERT: A 108 GLN cc_start: 0.9305 (mt0) cc_final: 0.9006 (mt0) REVERT: E 12 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8080 (ttmm) REVERT: E 62 GLN cc_start: 0.9074 (tp-100) cc_final: 0.8783 (tp-100) REVERT: E 81 MET cc_start: 0.8107 (ppp) cc_final: 0.7837 (ppp) REVERT: F 60 TYR cc_start: 0.8829 (m-80) cc_final: 0.8259 (m-80) REVERT: F 73 ASP cc_start: 0.7320 (t0) cc_final: 0.7000 (t0) REVERT: F 89 GLU cc_start: 0.9129 (pm20) cc_final: 0.8861 (pm20) REVERT: F 106 TYR cc_start: 0.8162 (t80) cc_final: 0.7789 (t80) REVERT: F 114 THR cc_start: 0.8856 (m) cc_final: 0.8248 (p) REVERT: G 19 VAL cc_start: 0.8953 (t) cc_final: 0.8689 (p) REVERT: I 141 LEU cc_start: 0.9389 (mp) cc_final: 0.8628 (tp) REVERT: I 143 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8939 (mp0) REVERT: I 174 GLN cc_start: 0.8792 (mp10) cc_final: 0.8250 (mp10) REVERT: I 210 LEU cc_start: 0.9294 (tp) cc_final: 0.9025 (tt) REVERT: I 211 GLN cc_start: 0.7870 (mt0) cc_final: 0.7530 (mt0) REVERT: J 74 ASP cc_start: 0.8654 (t0) cc_final: 0.8283 (t0) REVERT: K 73 ASP cc_start: 0.8166 (t0) cc_final: 0.7746 (t0) REVERT: L 36 GLN cc_start: 0.7154 (tt0) cc_final: 0.6498 (tm-30) REVERT: L 41 GLN cc_start: 0.6556 (mm-40) cc_final: 0.6025 (mp10) REVERT: L 60 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7504 (mtp180) REVERT: L 85 TYR cc_start: 0.8013 (m-80) cc_final: 0.7669 (m-10) REVERT: M 5 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7800 (tm-30) REVERT: M 16 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8670 (tt0) REVERT: M 32 TYR cc_start: 0.8423 (m-80) cc_final: 0.8144 (m-10) REVERT: M 52 ASP cc_start: 0.8302 (t0) cc_final: 0.7684 (t0) REVERT: M 111 GLN cc_start: 0.8211 (mp10) cc_final: 0.7458 (pm20) REVERT: N 43 GLN cc_start: 0.8831 (mp10) cc_final: 0.8383 (mp10) REVERT: N 91 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.8958 (t) REVERT: O 42 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8878 (mtmm) REVERT: P 10 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7970 (mm-30) REVERT: P 43 GLN cc_start: 0.8559 (mp10) cc_final: 0.8007 (mp10) REVERT: P 54 TYR cc_start: 0.9469 (t80) cc_final: 0.8851 (t80) REVERT: P 55 ASN cc_start: 0.9187 (m-40) cc_final: 0.8768 (m-40) REVERT: P 82 GLU cc_start: 0.8962 (tt0) cc_final: 0.8626 (tp30) REVERT: P 90 ASP cc_start: 0.8845 (m-30) cc_final: 0.8048 (m-30) REVERT: P 110 ASP cc_start: 0.8675 (t0) cc_final: 0.8275 (p0) REVERT: Q 22 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7704 (ttm-80) outliers start: 24 outliers final: 10 residues processed: 321 average time/residue: 0.1545 time to fit residues: 74.4466 Evaluate side-chains 290 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 279 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain Q residue 44 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 123 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 214 GLN A 252 HIS D 96 ASN ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 ASN M 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.046398 restraints weight = 60492.665| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.42 r_work: 0.2621 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.117 19908 Z= 0.405 Angle : 0.747 12.651 27100 Z= 0.382 Chirality : 0.048 0.290 3010 Planarity : 0.005 0.052 3463 Dihedral : 6.108 83.915 2808 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.31 % Allowed : 10.32 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.01 (0.17), residues: 2440 helix: 0.13 (0.31), residues: 277 sheet: 0.00 (0.16), residues: 966 loop : 0.16 (0.19), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 87 TYR 0.039 0.002 TYR I 181 PHE 0.031 0.002 PHE J 55 TRP 0.013 0.002 TRP E 113 HIS 0.008 0.002 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00939 / 0.40 (19883) covalent geometry : angle 0.73911 / 0.38 (27047) SS BOND : bond 0.00738 / 0.32 ( 22) SS BOND : angle 1.92815 / 1.12 ( 44) hydrogen bonds : bond 0.04103 / 2.73 ( 739) hydrogen bonds : angle 5.72864 / 4.01 ( 1965) link_NAG-ASN : bond 0.00981 / 0.51 ( 3) link_NAG-ASN : angle 4.61199 / 1.94 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 276 time to evaluate : 0.947 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 103 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8399 (mt-10) REVERT: A 108 GLN cc_start: 0.9277 (mt0) cc_final: 0.8963 (mt0) REVERT: A 354 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8560 (mm110) REVERT: D 85 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8966 (mt-10) REVERT: E 81 MET cc_start: 0.8134 (ppp) cc_final: 0.7797 (ppp) REVERT: F 60 TYR cc_start: 0.8811 (m-80) cc_final: 0.8228 (m-80) REVERT: F 73 ASP cc_start: 0.7581 (t0) cc_final: 0.7215 (t0) REVERT: F 89 GLU cc_start: 0.9183 (pm20) cc_final: 0.8911 (pm20) REVERT: F 114 THR cc_start: 0.8943 (m) cc_final: 0.8390 (p) REVERT: I 141 LEU cc_start: 0.9349 (mp) cc_final: 0.9016 (tp) REVERT: I 174 GLN cc_start: 0.8992 (mp10) cc_final: 0.8370 (mp10) REVERT: I 210 LEU cc_start: 0.9250 (tp) cc_final: 0.8786 (tt) REVERT: I 214 ASP cc_start: 0.8501 (m-30) cc_final: 0.8086 (m-30) REVERT: J 3 GLN cc_start: 0.8981 (mt0) cc_final: 0.8749 (mp10) REVERT: J 48 ASP cc_start: 0.9033 (t0) cc_final: 0.8774 (t0) REVERT: J 74 ASP cc_start: 0.8725 (t0) cc_final: 0.8404 (t0) REVERT: J 75 MET cc_start: 0.9148 (tpp) cc_final: 0.8938 (ttt) REVERT: K 57 ASP cc_start: 0.8812 (t0) cc_final: 0.8558 (t0) REVERT: K 73 ASP cc_start: 0.8348 (t0) cc_final: 0.7925 (t0) REVERT: L 33 CYS cc_start: 0.8979 (m) cc_final: 0.8600 (m) REVERT: L 41 GLN cc_start: 0.6763 (mm-40) cc_final: 0.6249 (mp10) REVERT: L 48 TYR cc_start: 0.8417 (p90) cc_final: 0.8084 (p90) REVERT: L 85 TYR cc_start: 0.8023 (m-80) cc_final: 0.7654 (m-80) REVERT: M 5 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7760 (tm-30) REVERT: M 16 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8628 (tt0) REVERT: M 32 TYR cc_start: 0.8432 (m-80) cc_final: 0.8179 (m-10) REVERT: M 52 ASP cc_start: 0.8542 (t0) cc_final: 0.8063 (t0) REVERT: M 77 GLN cc_start: 0.7599 (pp30) cc_final: 0.7381 (pp30) REVERT: M 94 TYR cc_start: 0.8089 (m-80) cc_final: 0.7560 (m-80) REVERT: M 111 GLN cc_start: 0.8228 (mp10) cc_final: 0.7463 (pm20) REVERT: N 43 GLN cc_start: 0.9060 (mp10) cc_final: 0.8509 (mp10) REVERT: O 70 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8157 (m-30) REVERT: P 10 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8367 (mm-30) REVERT: P 54 TYR cc_start: 0.9507 (t80) cc_final: 0.8878 (t80) REVERT: P 90 ASP cc_start: 0.8825 (m-30) cc_final: 0.8077 (m-30) REVERT: Q 22 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7852 (ttm-80) REVERT: Q 104 GLU cc_start: 0.6326 (pm20) cc_final: 0.6092 (pm20) outliers start: 49 outliers final: 30 residues processed: 312 average time/residue: 0.1519 time to fit residues: 71.4961 Evaluate side-chains 295 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain P residue 75 PHE Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 73 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 122 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 HIS ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.047974 restraints weight = 59160.435| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.42 r_work: 0.2661 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19908 Z= 0.205 Angle : 0.604 11.240 27100 Z= 0.311 Chirality : 0.044 0.202 3010 Planarity : 0.004 0.054 3463 Dihedral : 5.870 84.044 2808 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.07 % Allowed : 11.68 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.15 (0.17), residues: 2440 helix: 0.52 (0.31), residues: 275 sheet: 0.09 (0.16), residues: 954 loop : 0.18 (0.19), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 87 TYR 0.024 0.001 TYR I 181 PHE 0.016 0.002 PHE J 55 TRP 0.015 0.001 TRP H 50 HIS 0.006 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (19883) covalent geometry : angle 0.59684 / 0.31 (27047) SS BOND : bond 0.00352 / 0.17 ( 22) SS BOND : angle 1.43567 / 0.83 ( 44) hydrogen bonds : bond 0.03314 / 2.20 ( 739) hydrogen bonds : angle 5.37580 / 3.76 ( 1965) link_NAG-ASN : bond 0.00727 / 0.38 ( 3) link_NAG-ASN : angle 4.22597 / 1.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 0.798 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 103 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8354 (mt-10) REVERT: A 108 GLN cc_start: 0.9262 (mt0) cc_final: 0.8948 (mt0) REVERT: D 28 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7386 (p0) REVERT: D 85 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8966 (mt-10) REVERT: E 34 MET cc_start: 0.9029 (tpp) cc_final: 0.8339 (tpp) REVERT: F 60 TYR cc_start: 0.8714 (m-80) cc_final: 0.8042 (m-80) REVERT: F 73 ASP cc_start: 0.7472 (t0) cc_final: 0.7107 (t0) REVERT: F 89 GLU cc_start: 0.9197 (pm20) cc_final: 0.8919 (pm20) REVERT: F 106 TYR cc_start: 0.8262 (t80) cc_final: 0.7946 (t80) REVERT: F 114 THR cc_start: 0.8952 (m) cc_final: 0.8463 (p) REVERT: H 5 MET cc_start: 0.9196 (mmm) cc_final: 0.8967 (mmt) REVERT: I 141 LEU cc_start: 0.9327 (mp) cc_final: 0.8974 (tp) REVERT: I 174 GLN cc_start: 0.9011 (mp10) cc_final: 0.8368 (mp10) REVERT: I 210 LEU cc_start: 0.9268 (tp) cc_final: 0.8831 (tt) REVERT: I 211 GLN cc_start: 0.7828 (mt0) cc_final: 0.7510 (mt0) REVERT: I 214 ASP cc_start: 0.8429 (m-30) cc_final: 0.8218 (m-30) REVERT: J 3 GLN cc_start: 0.8965 (mt0) cc_final: 0.8704 (mp10) REVERT: J 48 ASP cc_start: 0.9017 (t0) cc_final: 0.8729 (t0) REVERT: J 74 ASP cc_start: 0.8749 (t0) cc_final: 0.8397 (t0) REVERT: K 57 ASP cc_start: 0.8775 (t0) cc_final: 0.8492 (t0) REVERT: K 73 ASP cc_start: 0.8354 (t0) cc_final: 0.7877 (t0) REVERT: L 41 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6626 (mp10) REVERT: L 85 TYR cc_start: 0.8179 (m-80) cc_final: 0.7768 (m-10) REVERT: M 5 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7780 (tm-30) REVERT: M 16 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8651 (tt0) REVERT: M 32 TYR cc_start: 0.8438 (m-80) cc_final: 0.8212 (m-10) REVERT: M 46 GLU cc_start: 0.8777 (tt0) cc_final: 0.8228 (tt0) REVERT: M 52 ASP cc_start: 0.8539 (t0) cc_final: 0.8079 (t0) REVERT: M 94 TYR cc_start: 0.8101 (m-80) cc_final: 0.7622 (m-80) REVERT: M 111 GLN cc_start: 0.8202 (mp10) cc_final: 0.7383 (pm20) REVERT: N 43 GLN cc_start: 0.8958 (mp10) cc_final: 0.8405 (mp10) REVERT: N 70 MET cc_start: 0.9053 (mtt) cc_final: 0.8527 (mtt) REVERT: O 70 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: P 10 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8402 (mm-30) REVERT: P 54 TYR cc_start: 0.9500 (t80) cc_final: 0.8916 (t80) REVERT: P 82 GLU cc_start: 0.9038 (tt0) cc_final: 0.8647 (tp30) REVERT: P 87 ARG cc_start: 0.8918 (mtm110) cc_final: 0.7651 (mtm-85) REVERT: P 90 ASP cc_start: 0.8910 (m-30) cc_final: 0.7767 (m-30) REVERT: Q 22 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7800 (ttm-80) outliers start: 44 outliers final: 30 residues processed: 310 average time/residue: 0.1448 time to fit residues: 68.0976 Evaluate side-chains 298 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 266 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain Q residue 44 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 174 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 144 optimal weight: 0.0000 chunk 220 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 239 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 252 HIS ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 ASN M 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.069497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.049897 restraints weight = 58814.504| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.39 r_work: 0.2733 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 19908 Z= 0.114 Angle : 0.577 13.621 27100 Z= 0.293 Chirality : 0.042 0.299 3010 Planarity : 0.004 0.054 3463 Dihedral : 5.602 84.643 2808 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.55 % Allowed : 12.81 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.32 (0.17), residues: 2440 helix: 0.80 (0.32), residues: 276 sheet: 0.24 (0.17), residues: 940 loop : 0.20 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 87 TYR 0.030 0.001 TYR I 181 PHE 0.020 0.001 PHE A 317 TRP 0.014 0.001 TRP H 50 HIS 0.005 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (19883) covalent geometry : angle 0.56929 / 0.29 (27047) SS BOND : bond 0.00284 / 0.13 ( 22) SS BOND : angle 1.60902 / 0.97 ( 44) hydrogen bonds : bond 0.02928 / 1.95 ( 739) hydrogen bonds : angle 5.08519 / 3.55 ( 1965) link_NAG-ASN : bond 0.00621 / 0.33 ( 3) link_NAG-ASN : angle 3.92611 / 1.66 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 0.769 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 103 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8352 (mt-10) REVERT: A 658 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8335 (t70) REVERT: D 16 GLN cc_start: 0.9153 (tt0) cc_final: 0.8708 (pt0) REVERT: D 28 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7368 (p0) REVERT: D 85 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8940 (mt-10) REVERT: E 34 MET cc_start: 0.8951 (tpp) cc_final: 0.8263 (tpp) REVERT: F 18 LEU cc_start: 0.8396 (tp) cc_final: 0.8186 (tt) REVERT: F 60 TYR cc_start: 0.8766 (m-80) cc_final: 0.8071 (m-80) REVERT: F 73 ASP cc_start: 0.7443 (t0) cc_final: 0.6941 (t0) REVERT: F 89 GLU cc_start: 0.9213 (pm20) cc_final: 0.8939 (pm20) REVERT: F 106 TYR cc_start: 0.8317 (t80) cc_final: 0.7966 (t80) REVERT: F 114 THR cc_start: 0.8955 (m) cc_final: 0.8470 (p) REVERT: G 1 ASP cc_start: 0.7904 (t0) cc_final: 0.7480 (t0) REVERT: G 3 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8389 (mm-40) REVERT: I 130 MET cc_start: 0.8771 (mmm) cc_final: 0.8209 (mmm) REVERT: I 141 LEU cc_start: 0.9332 (mp) cc_final: 0.8711 (tp) REVERT: I 143 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8969 (mp0) REVERT: I 174 GLN cc_start: 0.8986 (mp10) cc_final: 0.8382 (mp10) REVERT: I 210 LEU cc_start: 0.9261 (tp) cc_final: 0.9018 (tt) REVERT: I 211 GLN cc_start: 0.7829 (mt0) cc_final: 0.7464 (mt0) REVERT: I 214 ASP cc_start: 0.8403 (m-30) cc_final: 0.8178 (m-30) REVERT: J 3 GLN cc_start: 0.8933 (mt0) cc_final: 0.8687 (mp10) REVERT: J 48 ASP cc_start: 0.9012 (t0) cc_final: 0.8750 (t0) REVERT: J 74 ASP cc_start: 0.8745 (t0) cc_final: 0.8368 (t0) REVERT: K 57 ASP cc_start: 0.8741 (t0) cc_final: 0.8456 (t0) REVERT: K 73 ASP cc_start: 0.8368 (t0) cc_final: 0.7846 (t0) REVERT: L 26 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8002 (mmmt) REVERT: L 41 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6634 (mp10) REVERT: L 85 TYR cc_start: 0.8248 (m-80) cc_final: 0.7892 (m-10) REVERT: L 86 TYR cc_start: 0.7950 (m-80) cc_final: 0.7239 (m-80) REVERT: M 5 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7983 (tm-30) REVERT: M 16 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8661 (tt0) REVERT: M 32 TYR cc_start: 0.8422 (m-80) cc_final: 0.8183 (m-10) REVERT: M 52 ASP cc_start: 0.8555 (t0) cc_final: 0.8209 (t0) REVERT: M 59 TYR cc_start: 0.8914 (m-10) cc_final: 0.8654 (m-10) REVERT: M 94 TYR cc_start: 0.8083 (m-80) cc_final: 0.7823 (m-80) REVERT: M 111 GLN cc_start: 0.8211 (mp10) cc_final: 0.7389 (pm20) REVERT: N 43 GLN cc_start: 0.8958 (mp10) cc_final: 0.8394 (mp10) REVERT: O 42 LYS cc_start: 0.9155 (mmmm) cc_final: 0.8856 (mtmm) REVERT: P 10 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8284 (mm-30) REVERT: P 43 GLN cc_start: 0.8490 (mp10) cc_final: 0.7959 (mp10) REVERT: P 54 TYR cc_start: 0.9493 (t80) cc_final: 0.8878 (t80) REVERT: P 55 ASN cc_start: 0.9266 (m-40) cc_final: 0.8913 (m-40) REVERT: P 82 GLU cc_start: 0.9032 (tt0) cc_final: 0.8602 (tp30) REVERT: P 89 ASP cc_start: 0.9166 (p0) cc_final: 0.8862 (p0) REVERT: P 90 ASP cc_start: 0.8976 (m-30) cc_final: 0.8177 (m-30) REVERT: Q 22 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7682 (ttm-80) REVERT: Q 99 GLN cc_start: 0.8694 (pt0) cc_final: 0.8393 (pm20) outliers start: 33 outliers final: 19 residues processed: 311 average time/residue: 0.1580 time to fit residues: 74.0415 Evaluate side-chains 299 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain Q residue 44 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 123 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 42 optimal weight: 0.0050 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 112 HIS ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 ASN M 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.066733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.047064 restraints weight = 60020.221| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.40 r_work: 0.2636 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 19908 Z= 0.294 Angle : 0.653 11.887 27100 Z= 0.333 Chirality : 0.045 0.276 3010 Planarity : 0.004 0.059 3463 Dihedral : 5.782 84.274 2808 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.07 % Allowed : 13.19 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.14 (0.17), residues: 2440 helix: 0.66 (0.31), residues: 276 sheet: 0.11 (0.16), residues: 952 loop : 0.10 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 144 TYR 0.037 0.002 TYR I 181 PHE 0.027 0.002 PHE J 55 TRP 0.011 0.002 TRP F 47 HIS 0.007 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.29 (19883) covalent geometry : angle 0.64709 / 0.33 (27047) SS BOND : bond 0.00414 / 0.21 ( 22) SS BOND : angle 1.68526 / 0.98 ( 44) hydrogen bonds : bond 0.03508 / 2.34 ( 739) hydrogen bonds : angle 5.29809 / 3.70 ( 1965) link_NAG-ASN : bond 0.00597 / 0.31 ( 3) link_NAG-ASN : angle 3.65301 / 1.55 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 0.746 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 103 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8348 (mt-10) REVERT: A 658 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8367 (t70) REVERT: D 28 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7370 (p0) REVERT: D 85 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8986 (mt-10) REVERT: E 34 MET cc_start: 0.8985 (tpp) cc_final: 0.8068 (tpp) REVERT: F 18 LEU cc_start: 0.8417 (tp) cc_final: 0.8023 (tt) REVERT: F 60 TYR cc_start: 0.8733 (m-80) cc_final: 0.8009 (m-80) REVERT: F 73 ASP cc_start: 0.7599 (t0) cc_final: 0.7140 (t0) REVERT: F 82 GLN cc_start: 0.8646 (tt0) cc_final: 0.8185 (tp40) REVERT: F 89 GLU cc_start: 0.9199 (pm20) cc_final: 0.8913 (pm20) REVERT: F 114 THR cc_start: 0.8952 (m) cc_final: 0.8456 (p) REVERT: G 1 ASP cc_start: 0.8023 (t0) cc_final: 0.7645 (t0) REVERT: G 81 GLU cc_start: 0.8305 (pm20) cc_final: 0.8099 (pm20) REVERT: I 141 LEU cc_start: 0.9306 (mp) cc_final: 0.8989 (tp) REVERT: I 174 GLN cc_start: 0.9055 (mp10) cc_final: 0.8457 (mp10) REVERT: I 210 LEU cc_start: 0.9276 (tp) cc_final: 0.9036 (tt) REVERT: I 214 ASP cc_start: 0.8425 (m-30) cc_final: 0.8177 (m-30) REVERT: J 3 GLN cc_start: 0.9013 (mt0) cc_final: 0.8759 (mp10) REVERT: J 48 ASP cc_start: 0.9041 (t0) cc_final: 0.8775 (t0) REVERT: J 74 ASP cc_start: 0.8697 (t0) cc_final: 0.8271 (t0) REVERT: K 57 ASP cc_start: 0.8738 (t0) cc_final: 0.8452 (t0) REVERT: K 73 ASP cc_start: 0.8382 (t0) cc_final: 0.7868 (t0) REVERT: K 97 MET cc_start: 0.8841 (tmm) cc_final: 0.8436 (tmm) REVERT: L 33 CYS cc_start: 0.8973 (m) cc_final: 0.8628 (m) REVERT: L 41 GLN cc_start: 0.7388 (mm-40) cc_final: 0.6832 (mp10) REVERT: L 48 TYR cc_start: 0.8424 (p90) cc_final: 0.8156 (p90) REVERT: L 85 TYR cc_start: 0.8229 (m-80) cc_final: 0.7850 (m-10) REVERT: M 5 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7815 (tm-30) REVERT: M 16 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8646 (tt0) REVERT: M 32 TYR cc_start: 0.8431 (m-80) cc_final: 0.8194 (m-10) REVERT: M 52 ASP cc_start: 0.8561 (t0) cc_final: 0.8157 (t0) REVERT: M 94 TYR cc_start: 0.8045 (m-80) cc_final: 0.7800 (m-80) REVERT: M 111 GLN cc_start: 0.8202 (mp10) cc_final: 0.7432 (pm20) REVERT: N 43 GLN cc_start: 0.9009 (mp10) cc_final: 0.8378 (mp10) REVERT: N 70 MET cc_start: 0.9118 (mtt) cc_final: 0.8685 (mtt) REVERT: P 10 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8338 (mm-30) REVERT: P 43 GLN cc_start: 0.8395 (mp10) cc_final: 0.7881 (mp10) REVERT: P 54 TYR cc_start: 0.9497 (t80) cc_final: 0.8914 (t80) REVERT: P 82 GLU cc_start: 0.9034 (tt0) cc_final: 0.8640 (tp30) REVERT: P 87 ARG cc_start: 0.8751 (mtm110) cc_final: 0.8459 (mtm110) REVERT: P 89 ASP cc_start: 0.9177 (p0) cc_final: 0.8882 (p0) REVERT: P 90 ASP cc_start: 0.8908 (m-30) cc_final: 0.8166 (m-30) REVERT: Q 22 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7969 (ttm-80) REVERT: Q 104 GLU cc_start: 0.7075 (pm20) cc_final: 0.6428 (pm20) outliers start: 44 outliers final: 35 residues processed: 305 average time/residue: 0.1568 time to fit residues: 72.4617 Evaluate side-chains 301 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain P residue 75 PHE Chi-restraints excluded: chain Q residue 44 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 181 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 213 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 112 HIS M 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.069446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.049875 restraints weight = 58850.529| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.38 r_work: 0.2731 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19908 Z= 0.119 Angle : 0.591 15.866 27100 Z= 0.299 Chirality : 0.042 0.267 3010 Planarity : 0.004 0.055 3463 Dihedral : 5.490 84.189 2808 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.60 % Allowed : 13.85 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 (0.18), residues: 2440 helix: 0.97 (0.32), residues: 276 sheet: 0.25 (0.17), residues: 945 loop : 0.19 (0.19), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 144 TYR 0.036 0.001 TYR I 181 PHE 0.014 0.001 PHE A 317 TRP 0.016 0.001 TRP H 50 HIS 0.006 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (19883) covalent geometry : angle 0.58473 / 0.30 (27047) SS BOND : bond 0.00391 / 0.15 ( 22) SS BOND : angle 1.51060 / 0.88 ( 44) hydrogen bonds : bond 0.02888 / 1.94 ( 739) hydrogen bonds : angle 4.98261 / 3.47 ( 1965) link_NAG-ASN : bond 0.00474 / 0.25 ( 3) link_NAG-ASN : angle 3.41253 / 1.45 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 283 time to evaluate : 0.985 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: A 103 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8355 (mt-10) REVERT: A 658 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8387 (t70) REVERT: D 16 GLN cc_start: 0.9183 (tt0) cc_final: 0.8694 (pt0) REVERT: D 28 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7424 (p0) REVERT: D 85 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8988 (mt-10) REVERT: E 34 MET cc_start: 0.8922 (tpp) cc_final: 0.8008 (tpp) REVERT: E 81 MET cc_start: 0.7972 (ppp) cc_final: 0.7724 (ppp) REVERT: F 18 LEU cc_start: 0.8484 (tp) cc_final: 0.8095 (tt) REVERT: F 60 TYR cc_start: 0.8763 (m-80) cc_final: 0.8102 (m-80) REVERT: F 73 ASP cc_start: 0.7519 (t0) cc_final: 0.7009 (t0) REVERT: F 82 GLN cc_start: 0.8610 (tt0) cc_final: 0.8196 (tp40) REVERT: F 86 LEU cc_start: 0.9010 (mt) cc_final: 0.8726 (mp) REVERT: F 89 GLU cc_start: 0.9232 (pm20) cc_final: 0.8937 (pm20) REVERT: F 114 THR cc_start: 0.8978 (m) cc_final: 0.8494 (p) REVERT: G 53 ARG cc_start: 0.8737 (mtm-85) cc_final: 0.8506 (mtm-85) REVERT: G 81 GLU cc_start: 0.8486 (pm20) cc_final: 0.8241 (pm20) REVERT: I 130 MET cc_start: 0.8741 (mmm) cc_final: 0.8410 (mmm) REVERT: I 141 LEU cc_start: 0.9313 (mp) cc_final: 0.9002 (tp) REVERT: I 174 GLN cc_start: 0.9023 (mp10) cc_final: 0.8430 (mp10) REVERT: I 210 LEU cc_start: 0.9293 (tp) cc_final: 0.9067 (tt) REVERT: I 214 ASP cc_start: 0.8431 (m-30) cc_final: 0.8186 (m-30) REVERT: J 48 ASP cc_start: 0.9026 (t0) cc_final: 0.8760 (t0) REVERT: J 74 ASP cc_start: 0.8774 (t0) cc_final: 0.8350 (t0) REVERT: K 57 ASP cc_start: 0.8663 (t0) cc_final: 0.8362 (t0) REVERT: K 73 ASP cc_start: 0.8402 (t0) cc_final: 0.7863 (t0) REVERT: L 41 GLN cc_start: 0.7354 (mm-40) cc_final: 0.6769 (mp10) REVERT: L 85 TYR cc_start: 0.8283 (m-80) cc_final: 0.7952 (m-10) REVERT: L 86 TYR cc_start: 0.7781 (m-80) cc_final: 0.7171 (m-80) REVERT: M 5 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7955 (tm-30) REVERT: M 16 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8661 (tt0) REVERT: M 32 TYR cc_start: 0.8427 (m-80) cc_final: 0.8191 (m-10) REVERT: M 52 ASP cc_start: 0.8566 (t0) cc_final: 0.8165 (t0) REVERT: M 59 TYR cc_start: 0.8886 (m-10) cc_final: 0.8640 (m-10) REVERT: M 75 LYS cc_start: 0.8740 (pttp) cc_final: 0.8526 (pttp) REVERT: M 111 GLN cc_start: 0.8182 (mp10) cc_final: 0.7315 (pm20) REVERT: N 43 GLN cc_start: 0.9000 (mp10) cc_final: 0.8731 (mp10) REVERT: P 10 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8364 (mm-30) REVERT: P 43 GLN cc_start: 0.8426 (mp10) cc_final: 0.7880 (mp10) REVERT: P 54 TYR cc_start: 0.9501 (t80) cc_final: 0.8876 (t80) REVERT: P 55 ASN cc_start: 0.9270 (m-40) cc_final: 0.8909 (m-40) REVERT: P 82 GLU cc_start: 0.9027 (tt0) cc_final: 0.8620 (tp30) REVERT: P 87 ARG cc_start: 0.8716 (mtm110) cc_final: 0.8386 (mtm110) REVERT: P 89 ASP cc_start: 0.9174 (p0) cc_final: 0.8750 (p0) REVERT: P 90 ASP cc_start: 0.8911 (m-30) cc_final: 0.7947 (m-30) REVERT: P 110 ASP cc_start: 0.8726 (t0) cc_final: 0.8330 (p0) REVERT: Q 22 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7833 (ttm-80) REVERT: Q 99 GLN cc_start: 0.8955 (pt0) cc_final: 0.8642 (pm20) REVERT: Q 104 GLU cc_start: 0.7164 (pm20) cc_final: 0.6922 (pm20) outliers start: 34 outliers final: 25 residues processed: 309 average time/residue: 0.1538 time to fit residues: 72.1667 Evaluate side-chains 299 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain Q residue 44 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 17 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 142 optimal weight: 0.0770 chunk 167 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 112 HIS ** J 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.069282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.049573 restraints weight = 58758.722| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.40 r_work: 0.2725 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19908 Z= 0.141 Angle : 0.590 15.051 27100 Z= 0.299 Chirality : 0.043 0.252 3010 Planarity : 0.004 0.053 3463 Dihedral : 5.434 84.882 2808 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.60 % Allowed : 13.71 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.43 (0.18), residues: 2440 helix: 1.02 (0.32), residues: 276 sheet: 0.29 (0.17), residues: 958 loop : 0.27 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 16 TYR 0.032 0.001 TYR I 181 PHE 0.036 0.001 PHE M 78 TRP 0.013 0.001 TRP H 50 HIS 0.006 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (19883) covalent geometry : angle 0.58419 / 0.30 (27047) SS BOND : bond 0.00373 / 0.16 ( 22) SS BOND : angle 1.44659 / 0.85 ( 44) hydrogen bonds : bond 0.02935 / 1.98 ( 739) hydrogen bonds : angle 4.93015 / 3.44 ( 1965) link_NAG-ASN : bond 0.00458 / 0.24 ( 3) link_NAG-ASN : angle 3.27729 / 1.39 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 0.793 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: 0.8794 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 103 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8336 (mt-10) REVERT: A 658 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8376 (t70) REVERT: D 16 GLN cc_start: 0.9179 (tt0) cc_final: 0.8657 (pt0) REVERT: D 28 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7411 (p0) REVERT: D 85 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8986 (mt-10) REVERT: E 34 MET cc_start: 0.8913 (tpp) cc_final: 0.8016 (tpp) REVERT: E 81 MET cc_start: 0.7936 (ppp) cc_final: 0.7651 (ppp) REVERT: F 60 TYR cc_start: 0.8772 (m-80) cc_final: 0.8060 (m-80) REVERT: F 73 ASP cc_start: 0.7498 (t0) cc_final: 0.7059 (t0) REVERT: F 82 GLN cc_start: 0.8664 (tt0) cc_final: 0.8233 (tp40) REVERT: F 86 LEU cc_start: 0.8996 (mt) cc_final: 0.8718 (mp) REVERT: F 89 GLU cc_start: 0.9226 (pm20) cc_final: 0.8934 (pm20) REVERT: F 114 THR cc_start: 0.8963 (m) cc_final: 0.8485 (p) REVERT: I 130 MET cc_start: 0.8735 (mmm) cc_final: 0.8024 (mmm) REVERT: I 141 LEU cc_start: 0.9297 (mp) cc_final: 0.8998 (tp) REVERT: I 174 GLN cc_start: 0.8991 (mp10) cc_final: 0.8387 (mp10) REVERT: I 210 LEU cc_start: 0.9289 (tp) cc_final: 0.9058 (tt) REVERT: I 214 ASP cc_start: 0.8416 (m-30) cc_final: 0.8174 (m-30) REVERT: J 1 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8029 (pp30) REVERT: J 48 ASP cc_start: 0.9039 (t0) cc_final: 0.8768 (t0) REVERT: J 74 ASP cc_start: 0.8713 (t0) cc_final: 0.8271 (t0) REVERT: K 57 ASP cc_start: 0.8649 (t0) cc_final: 0.8354 (t0) REVERT: K 73 ASP cc_start: 0.8374 (t0) cc_final: 0.7830 (t0) REVERT: K 97 MET cc_start: 0.8682 (tmm) cc_final: 0.8305 (tmm) REVERT: L 26 LYS cc_start: 0.8512 (mtpp) cc_final: 0.7989 (mmmt) REVERT: L 41 GLN cc_start: 0.7372 (mm-40) cc_final: 0.6764 (mp10) REVERT: L 86 TYR cc_start: 0.7847 (m-80) cc_final: 0.7217 (m-80) REVERT: M 5 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7982 (tm-30) REVERT: M 16 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8659 (tt0) REVERT: M 32 TYR cc_start: 0.8445 (m-80) cc_final: 0.8210 (m-10) REVERT: M 46 GLU cc_start: 0.8771 (tt0) cc_final: 0.8190 (tt0) REVERT: M 52 ASP cc_start: 0.8557 (t0) cc_final: 0.8141 (t0) REVERT: M 59 TYR cc_start: 0.8875 (m-10) cc_final: 0.8639 (m-10) REVERT: M 66 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8298 (ttt180) REVERT: M 111 GLN cc_start: 0.8149 (mp10) cc_final: 0.7358 (pm20) REVERT: N 43 GLN cc_start: 0.9014 (mp10) cc_final: 0.8750 (mp10) REVERT: P 10 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8343 (mm-30) REVERT: P 43 GLN cc_start: 0.8412 (mp10) cc_final: 0.7833 (mp10) REVERT: P 48 MET cc_start: 0.9141 (mmm) cc_final: 0.8940 (mmt) REVERT: P 54 TYR cc_start: 0.9499 (t80) cc_final: 0.8839 (t80) REVERT: P 55 ASN cc_start: 0.9184 (m-40) cc_final: 0.8770 (m-40) REVERT: P 82 GLU cc_start: 0.9019 (tt0) cc_final: 0.8625 (tp30) REVERT: P 87 ARG cc_start: 0.8719 (mtm110) cc_final: 0.8377 (mtm110) REVERT: P 89 ASP cc_start: 0.9167 (p0) cc_final: 0.8743 (p0) REVERT: P 90 ASP cc_start: 0.8843 (m-30) cc_final: 0.7938 (m-30) REVERT: Q 22 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7784 (ttm-80) REVERT: Q 99 GLN cc_start: 0.8901 (pt0) cc_final: 0.8530 (pm20) REVERT: Q 104 GLU cc_start: 0.7192 (pm20) cc_final: 0.6933 (pm20) outliers start: 34 outliers final: 26 residues processed: 301 average time/residue: 0.1559 time to fit residues: 71.4395 Evaluate side-chains 299 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain Q residue 44 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 211 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 chunk 231 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN J 3 GLN M 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.067876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.048100 restraints weight = 59590.955| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.41 r_work: 0.2667 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 19908 Z= 0.208 Angle : 0.623 14.581 27100 Z= 0.316 Chirality : 0.043 0.249 3010 Planarity : 0.004 0.053 3463 Dihedral : 5.514 85.641 2808 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.70 % Allowed : 13.75 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.37 (0.17), residues: 2440 helix: 0.92 (0.32), residues: 276 sheet: 0.27 (0.17), residues: 958 loop : 0.21 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 16 TYR 0.031 0.001 TYR I 181 PHE 0.033 0.002 PHE M 78 TRP 0.011 0.001 TRP F 52 HIS 0.007 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (19883) covalent geometry : angle 0.61775 / 0.31 (27047) SS BOND : bond 0.00390 / 0.18 ( 22) SS BOND : angle 1.45876 / 0.85 ( 44) hydrogen bonds : bond 0.03137 / 2.11 ( 739) hydrogen bonds : angle 4.99240 / 3.48 ( 1965) link_NAG-ASN : bond 0.00447 / 0.23 ( 3) link_NAG-ASN : angle 3.17685 / 1.35 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 0.784 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 103 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8322 (mt-10) REVERT: A 658 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8404 (t70) REVERT: D 28 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7445 (p0) REVERT: D 85 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8977 (mt-10) REVERT: E 34 MET cc_start: 0.8940 (tpp) cc_final: 0.8064 (tpp) REVERT: E 81 MET cc_start: 0.7945 (ppp) cc_final: 0.7682 (ppp) REVERT: F 60 TYR cc_start: 0.8802 (m-80) cc_final: 0.8082 (m-80) REVERT: F 73 ASP cc_start: 0.7605 (t0) cc_final: 0.7149 (t0) REVERT: F 82 GLN cc_start: 0.8622 (tt0) cc_final: 0.8168 (tp40) REVERT: F 86 LEU cc_start: 0.9023 (mt) cc_final: 0.8732 (mp) REVERT: F 89 GLU cc_start: 0.9203 (pm20) cc_final: 0.8919 (pm20) REVERT: F 106 TYR cc_start: 0.8332 (t80) cc_final: 0.8029 (t80) REVERT: F 114 THR cc_start: 0.8946 (m) cc_final: 0.8468 (p) REVERT: I 130 MET cc_start: 0.8801 (mmm) cc_final: 0.8089 (mmm) REVERT: I 141 LEU cc_start: 0.9306 (mp) cc_final: 0.9020 (tp) REVERT: I 174 GLN cc_start: 0.9041 (mp10) cc_final: 0.8438 (mp10) REVERT: I 210 LEU cc_start: 0.9317 (tp) cc_final: 0.9078 (tt) REVERT: I 214 ASP cc_start: 0.8414 (m-30) cc_final: 0.8187 (m-30) REVERT: J 1 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8156 (tm-30) REVERT: J 3 GLN cc_start: 0.8936 (mp-120) cc_final: 0.8641 (mp10) REVERT: J 48 ASP cc_start: 0.9050 (t0) cc_final: 0.8789 (t0) REVERT: J 74 ASP cc_start: 0.8715 (t0) cc_final: 0.8272 (t0) REVERT: K 57 ASP cc_start: 0.8694 (t0) cc_final: 0.8405 (t0) REVERT: K 73 ASP cc_start: 0.8395 (t0) cc_final: 0.7865 (t0) REVERT: K 97 MET cc_start: 0.8775 (tmm) cc_final: 0.8391 (tmm) REVERT: L 41 GLN cc_start: 0.7454 (mm-40) cc_final: 0.6826 (mp-120) REVERT: L 85 TYR cc_start: 0.8399 (m-80) cc_final: 0.8105 (m-10) REVERT: M 5 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7902 (tm-30) REVERT: M 16 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8599 (tt0) REVERT: M 32 TYR cc_start: 0.8483 (m-80) cc_final: 0.8245 (m-10) REVERT: M 52 ASP cc_start: 0.8561 (t0) cc_final: 0.8170 (t0) REVERT: M 59 TYR cc_start: 0.8878 (m-10) cc_final: 0.8622 (m-10) REVERT: M 66 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8455 (ttt180) REVERT: M 111 GLN cc_start: 0.8142 (mp10) cc_final: 0.7383 (pm20) REVERT: N 43 GLN cc_start: 0.9062 (mp10) cc_final: 0.8788 (mp10) REVERT: N 70 MET cc_start: 0.9023 (mtt) cc_final: 0.8509 (mtt) REVERT: P 10 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8393 (mm-30) REVERT: P 43 GLN cc_start: 0.8433 (mp10) cc_final: 0.7881 (mp10) REVERT: P 48 MET cc_start: 0.9170 (mmm) cc_final: 0.8938 (mmt) REVERT: P 54 TYR cc_start: 0.9488 (t80) cc_final: 0.8875 (t80) REVERT: P 55 ASN cc_start: 0.9214 (m-40) cc_final: 0.8839 (m-40) REVERT: P 82 GLU cc_start: 0.9035 (tt0) cc_final: 0.8642 (tp30) REVERT: P 87 ARG cc_start: 0.8674 (mtm110) cc_final: 0.8356 (mtm110) REVERT: P 90 ASP cc_start: 0.8770 (m-30) cc_final: 0.7938 (m-30) REVERT: Q 22 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7872 (ttm-80) REVERT: Q 104 GLU cc_start: 0.7174 (pm20) cc_final: 0.6933 (pm20) outliers start: 36 outliers final: 30 residues processed: 298 average time/residue: 0.1565 time to fit residues: 70.7689 Evaluate side-chains 297 residues out of total 2126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 265 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 658 ASP Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain P residue 75 PHE Chi-restraints excluded: chain Q residue 44 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 118 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 48 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 112 HIS G 3 GLN M 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.050534 restraints weight = 58715.608| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.39 r_work: 0.2750 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19908 Z= 0.109 Angle : 0.580 14.440 27100 Z= 0.294 Chirality : 0.042 0.241 3010 Planarity : 0.004 0.055 3463 Dihedral : 5.303 86.163 2808 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.60 % Allowed : 13.80 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: 0.55 (0.18), residues: 2440 helix: 1.11 (0.32), residues: 276 sheet: 0.41 (0.17), residues: 935 loop : 0.31 (0.19), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 16 TYR 0.032 0.001 TYR I 181 PHE 0.031 0.001 PHE M 78 TRP 0.016 0.001 TRP H 50 HIS 0.006 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (19883) covalent geometry : angle 0.57537 / 0.29 (27047) SS BOND : bond 0.00331 / 0.14 ( 22) SS BOND : angle 1.32779 / 0.76 ( 44) hydrogen bonds : bond 0.02729 / 1.84 ( 739) hydrogen bonds : angle 4.80107 / 3.34 ( 1965) link_NAG-ASN : bond 0.00407 / 0.21 ( 3) link_NAG-ASN : angle 3.02954 / 1.29 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4481.60 seconds wall clock time: 77 minutes 59.74 seconds (4679.74 seconds total)