Starting phenix.real_space_refine on Sun Aug 24 11:21:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eyx_28723/08_2025/8eyx_28723_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyx_28723/08_2025/8eyx_28723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eyx_28723/08_2025/8eyx_28723_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyx_28723/08_2025/8eyx_28723_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eyx_28723/08_2025/8eyx_28723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyx_28723/08_2025/8eyx_28723.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6287 atoms to isotropic. 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 113 5.16 5 C 9082 2.51 5 N 2447 2.21 5 O 2656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14298 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6572 Classifications: {'peptide': 815} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 769} Chain breaks: 4 Chain: "B" Number of atoms: 6263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6263 Classifications: {'peptide': 772} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 730} Chain breaks: 5 Chain: "D" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Chain: "E" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "F" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Chain: "G" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Time building chain proxies: 3.65, per 1000 atoms: 0.26 Number of scatterers: 14298 At special positions: 0 Unit cell: (145.8, 140.4, 176.04, 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 113 16.00 O 2656 8.00 N 2447 7.00 C 9082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.02 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.02 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.02 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 62 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 62 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 66 " distance=2.03 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS G 62 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 66 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 605.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3334 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 34 sheets defined 17.8% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.542A pdb=" N ARG A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.525A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.703A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.994A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 378 through 382 removed outlier: 4.371A pdb=" N PHE A 381 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 448 through 452 removed outlier: 4.242A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 644 Processing helix chain 'A' and resid 706 through 716 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.517A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.589A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.537A pdb=" N ARG B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.567A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.654A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.727A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 645 removed outlier: 4.215A pdb=" N PHE B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 640 through 645' Processing helix chain 'B' and resid 691 through 716 Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'D' and resid 8 through 19 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.570A pdb=" N ASN D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 67 through 73 removed outlier: 3.516A pdb=" N ASN E 73 " --> pdb=" O TYR E 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.557A pdb=" N VAL F 12 " --> pdb=" O GLY F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 Processing helix chain 'F' and resid 67 through 75 removed outlier: 3.774A pdb=" N GLN F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU F 72 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 19 removed outlier: 3.540A pdb=" N VAL G 12 " --> pdb=" O GLY G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 67 through 75 removed outlier: 4.262A pdb=" N GLU G 72 " --> pdb=" O TYR G 69 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN G 73 " --> pdb=" O GLN G 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 5.802A pdb=" N ILE A 13 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET A 38 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.329A pdb=" N HIS A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 232 Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA8, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 321 removed outlier: 6.680A pdb=" N VAL A 335 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN A 313 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A 337 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 315 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N SER A 339 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 317 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 341 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 311 through 321 removed outlier: 6.680A pdb=" N VAL A 335 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN A 313 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A 337 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 315 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N SER A 339 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 317 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 341 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU A 368 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N LEU A 403 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A 370 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB3, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.258A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.743A pdb=" N THR A 530 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 507 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 504 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 601 through 609 removed outlier: 6.553A pdb=" N LYS A 616 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER A 605 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A 614 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER A 607 " --> pdb=" O GLN A 612 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLN A 612 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 761 through 764 Processing sheet with id=AB7, first strand: chain 'A' and resid 820 through 824 Processing sheet with id=AB8, first strand: chain 'A' and resid 859 through 864 Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.122A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AC3, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AC4, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC5, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC6, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AC7, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.315A pdb=" N LYS B 319 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 340 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG B 371 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE B 342 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 335 through 336 Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 473 removed outlier: 6.127A pdb=" N GLU B 471 " --> pdb=" O LYS B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 477 through 480 Processing sheet with id=AD2, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.636A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 567 " --> pdb=" O PHE B 506 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 601 through 609 removed outlier: 5.222A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN B 612 " --> pdb=" O ASN B 608 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 761 through 764 Processing sheet with id=AD5, first strand: chain 'B' and resid 761 through 764 Processing sheet with id=AD6, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD7, first strand: chain 'B' and resid 859 through 864 removed outlier: 3.605A pdb=" N PHE B 905 " --> pdb=" O TYR B 884 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2382 1.32 - 1.44: 4034 1.44 - 1.57: 8086 1.57 - 1.69: 1 1.69 - 1.82: 138 Bond restraints: 14641 Sorted by residual: bond pdb=" CB TRP A 529 " pdb=" CG TRP A 529 " ideal model delta sigma weight residual 1.498 1.765 -0.267 3.10e-02 1.04e+03 7.40e+01 bond pdb=" CA TRP A 529 " pdb=" CB TRP A 529 " ideal model delta sigma weight residual 1.530 1.597 -0.066 1.69e-02 3.50e+03 1.55e+01 bond pdb=" N PRO B 548 " pdb=" CD PRO B 548 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.11e+01 bond pdb=" CA CYS A 468 " pdb=" C CYS A 468 " ideal model delta sigma weight residual 1.527 1.488 0.039 1.20e-02 6.94e+03 1.05e+01 bond pdb=" CA TRP A 529 " pdb=" C TRP A 529 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.34e-02 5.57e+03 7.55e+00 ... (remaining 14636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 19513 2.48 - 4.97: 284 4.97 - 7.45: 29 7.45 - 9.94: 5 9.94 - 12.42: 4 Bond angle restraints: 19835 Sorted by residual: angle pdb=" CA PRO B 548 " pdb=" N PRO B 548 " pdb=" CD PRO B 548 " ideal model delta sigma weight residual 112.00 99.58 12.42 1.40e+00 5.10e-01 7.87e+01 angle pdb=" N ALA A 466 " pdb=" CA ALA A 466 " pdb=" C ALA A 466 " ideal model delta sigma weight residual 108.99 119.30 -10.31 1.57e+00 4.06e-01 4.31e+01 angle pdb=" N PHE F 25 " pdb=" CA PHE F 25 " pdb=" C PHE F 25 " ideal model delta sigma weight residual 112.54 106.28 6.26 1.22e+00 6.72e-01 2.63e+01 angle pdb=" N CYS A 468 " pdb=" CA CYS A 468 " pdb=" C CYS A 468 " ideal model delta sigma weight residual 109.83 102.08 7.75 1.55e+00 4.16e-01 2.50e+01 angle pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 ... (remaining 19830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.37: 8287 20.37 - 40.74: 487 40.74 - 61.11: 69 61.11 - 81.48: 21 81.48 - 101.85: 2 Dihedral angle restraints: 8866 sinusoidal: 3695 harmonic: 5171 Sorted by residual: dihedral pdb=" CA PRO B 272 " pdb=" C PRO B 272 " pdb=" N GLY B 273 " pdb=" CA GLY B 273 " ideal model delta harmonic sigma weight residual -180.00 -78.15 -101.85 0 5.00e+00 4.00e-02 4.15e+02 dihedral pdb=" CA THR A 580 " pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta harmonic sigma weight residual 180.00 147.84 32.16 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -138.17 52.17 1 1.00e+01 1.00e-02 3.71e+01 ... (remaining 8863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1673 0.051 - 0.101: 379 0.101 - 0.152: 81 0.152 - 0.202: 16 0.202 - 0.253: 1 Chirality restraints: 2150 Sorted by residual: chirality pdb=" CA TRP A 529 " pdb=" N TRP A 529 " pdb=" C TRP A 529 " pdb=" CB TRP A 529 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU A 770 " pdb=" CB LEU A 770 " pdb=" CD1 LEU A 770 " pdb=" CD2 LEU A 770 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" CG LEU B 358 " pdb=" CB LEU B 358 " pdb=" CD1 LEU B 358 " pdb=" CD2 LEU B 358 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.70e-01 ... (remaining 2147 not shown) Planarity restraints: 2564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 547 " -0.062 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 548 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 548 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 548 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 580 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C THR A 580 " -0.053 2.00e-02 2.50e+03 pdb=" O THR A 580 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 581 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 271 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO A 272 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.043 5.00e-02 4.00e+02 ... (remaining 2561 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 186 2.48 - 3.09: 10866 3.09 - 3.69: 24089 3.69 - 4.30: 34183 4.30 - 4.90: 53282 Nonbonded interactions: 122606 Sorted by model distance: nonbonded pdb=" CD2 PHE B 506 " pdb=" NE1 TRP B 529 " model vdw 1.876 2.736 nonbonded pdb=" CG ARG B 267 " pdb=" NE2 GLN B 276 " model vdw 1.937 3.520 nonbonded pdb=" O GLN A 260 " pdb=" CD2 PHE A 264 " model vdw 1.960 3.340 nonbonded pdb=" OE1 GLN B 521 " pdb=" N ASN B 527 " model vdw 2.014 3.120 nonbonded pdb=" O THR B 516 " pdb=" CD2 PHE B 518 " model vdw 2.068 3.340 ... (remaining 122601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 151 or resid 208 through 540 or resid 548 throug \ h 908)) selection = (chain 'B' and (resid 5 through 521 or resid 527 through 540 or resid 548 throug \ h 658 or resid 705 through 908)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 4 through 26 or resid 56 through 76)) selection = (chain 'F' and (resid 4 through 26 or resid 56 through 76)) selection = (chain 'G' and (resid 4 through 26 or resid 56 through 76)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.100 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 0.007 0.427 14682 Z= 0.447 Angle : 0.759 12.422 19915 Z= 0.410 Chirality : 0.046 0.253 2150 Planarity : 0.005 0.086 2564 Dihedral : 12.875 101.852 5412 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 33.88 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.74 % Favored : 89.68 % Rotamer: Outliers : 1.18 % Allowed : 1.24 % Favored : 97.58 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.20), residues: 1735 helix: -0.98 (0.32), residues: 236 sheet: -0.65 (0.29), residues: 334 loop : -1.39 (0.19), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 383 TYR 0.038 0.002 TYR A 512 PHE 0.016 0.002 PHE B 400 TRP 0.026 0.002 TRP A 529 HIS 0.010 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00576 (14641) covalent geometry : angle 0.75813 (19835) SS BOND : bond 0.00379 ( 40) SS BOND : angle 0.95709 ( 80) hydrogen bonds : bond 0.19371 ( 361) hydrogen bonds : angle 8.31155 ( 942) Misc. bond : bond 0.42684 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7681 (pmm) cc_final: 0.7029 (pmm) REVERT: A 91 TYR cc_start: 0.8771 (m-10) cc_final: 0.8376 (m-10) REVERT: A 137 LEU cc_start: 0.9394 (tp) cc_final: 0.9148 (tp) REVERT: A 833 MET cc_start: 0.8869 (tpt) cc_final: 0.8488 (tpt) REVERT: B 379 LEU cc_start: 0.9097 (tt) cc_final: 0.8459 (tt) REVERT: B 833 MET cc_start: 0.9231 (mmp) cc_final: 0.8629 (mmp) REVERT: E 11 LEU cc_start: 0.9378 (tt) cc_final: 0.9163 (tp) REVERT: E 69 TYR cc_start: 0.9026 (t80) cc_final: 0.8758 (t80) outliers start: 19 outliers final: 5 residues processed: 115 average time/residue: 0.1378 time to fit residues: 23.2932 Evaluate side-chains 70 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN A 199 HIS ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 431 ASN ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 343 ASN ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 GLN F 60 GLN G 60 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.046980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.029526 restraints weight = 156651.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.030458 restraints weight = 87959.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.031106 restraints weight = 60404.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.031506 restraints weight = 46879.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.031728 restraints weight = 39585.946| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 14682 Z= 0.286 Angle : 0.738 10.156 19915 Z= 0.379 Chirality : 0.045 0.170 2150 Planarity : 0.005 0.069 2564 Dihedral : 5.671 58.677 1935 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 24.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.99 % Favored : 90.66 % Rotamer: Outliers : 0.06 % Allowed : 5.28 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.20), residues: 1735 helix: -0.51 (0.32), residues: 234 sheet: -0.73 (0.28), residues: 344 loop : -1.36 (0.19), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 479 TYR 0.028 0.002 TYR A 581 PHE 0.026 0.002 PHE A 264 TRP 0.018 0.002 TRP B 529 HIS 0.009 0.002 HIS B 386 Details of bonding type rmsd covalent geometry : bond 0.00613 (14641) covalent geometry : angle 0.73676 (19835) SS BOND : bond 0.00389 ( 40) SS BOND : angle 1.05061 ( 80) hydrogen bonds : bond 0.05218 ( 361) hydrogen bonds : angle 7.62422 ( 942) Misc. bond : bond 0.00457 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7939 (pmm) cc_final: 0.7223 (pmm) REVERT: A 404 ASP cc_start: 0.8790 (m-30) cc_final: 0.8564 (m-30) REVERT: B 379 LEU cc_start: 0.9278 (tt) cc_final: 0.8695 (tt) REVERT: B 833 MET cc_start: 0.9040 (mmp) cc_final: 0.8456 (mmp) REVERT: E 11 LEU cc_start: 0.9556 (tt) cc_final: 0.9263 (tp) REVERT: E 15 LEU cc_start: 0.9711 (mm) cc_final: 0.9431 (mm) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.1154 time to fit residues: 14.6333 Evaluate side-chains 57 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 136 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 132 optimal weight: 0.0970 chunk 108 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 77 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 431 ASN ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 343 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN G 60 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.048289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.030384 restraints weight = 153249.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.031469 restraints weight = 84620.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.032174 restraints weight = 57254.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.032656 restraints weight = 43966.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.032911 restraints weight = 36930.373| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14682 Z= 0.141 Angle : 0.611 9.887 19915 Z= 0.317 Chirality : 0.044 0.192 2150 Planarity : 0.004 0.067 2564 Dihedral : 5.400 50.749 1935 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.86 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.21), residues: 1735 helix: -0.04 (0.33), residues: 232 sheet: -0.52 (0.28), residues: 355 loop : -1.29 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 22 TYR 0.020 0.001 TYR A 581 PHE 0.026 0.001 PHE B 506 TRP 0.021 0.002 TRP B 529 HIS 0.010 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00309 (14641) covalent geometry : angle 0.60794 (19835) SS BOND : bond 0.00455 ( 40) SS BOND : angle 1.14007 ( 80) hydrogen bonds : bond 0.04364 ( 361) hydrogen bonds : angle 7.03449 ( 942) Misc. bond : bond 0.01196 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7751 (pmm) cc_final: 0.7469 (pmm) REVERT: A 36 LEU cc_start: 0.9307 (pt) cc_final: 0.8734 (pt) REVERT: A 404 ASP cc_start: 0.8723 (m-30) cc_final: 0.8520 (m-30) REVERT: A 581 TYR cc_start: 0.5214 (m-10) cc_final: 0.4572 (m-10) REVERT: B 379 LEU cc_start: 0.9272 (tt) cc_final: 0.8880 (tt) REVERT: B 833 MET cc_start: 0.9059 (mmp) cc_final: 0.8550 (mmp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1225 time to fit residues: 16.2025 Evaluate side-chains 64 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 61 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 109 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 431 ASN A 470 ASN ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN B 32 HIS B 108 ASN B 275 HIS B 343 ASN ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN G 60 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.047011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.029383 restraints weight = 157964.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.030405 restraints weight = 88868.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.031074 restraints weight = 60633.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.031483 restraints weight = 46673.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.031767 restraints weight = 39642.376| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14682 Z= 0.241 Angle : 0.677 11.774 19915 Z= 0.346 Chirality : 0.044 0.183 2150 Planarity : 0.004 0.069 2564 Dihedral : 5.472 45.709 1935 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.82 % Favored : 90.89 % Rotamer: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.20), residues: 1735 helix: -0.22 (0.33), residues: 239 sheet: -0.66 (0.27), residues: 364 loop : -1.36 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 252 TYR 0.030 0.002 TYR A 581 PHE 0.021 0.002 PHE B 506 TRP 0.022 0.002 TRP B 529 HIS 0.009 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00520 (14641) covalent geometry : angle 0.67428 (19835) SS BOND : bond 0.00300 ( 40) SS BOND : angle 1.23440 ( 80) hydrogen bonds : bond 0.04399 ( 361) hydrogen bonds : angle 7.16925 ( 942) Misc. bond : bond 0.01047 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7793 (pmm) cc_final: 0.7380 (pmm) REVERT: A 34 GLN cc_start: 0.8778 (mt0) cc_final: 0.8578 (mt0) REVERT: A 36 LEU cc_start: 0.9345 (pt) cc_final: 0.8760 (pt) REVERT: A 91 TYR cc_start: 0.8808 (m-10) cc_final: 0.8481 (m-10) REVERT: A 404 ASP cc_start: 0.8818 (m-30) cc_final: 0.8594 (m-30) REVERT: A 504 MET cc_start: 0.8132 (pmm) cc_final: 0.7874 (pmm) REVERT: A 833 MET cc_start: 0.8973 (tpt) cc_final: 0.8749 (tpt) REVERT: B 379 LEU cc_start: 0.9280 (tt) cc_final: 0.8916 (tt) REVERT: B 833 MET cc_start: 0.9012 (mmp) cc_final: 0.8551 (mmp) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1081 time to fit residues: 13.3933 Evaluate side-chains 58 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 173 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 343 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN G 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.047891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.030093 restraints weight = 157863.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.031188 restraints weight = 87421.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.031894 restraints weight = 58729.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.032297 restraints weight = 45070.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.032469 restraints weight = 38062.084| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14682 Z= 0.146 Angle : 0.606 12.534 19915 Z= 0.312 Chirality : 0.044 0.208 2150 Planarity : 0.004 0.069 2564 Dihedral : 5.317 42.854 1935 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.32 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.20), residues: 1735 helix: -0.34 (0.32), residues: 251 sheet: -0.52 (0.28), residues: 365 loop : -1.32 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 252 TYR 0.020 0.001 TYR A 581 PHE 0.022 0.001 PHE A 477 TRP 0.016 0.001 TRP B 529 HIS 0.006 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00324 (14641) covalent geometry : angle 0.60321 (19835) SS BOND : bond 0.00234 ( 40) SS BOND : angle 1.07556 ( 80) hydrogen bonds : bond 0.03924 ( 361) hydrogen bonds : angle 6.86901 ( 942) Misc. bond : bond 0.00787 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9309 (pt) cc_final: 0.8698 (pt) REVERT: A 581 TYR cc_start: 0.4878 (m-10) cc_final: 0.4386 (m-10) REVERT: A 833 MET cc_start: 0.8980 (tpt) cc_final: 0.8755 (tpt) REVERT: B 358 LEU cc_start: 0.8803 (tt) cc_final: 0.8393 (mp) REVERT: B 833 MET cc_start: 0.8993 (mmp) cc_final: 0.8595 (mmp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1164 time to fit residues: 13.8013 Evaluate side-chains 60 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 139 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 50.0000 chunk 100 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 541 ASN ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 343 ASN F 60 GLN G 60 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.047410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.029750 restraints weight = 159814.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.030804 restraints weight = 88116.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.031477 restraints weight = 59529.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.031831 restraints weight = 45898.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.032166 restraints weight = 38982.160| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14682 Z= 0.180 Angle : 0.624 12.511 19915 Z= 0.318 Chirality : 0.044 0.173 2150 Planarity : 0.004 0.069 2564 Dihedral : 5.282 40.036 1935 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.30 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.20), residues: 1735 helix: -0.35 (0.32), residues: 252 sheet: -0.55 (0.28), residues: 364 loop : -1.35 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 252 TYR 0.025 0.002 TYR A 847 PHE 0.017 0.001 PHE B 506 TRP 0.017 0.002 TRP B 529 HIS 0.008 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00396 (14641) covalent geometry : angle 0.62055 (19835) SS BOND : bond 0.00276 ( 40) SS BOND : angle 1.15749 ( 80) hydrogen bonds : bond 0.03912 ( 361) hydrogen bonds : angle 6.86543 ( 942) Misc. bond : bond 0.00813 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 11 MET cc_start: 0.7719 (pmm) cc_final: 0.7392 (pmm) REVERT: A 36 LEU cc_start: 0.9326 (pt) cc_final: 0.8687 (pt) REVERT: A 91 TYR cc_start: 0.8644 (m-10) cc_final: 0.8340 (m-10) REVERT: A 404 ASP cc_start: 0.8801 (m-30) cc_final: 0.8548 (m-30) REVERT: A 833 MET cc_start: 0.8867 (tpt) cc_final: 0.8656 (tpt) REVERT: B 379 LEU cc_start: 0.9328 (tt) cc_final: 0.8710 (tt) REVERT: B 833 MET cc_start: 0.8950 (mmp) cc_final: 0.8592 (mmp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1136 time to fit residues: 13.3057 Evaluate side-chains 55 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 138 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 173 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN B 108 ASN B 343 ASN F 60 GLN G 60 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.047990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.030265 restraints weight = 155031.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.031368 restraints weight = 85854.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.032052 restraints weight = 57671.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.032359 restraints weight = 44169.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.032779 restraints weight = 38141.507| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14682 Z= 0.128 Angle : 0.592 10.624 19915 Z= 0.303 Chirality : 0.044 0.169 2150 Planarity : 0.004 0.068 2564 Dihedral : 5.170 38.717 1935 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.09 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.20), residues: 1735 helix: -0.40 (0.32), residues: 258 sheet: -0.47 (0.28), residues: 364 loop : -1.29 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 872 TYR 0.019 0.001 TYR A 91 PHE 0.019 0.001 PHE B 382 TRP 0.014 0.001 TRP B 412 HIS 0.011 0.001 HIS B 831 Details of bonding type rmsd covalent geometry : bond 0.00288 (14641) covalent geometry : angle 0.58924 (19835) SS BOND : bond 0.00224 ( 40) SS BOND : angle 1.04429 ( 80) hydrogen bonds : bond 0.03663 ( 361) hydrogen bonds : angle 6.61638 ( 942) Misc. bond : bond 0.00719 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9308 (pt) cc_final: 0.8703 (pt) REVERT: A 404 ASP cc_start: 0.8761 (m-30) cc_final: 0.8527 (m-30) REVERT: B 358 LEU cc_start: 0.8760 (tt) cc_final: 0.8393 (mp) REVERT: B 379 LEU cc_start: 0.9297 (tt) cc_final: 0.8870 (tt) REVERT: B 382 PHE cc_start: 0.9187 (m-80) cc_final: 0.8953 (m-80) REVERT: B 833 MET cc_start: 0.9111 (mmp) cc_final: 0.8635 (mmp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1139 time to fit residues: 14.4142 Evaluate side-chains 61 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 8 optimal weight: 0.1980 chunk 121 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 17 optimal weight: 0.0050 chunk 144 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN B 108 ASN B 343 ASN F 60 GLN G 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.048030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.030284 restraints weight = 154074.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.031380 restraints weight = 85354.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.032087 restraints weight = 57257.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.032558 restraints weight = 43897.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.032778 restraints weight = 36359.986| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14682 Z= 0.131 Angle : 0.609 10.023 19915 Z= 0.311 Chirality : 0.044 0.207 2150 Planarity : 0.004 0.068 2564 Dihedral : 5.175 37.639 1935 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.61 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.21), residues: 1735 helix: -0.38 (0.32), residues: 258 sheet: -0.43 (0.28), residues: 370 loop : -1.25 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 556 TYR 0.021 0.001 TYR A 91 PHE 0.015 0.001 PHE B 382 TRP 0.020 0.001 TRP B 529 HIS 0.006 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00293 (14641) covalent geometry : angle 0.60293 (19835) SS BOND : bond 0.00223 ( 40) SS BOND : angle 1.44137 ( 80) hydrogen bonds : bond 0.03699 ( 361) hydrogen bonds : angle 6.45876 ( 942) Misc. bond : bond 0.00747 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9309 (pt) cc_final: 0.8691 (pt) REVERT: A 404 ASP cc_start: 0.8759 (m-30) cc_final: 0.8532 (m-30) REVERT: A 504 MET cc_start: 0.8106 (pmm) cc_final: 0.7860 (pmm) REVERT: A 833 MET cc_start: 0.8794 (tpt) cc_final: 0.8487 (tpt) REVERT: B 358 LEU cc_start: 0.8799 (tt) cc_final: 0.8433 (mp) REVERT: B 379 LEU cc_start: 0.9199 (tt) cc_final: 0.8709 (tt) REVERT: B 382 PHE cc_start: 0.9215 (m-80) cc_final: 0.8971 (m-80) REVERT: B 833 MET cc_start: 0.9083 (mmp) cc_final: 0.8595 (mmp) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1133 time to fit residues: 14.3721 Evaluate side-chains 65 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 3 optimal weight: 1.9990 chunk 159 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 31 optimal weight: 0.0000 chunk 110 optimal weight: 0.7980 chunk 169 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 53 optimal weight: 0.0000 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN B 108 ASN B 343 ASN F 60 GLN G 60 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.048175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.030393 restraints weight = 152386.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.031515 restraints weight = 84771.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.032234 restraints weight = 56845.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.032703 restraints weight = 43247.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.032950 restraints weight = 36259.586| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14682 Z= 0.119 Angle : 0.599 9.892 19915 Z= 0.305 Chirality : 0.044 0.191 2150 Planarity : 0.004 0.068 2564 Dihedral : 5.157 36.885 1935 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.26 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.21), residues: 1735 helix: -0.38 (0.32), residues: 258 sheet: -0.38 (0.28), residues: 369 loop : -1.19 (0.20), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 22 TYR 0.018 0.001 TYR A 581 PHE 0.020 0.001 PHE G 24 TRP 0.018 0.001 TRP B 529 HIS 0.006 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00269 (14641) covalent geometry : angle 0.59481 (19835) SS BOND : bond 0.00326 ( 40) SS BOND : angle 1.29132 ( 80) hydrogen bonds : bond 0.03580 ( 361) hydrogen bonds : angle 6.34363 ( 942) Misc. bond : bond 0.00737 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9303 (pt) cc_final: 0.8676 (pt) REVERT: A 404 ASP cc_start: 0.8746 (m-30) cc_final: 0.8508 (m-30) REVERT: A 581 TYR cc_start: 0.4884 (m-10) cc_final: 0.4515 (m-10) REVERT: A 833 MET cc_start: 0.8757 (tpt) cc_final: 0.8436 (tpt) REVERT: B 358 LEU cc_start: 0.8811 (tt) cc_final: 0.8461 (mp) REVERT: B 379 LEU cc_start: 0.9186 (tt) cc_final: 0.8668 (tt) REVERT: B 382 PHE cc_start: 0.9207 (m-80) cc_final: 0.8970 (m-80) REVERT: B 833 MET cc_start: 0.9073 (mmp) cc_final: 0.8577 (mmp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1015 time to fit residues: 13.2866 Evaluate side-chains 63 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 127 optimal weight: 6.9990 chunk 160 optimal weight: 40.0000 chunk 71 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 169 optimal weight: 0.5980 chunk 20 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN B 108 ASN B 343 ASN F 60 GLN G 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.047770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.030081 restraints weight = 156528.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.031154 restraints weight = 86855.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.031855 restraints weight = 58526.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.032306 restraints weight = 44733.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.032482 restraints weight = 37529.825| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14682 Z= 0.143 Angle : 0.603 9.296 19915 Z= 0.307 Chirality : 0.044 0.202 2150 Planarity : 0.004 0.067 2564 Dihedral : 5.169 35.861 1935 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.01 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.21), residues: 1735 helix: -0.03 (0.33), residues: 244 sheet: -0.43 (0.28), residues: 368 loop : -1.15 (0.20), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 252 TYR 0.023 0.001 TYR A 91 PHE 0.016 0.001 PHE B 506 TRP 0.023 0.002 TRP A 553 HIS 0.008 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00318 (14641) covalent geometry : angle 0.59986 (19835) SS BOND : bond 0.00304 ( 40) SS BOND : angle 1.13289 ( 80) hydrogen bonds : bond 0.03608 ( 361) hydrogen bonds : angle 6.33843 ( 942) Misc. bond : bond 0.00793 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 11 MET cc_start: 0.7576 (pmm) cc_final: 0.7371 (pmm) REVERT: A 404 ASP cc_start: 0.8692 (m-30) cc_final: 0.8470 (m-30) REVERT: A 504 MET cc_start: 0.7894 (pmm) cc_final: 0.7669 (pmm) REVERT: A 833 MET cc_start: 0.8808 (tpt) cc_final: 0.8463 (tpt) REVERT: B 56 MET cc_start: 0.8026 (tpt) cc_final: 0.6842 (mmt) REVERT: B 358 LEU cc_start: 0.8858 (tt) cc_final: 0.8485 (mp) REVERT: B 379 LEU cc_start: 0.9175 (tt) cc_final: 0.8660 (tt) REVERT: B 382 PHE cc_start: 0.9222 (m-80) cc_final: 0.9000 (m-80) REVERT: B 833 MET cc_start: 0.9070 (mmp) cc_final: 0.8588 (mmp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1042 time to fit residues: 12.5638 Evaluate side-chains 60 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 86 optimal weight: 0.0370 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 overall best weight: 2.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 343 ASN F 60 GLN G 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.047753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.030090 restraints weight = 156608.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.031176 restraints weight = 86924.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.031877 restraints weight = 58292.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.032265 restraints weight = 44813.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.032607 restraints weight = 37740.256| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14682 Z= 0.139 Angle : 0.594 9.064 19915 Z= 0.303 Chirality : 0.043 0.190 2150 Planarity : 0.004 0.067 2564 Dihedral : 5.154 35.302 1935 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.49 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.21), residues: 1735 helix: -0.18 (0.33), residues: 250 sheet: -0.33 (0.28), residues: 362 loop : -1.17 (0.20), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.013 0.001 TYR A 847 PHE 0.013 0.001 PHE B 382 TRP 0.018 0.001 TRP B 529 HIS 0.007 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00311 (14641) covalent geometry : angle 0.59099 (19835) SS BOND : bond 0.00234 ( 40) SS BOND : angle 1.07895 ( 80) hydrogen bonds : bond 0.03566 ( 361) hydrogen bonds : angle 6.29997 ( 942) Misc. bond : bond 0.00755 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3518.91 seconds wall clock time: 61 minutes 25.92 seconds (3685.92 seconds total)