Starting phenix.real_space_refine on Tue Dec 31 21:43:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stk_25431/12_2024/7stk_25431_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stk_25431/12_2024/7stk_25431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7stk_25431/12_2024/7stk_25431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stk_25431/12_2024/7stk_25431.map" model { file = "/net/cci-nas-00/data/ceres_data/7stk_25431/12_2024/7stk_25431_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stk_25431/12_2024/7stk_25431_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3406 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 116 5.16 5 C 8828 2.51 5 N 2389 2.21 5 O 2578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13911 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6579 Classifications: {'peptide': 815} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 770} Chain breaks: 8 Chain: "B" Number of atoms: 6621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6621 Classifications: {'peptide': 820} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 773} Chain breaks: 6 Chain: "C" 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: "D" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 335 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain breaks: 1 Time building chain proxies: 8.13, per 1000 atoms: 0.58 Number of scatterers: 13911 At special positions: 0 Unit cell: (133.92, 128.52, 177.12, 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 116 16.00 O 2578 8.00 N 2389 7.00 C 8828 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=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 860 " distance=2.03 Simple disulfide: pdb=" SG CYS A 682 " - pdb=" SG CYS B 685 " distance=2.34 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 860 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 66 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.8 seconds 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 32 sheets defined 15.9% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.734A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.905A pdb=" N ARG A 47 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 4.531A pdb=" N LEU A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.555A pdb=" N ILE A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.709A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.491A pdb=" N GLU A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.915A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.759A pdb=" N LEU A 500 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.746A pdb=" N GLU A 643 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 714 Processing helix chain 'A' and resid 863 through 870 Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.982A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 71 through 75 removed outlier: 4.153A pdb=" N ASP B 74 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.609A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN B 268 " --> pdb=" O PHE B 264 " (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 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.515A pdb=" N PHE B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.918A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 689 through 695 Processing helix chain 'B' and resid 704 through 715 Processing helix chain 'B' and resid 863 through 869 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.801A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.593A pdb=" N LEU C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 67 through 72' Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 67 through 74 removed outlier: 3.590A pdb=" N LEU D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR D 74 " --> pdb=" O GLN D 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.657A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N MET A 98 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLU A 97 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR A 144 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 119 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.869A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) 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 212 through 216 removed outlier: 5.994A pdb=" N LEU A 213 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N CYS A 228 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASN A 215 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233 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 292 through 293 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 314 removed outlier: 4.154A pdb=" N ILE A 314 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER A 339 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.382A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LYS A 369 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 340 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ARG A 371 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE A 342 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 475 through 480 Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 534 Processing sheet with id=AB3, first strand: chain 'A' and resid 599 through 605 removed outlier: 5.595A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 759 through 762 removed outlier: 4.166A pdb=" N GLY A 778 " --> pdb=" O GLN A 635 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 819 through 822 Processing sheet with id=AB6, first strand: chain 'A' and resid 859 through 862 removed outlier: 3.605A pdb=" N LEU A 844 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL A 886 " --> pdb=" O TRP A 897 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TRP A 897 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 888 " --> pdb=" O GLY A 895 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 880 through 882 removed outlier: 3.717A pdb=" N PHE A 903 " --> pdb=" O TYR A 882 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.544A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ARG B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL B 94 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLU B 120 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE B 96 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASN B 122 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 145 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU B 120 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU B 147 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.569A pdb=" N ILE B 29 " --> pdb=" O MET B 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC2, first strand: chain 'B' and resid 212 through 216 removed outlier: 6.172A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC4, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC5, first strand: chain 'B' and resid 318 through 321 removed outlier: 8.493A pdb=" N HIS B 429 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 335 through 336 Processing sheet with id=AC7, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC8, first strand: chain 'B' and resid 477 through 479 Processing sheet with id=AC9, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.667A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 599 through 604 removed outlier: 7.084A pdb=" N LYS B 614 " --> pdb=" O PRO B 601 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER B 603 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 612 " --> pdb=" O SER B 603 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.774A pdb=" N GLU B 760 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 788 " --> pdb=" O ARG B 794 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 759 through 762 removed outlier: 3.774A pdb=" N GLU B 760 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 819 through 822 removed outlier: 3.522A pdb=" N CYS B 872 " --> pdb=" O LEU B 830 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 856 through 862 339 hydrogen bonds defined for protein. 843 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: 5.12 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4549 1.34 - 1.46: 3051 1.46 - 1.58: 6506 1.58 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 14246 Sorted by residual: bond pdb=" CA GLU A 469 " pdb=" C GLU A 469 " ideal model delta sigma weight residual 1.523 1.501 0.022 1.35e-02 5.49e+03 2.64e+00 bond pdb=" N CYS A 468 " pdb=" CA CYS A 468 " ideal model delta sigma weight residual 1.455 1.473 -0.018 1.33e-02 5.65e+03 1.83e+00 bond pdb=" CA GLU A 471 " pdb=" C GLU A 471 " ideal model delta sigma weight residual 1.519 1.504 0.015 1.14e-02 7.69e+03 1.74e+00 bond pdb=" C CYS A 682 " pdb=" N CYS A 683 " ideal model delta sigma weight residual 1.332 1.315 0.018 1.40e-02 5.10e+03 1.58e+00 bond pdb=" CA GLU A 469 " pdb=" CB GLU A 469 " ideal model delta sigma weight residual 1.529 1.510 0.019 1.58e-02 4.01e+03 1.46e+00 ... (remaining 14241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 19176 2.79 - 5.58: 114 5.58 - 8.36: 9 8.36 - 11.15: 0 11.15 - 13.94: 1 Bond angle restraints: 19300 Sorted by residual: angle pdb=" N GLU A 469 " pdb=" CA GLU A 469 " pdb=" C GLU A 469 " ideal model delta sigma weight residual 111.33 97.39 13.94 1.21e+00 6.83e-01 1.33e+02 angle pdb=" C SER A 467 " pdb=" N CYS A 468 " pdb=" CA CYS A 468 " ideal model delta sigma weight residual 122.49 115.96 6.53 1.55e+00 4.16e-01 1.77e+01 angle pdb=" C PHE B 714 " pdb=" N VAL B 715 " pdb=" CA VAL B 715 " ideal model delta sigma weight residual 122.13 129.66 -7.53 1.85e+00 2.92e-01 1.66e+01 angle pdb=" N ASN A 470 " pdb=" CA ASN A 470 " pdb=" C ASN A 470 " ideal model delta sigma weight residual 110.80 117.91 -7.11 2.13e+00 2.20e-01 1.11e+01 angle pdb=" C VAL A 99 " pdb=" N HIS A 100 " pdb=" CA HIS A 100 " ideal model delta sigma weight residual 121.54 127.02 -5.48 1.91e+00 2.74e-01 8.23e+00 ... (remaining 19295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 7743 17.46 - 34.92: 738 34.92 - 52.38: 118 52.38 - 69.84: 30 69.84 - 87.30: 20 Dihedral angle restraints: 8649 sinusoidal: 3612 harmonic: 5037 Sorted by residual: dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 -179.70 -87.30 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS D 7 " pdb=" SG CYS D 7 " pdb=" SG CYS D 62 " pdb=" CB CYS D 62 " ideal model delta sinusoidal sigma weight residual 93.00 12.44 80.56 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" CB CYS C 7 " pdb=" SG CYS C 7 " pdb=" SG CYS C 62 " pdb=" CB CYS C 62 " ideal model delta sinusoidal sigma weight residual 93.00 26.25 66.75 1 1.00e+01 1.00e-02 5.81e+01 ... (remaining 8646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1655 0.050 - 0.101: 349 0.101 - 0.151: 86 0.151 - 0.202: 4 0.202 - 0.252: 1 Chirality restraints: 2095 Sorted by residual: chirality pdb=" CA CYS A 468 " pdb=" N CYS A 468 " pdb=" C CYS A 468 " pdb=" CB CYS A 468 " 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=" CA ASN A 470 " pdb=" N ASN A 470 " pdb=" C ASN A 470 " pdb=" CB ASN A 470 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 2092 not shown) Planarity restraints: 2493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 682 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C CYS A 682 " -0.036 2.00e-02 2.50e+03 pdb=" O CYS A 682 " 0.014 2.00e-02 2.50e+03 pdb=" N CYS A 683 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 43 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 467 " -0.008 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C SER A 467 " 0.026 2.00e-02 2.50e+03 pdb=" O SER A 467 " -0.010 2.00e-02 2.50e+03 pdb=" N CYS A 468 " -0.009 2.00e-02 2.50e+03 ... (remaining 2490 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 486 2.70 - 3.25: 14194 3.25 - 3.80: 22891 3.80 - 4.35: 29092 4.35 - 4.90: 47041 Nonbonded interactions: 113704 Sorted by model distance: nonbonded pdb=" O GLU D 59 " pdb=" OG1 THR D 63 " model vdw 2.147 3.040 nonbonded pdb=" NH2 ARG A 14 " pdb=" O VAL B 712 " model vdw 2.171 3.120 nonbonded pdb=" O SER B 878 " pdb=" OH TYR B 882 " model vdw 2.173 3.040 nonbonded pdb=" O PRO A 77 " pdb=" ND2 ASN A 108 " model vdw 2.186 3.120 nonbonded pdb=" O GLN B 513 " pdb=" OH TYR B 587 " model vdw 2.212 3.040 ... (remaining 113699 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 3 through 518 or resid 528 through 905)) selection = (chain 'B' and (resid 3 through 314 or resid 317 through 346 or resid 351 throug \ h 539 or resid 547 through 717 or resid 756 through 905)) } ncs_group { reference = (chain 'C' and (resid 4 through 25 or resid 56 through 76)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.560 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14246 Z= 0.248 Angle : 0.592 13.941 19300 Z= 0.315 Chirality : 0.044 0.252 2095 Planarity : 0.003 0.040 2493 Dihedral : 13.676 86.409 5273 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.12 % Favored : 92.47 % Rotamer: Outliers : 0.19 % Allowed : 0.70 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.22), residues: 1686 helix: -0.21 (0.39), residues: 201 sheet: -0.16 (0.29), residues: 372 loop : -0.89 (0.20), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 414 HIS 0.008 0.001 HIS B 829 PHE 0.022 0.001 PHE A 46 TYR 0.012 0.001 TYR B 708 ARG 0.004 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 1.665 Fit side-chains REVERT: A 32 HIS cc_start: 0.9095 (p90) cc_final: 0.8705 (p-80) REVERT: A 88 PHE cc_start: 0.8597 (t80) cc_final: 0.8175 (t80) outliers start: 3 outliers final: 1 residues processed: 62 average time/residue: 0.2167 time to fit residues: 23.2500 Evaluate side-chains 44 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 30.0000 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 155 optimal weight: 50.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 431 ASN ** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14246 Z= 0.412 Angle : 0.674 9.006 19300 Z= 0.345 Chirality : 0.046 0.164 2095 Planarity : 0.004 0.043 2493 Dihedral : 4.560 28.214 1880 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.53 % Favored : 92.17 % Rotamer: Outliers : 0.51 % Allowed : 6.62 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.21), residues: 1686 helix: -0.38 (0.36), residues: 206 sheet: -0.15 (0.29), residues: 367 loop : -1.02 (0.20), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 414 HIS 0.004 0.001 HIS B 209 PHE 0.014 0.002 PHE B 427 TYR 0.015 0.002 TYR B 800 ARG 0.005 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.595 Fit side-chains REVERT: A 32 HIS cc_start: 0.9123 (p90) cc_final: 0.8764 (p-80) REVERT: B 831 MET cc_start: 0.7683 (mmm) cc_final: 0.7411 (mmm) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.2097 time to fit residues: 19.0750 Evaluate side-chains 49 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 168 optimal weight: 0.0170 chunk 138 optimal weight: 9.9990 chunk 154 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN A 313 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 HIS B 34 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14246 Z= 0.147 Angle : 0.564 9.393 19300 Z= 0.289 Chirality : 0.044 0.206 2095 Planarity : 0.003 0.038 2493 Dihedral : 4.272 27.633 1879 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.93 % Favored : 93.77 % Rotamer: Outliers : 0.70 % Allowed : 9.41 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.21), residues: 1686 helix: -0.32 (0.36), residues: 222 sheet: -0.02 (0.29), residues: 364 loop : -0.97 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 414 HIS 0.003 0.001 HIS B 829 PHE 0.027 0.001 PHE A 88 TYR 0.013 0.001 TYR B 708 ARG 0.003 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 1.621 Fit side-chains REVERT: A 32 HIS cc_start: 0.9079 (p90) cc_final: 0.8703 (p-80) REVERT: B 401 TYR cc_start: 0.8657 (t80) cc_final: 0.8310 (t80) REVERT: D 60 GLN cc_start: 0.9021 (tt0) cc_final: 0.8023 (tm-30) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.2066 time to fit residues: 21.8146 Evaluate side-chains 56 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain B residue 696 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 30.0000 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 17 optimal weight: 30.0000 chunk 74 optimal weight: 7.9990 chunk 104 optimal weight: 0.4980 chunk 156 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14246 Z= 0.229 Angle : 0.567 9.553 19300 Z= 0.288 Chirality : 0.044 0.183 2095 Planarity : 0.003 0.039 2493 Dihedral : 4.252 27.454 1879 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.70 % Favored : 93.00 % Rotamer: Outliers : 1.02 % Allowed : 11.20 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.22), residues: 1686 helix: -0.37 (0.36), residues: 222 sheet: -0.01 (0.29), residues: 364 loop : -0.93 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 414 HIS 0.003 0.001 HIS B 829 PHE 0.012 0.001 PHE A 518 TYR 0.014 0.001 TYR B 708 ARG 0.004 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 1.724 Fit side-chains REVERT: A 32 HIS cc_start: 0.9092 (p90) cc_final: 0.8726 (p-80) outliers start: 16 outliers final: 12 residues processed: 56 average time/residue: 0.2130 time to fit residues: 21.0123 Evaluate side-chains 57 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14246 Z= 0.289 Angle : 0.603 12.589 19300 Z= 0.303 Chirality : 0.044 0.176 2095 Planarity : 0.004 0.040 2493 Dihedral : 4.387 27.724 1879 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.24 % Favored : 92.47 % Rotamer: Outliers : 1.27 % Allowed : 11.96 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1686 helix: -0.52 (0.36), residues: 218 sheet: -0.07 (0.29), residues: 364 loop : -0.91 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 414 HIS 0.004 0.001 HIS B 440 PHE 0.020 0.001 PHE A 88 TYR 0.014 0.001 TYR B 708 ARG 0.004 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 1.724 Fit side-chains revert: symmetry clash REVERT: A 32 HIS cc_start: 0.9128 (p90) cc_final: 0.8738 (p-80) REVERT: A 69 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8100 (mm) REVERT: A 469 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: D 60 GLN cc_start: 0.9014 (tt0) cc_final: 0.7908 (tm-30) outliers start: 20 outliers final: 16 residues processed: 57 average time/residue: 0.2149 time to fit residues: 21.4478 Evaluate side-chains 64 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 165 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 0.0060 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14246 Z= 0.155 Angle : 0.554 10.677 19300 Z= 0.279 Chirality : 0.043 0.183 2095 Planarity : 0.003 0.040 2493 Dihedral : 4.212 27.081 1879 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.35 % Favored : 93.36 % Rotamer: Outliers : 1.34 % Allowed : 13.49 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1686 helix: -0.42 (0.36), residues: 224 sheet: -0.06 (0.29), residues: 364 loop : -0.88 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 414 HIS 0.002 0.000 HIS A 429 PHE 0.015 0.001 PHE A 705 TYR 0.017 0.001 TYR C 69 ARG 0.002 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: A 32 HIS cc_start: 0.9123 (p90) cc_final: 0.8748 (p-80) REVERT: A 69 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8378 (mm) REVERT: B 401 TYR cc_start: 0.8742 (t80) cc_final: 0.8326 (t80) REVERT: D 60 GLN cc_start: 0.9008 (tt0) cc_final: 0.7908 (tm-30) outliers start: 21 outliers final: 15 residues processed: 64 average time/residue: 0.2054 time to fit residues: 22.8425 Evaluate side-chains 65 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 682 CYS Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 120 optimal weight: 0.0370 chunk 93 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14246 Z= 0.277 Angle : 0.592 9.934 19300 Z= 0.297 Chirality : 0.043 0.169 2095 Planarity : 0.003 0.041 2493 Dihedral : 4.311 27.674 1879 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.41 % Favored : 92.29 % Rotamer: Outliers : 1.59 % Allowed : 13.99 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1686 helix: -0.28 (0.37), residues: 209 sheet: -0.11 (0.29), residues: 362 loop : -0.84 (0.20), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 414 HIS 0.003 0.001 HIS B 32 PHE 0.020 0.001 PHE A 88 TYR 0.015 0.001 TYR B 708 ARG 0.004 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 1.790 Fit side-chains revert: symmetry clash REVERT: A 32 HIS cc_start: 0.9102 (p90) cc_final: 0.8684 (p-80) REVERT: A 69 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8198 (mm) REVERT: A 582 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8859 (tttt) outliers start: 25 outliers final: 19 residues processed: 66 average time/residue: 0.2134 time to fit residues: 24.4537 Evaluate side-chains 67 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 682 CYS Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14246 Z= 0.173 Angle : 0.565 10.729 19300 Z= 0.285 Chirality : 0.043 0.178 2095 Planarity : 0.003 0.041 2493 Dihedral : 4.216 27.276 1879 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.58 % Favored : 93.12 % Rotamer: Outliers : 1.34 % Allowed : 14.63 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1686 helix: -0.28 (0.37), residues: 215 sheet: -0.11 (0.29), residues: 362 loop : -0.84 (0.20), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 414 HIS 0.009 0.001 HIS B 21 PHE 0.014 0.001 PHE B 482 TYR 0.018 0.001 TYR C 69 ARG 0.002 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: A 32 HIS cc_start: 0.9113 (p90) cc_final: 0.8742 (p-80) REVERT: A 69 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8297 (mm) REVERT: A 582 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8813 (tttt) outliers start: 21 outliers final: 19 residues processed: 57 average time/residue: 0.2184 time to fit residues: 21.6484 Evaluate side-chains 67 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 682 CYS Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 10.0000 chunk 157 optimal weight: 30.0000 chunk 144 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 66 optimal weight: 0.1980 chunk 120 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14246 Z= 0.217 Angle : 0.572 10.631 19300 Z= 0.287 Chirality : 0.043 0.175 2095 Planarity : 0.003 0.041 2493 Dihedral : 4.230 27.185 1879 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.00 % Favored : 92.70 % Rotamer: Outliers : 1.53 % Allowed : 14.38 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1686 helix: -0.23 (0.37), residues: 215 sheet: -0.10 (0.29), residues: 362 loop : -0.84 (0.20), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 414 HIS 0.002 0.001 HIS B 185 PHE 0.013 0.001 PHE B 503 TYR 0.016 0.001 TYR B 708 ARG 0.003 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 1.624 Fit side-chains revert: symmetry clash REVERT: A 32 HIS cc_start: 0.9112 (p90) cc_final: 0.8692 (p-80) REVERT: A 69 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8325 (mm) REVERT: A 582 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8827 (tttt) REVERT: D 59 GLU cc_start: 0.8702 (mp0) cc_final: 0.8446 (pm20) outliers start: 24 outliers final: 21 residues processed: 60 average time/residue: 0.2123 time to fit residues: 21.8790 Evaluate side-chains 68 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 682 CYS Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain D residue 10 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14246 Z= 0.317 Angle : 0.625 10.579 19300 Z= 0.313 Chirality : 0.044 0.170 2095 Planarity : 0.004 0.041 2493 Dihedral : 4.447 27.762 1879 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.47 % Favored : 92.23 % Rotamer: Outliers : 1.59 % Allowed : 14.38 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1686 helix: -0.26 (0.38), residues: 209 sheet: -0.15 (0.29), residues: 363 loop : -0.88 (0.20), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 414 HIS 0.003 0.001 HIS B 32 PHE 0.030 0.001 PHE A 88 TYR 0.020 0.001 TYR C 69 ARG 0.004 0.000 ARG A 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: A 69 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8262 (mm) REVERT: A 469 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: A 582 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8844 (tttt) REVERT: D 59 GLU cc_start: 0.8715 (mp0) cc_final: 0.8466 (pm20) outliers start: 25 outliers final: 17 residues processed: 60 average time/residue: 0.2175 time to fit residues: 22.3188 Evaluate side-chains 64 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 682 CYS Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.068509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.043767 restraints weight = 78299.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.044865 restraints weight = 50645.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.044904 restraints weight = 33039.191| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14246 Z= 0.272 Angle : 0.601 10.338 19300 Z= 0.302 Chirality : 0.044 0.173 2095 Planarity : 0.003 0.041 2493 Dihedral : 4.421 27.776 1879 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.35 % Favored : 92.41 % Rotamer: Outliers : 1.27 % Allowed : 14.76 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.22), residues: 1686 helix: -0.27 (0.38), residues: 209 sheet: -0.20 (0.29), residues: 369 loop : -0.90 (0.20), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 414 HIS 0.003 0.001 HIS B 440 PHE 0.026 0.001 PHE A 88 TYR 0.016 0.001 TYR B 708 ARG 0.004 0.000 ARG A 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2204.75 seconds wall clock time: 41 minutes 51.25 seconds (2511.25 seconds total)