Starting phenix.real_space_refine on Sun Mar 17 09:26:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stk_25431/03_2024/7stk_25431_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stk_25431/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stk_25431/03_2024/7stk_25431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stk_25431/03_2024/7stk_25431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stk_25431/03_2024/7stk_25431_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stk_25431/03_2024/7stk_25431_neut.pdb" } 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 Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 600": "OD1" <-> "OD2" Residue "B PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 21": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.22, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 5.07 Conformation dependent library (CDL) restraints added in 2.5 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: 1.68 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: 5.27 Time building geometry restraints manager: 5.57 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: 97.39 - 104.71: 250 104.71 - 112.04: 6898 112.04 - 119.37: 4819 119.37 - 126.69: 7089 126.69 - 134.02: 244 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 2.440 nonbonded pdb=" NH2 ARG A 14 " pdb=" O VAL B 712 " model vdw 2.171 2.520 nonbonded pdb=" O SER B 878 " pdb=" OH TYR B 882 " model vdw 2.173 2.440 nonbonded pdb=" O PRO A 77 " pdb=" ND2 ASN A 108 " model vdw 2.186 2.520 nonbonded pdb=" O GLN B 513 " pdb=" OH TYR B 587 " model vdw 2.212 2.440 ... (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 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 5.950 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 38.880 Find NCS groups from input model: 0.860 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.500 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 1.675 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: 0.2106 time to fit residues: 22.4499 Evaluate side-chains 44 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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: 20.0000 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 155 optimal weight: 40.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN A 313 GLN ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 14246 Z= 0.509 Angle : 0.726 8.768 19300 Z= 0.370 Chirality : 0.047 0.164 2095 Planarity : 0.005 0.040 2493 Dihedral : 4.742 28.096 1880 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.24 % Favored : 91.46 % Rotamer: Outliers : 0.70 % Allowed : 7.82 % Favored : 91.48 % 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: -1.24 (0.21), residues: 1686 helix: -0.45 (0.36), residues: 201 sheet: -0.34 (0.28), residues: 378 loop : -1.09 (0.20), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 414 HIS 0.005 0.001 HIS B 280 PHE 0.024 0.002 PHE B 482 TYR 0.021 0.002 TYR B 800 ARG 0.008 0.001 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 57 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 1.494 Fit side-chains REVERT: A 11 MET cc_start: 0.7965 (ppp) cc_final: 0.7568 (ppp) REVERT: A 32 HIS cc_start: 0.9144 (p90) cc_final: 0.8763 (p-80) outliers start: 11 outliers final: 9 residues processed: 52 average time/residue: 0.2057 time to fit residues: 18.7291 Evaluate side-chains 51 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 130 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 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: 1.9990 chunk 48 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 168 optimal weight: 0.0980 chunk 138 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1164 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= 0.162 Angle : 0.548 8.443 19300 Z= 0.282 Chirality : 0.044 0.180 2095 Planarity : 0.003 0.040 2493 Dihedral : 4.366 28.256 1879 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.17 % Favored : 93.53 % Rotamer: Outliers : 0.89 % Allowed : 10.31 % Favored : 88.80 % 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 (0.21), residues: 1686 helix: -0.03 (0.37), residues: 208 sheet: -0.14 (0.29), residues: 365 loop : -0.97 (0.20), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 414 HIS 0.005 0.001 HIS B 829 PHE 0.024 0.001 PHE A 88 TYR 0.012 0.001 TYR B 708 ARG 0.004 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 62 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 1.665 Fit side-chains REVERT: A 11 MET cc_start: 0.7812 (ppp) cc_final: 0.7323 (ppp) REVERT: A 32 HIS cc_start: 0.9122 (p90) cc_final: 0.8787 (p-80) outliers start: 14 outliers final: 9 residues processed: 55 average time/residue: 0.1948 time to fit residues: 18.9019 Evaluate side-chains 53 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 TRP 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 11 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 705 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 40.0000 chunk 17 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 14246 Z= 0.451 Angle : 0.675 8.554 19300 Z= 0.341 Chirality : 0.045 0.163 2095 Planarity : 0.004 0.040 2493 Dihedral : 4.697 28.778 1879 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.96 % Favored : 90.75 % Rotamer: Outliers : 1.84 % Allowed : 12.15 % Favored : 86.01 % 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: -1.24 (0.21), residues: 1686 helix: -0.49 (0.36), residues: 207 sheet: -0.38 (0.28), residues: 378 loop : -1.08 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 414 HIS 0.006 0.001 HIS B 32 PHE 0.028 0.002 PHE B 572 TYR 0.014 0.002 TYR B 708 ARG 0.009 0.001 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 71 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 42 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.7990 (ppp) cc_final: 0.7747 (ppp) REVERT: D 15 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9034 (mm) outliers start: 29 outliers final: 15 residues processed: 62 average time/residue: 0.1950 time to fit residues: 21.3926 Evaluate side-chains 58 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 133 TRP 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 B residue 11 MET Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 320 THR 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 D residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 148 optimal weight: 0.0970 chunk 41 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14246 Z= 0.146 Angle : 0.549 8.257 19300 Z= 0.280 Chirality : 0.043 0.170 2095 Planarity : 0.003 0.041 2493 Dihedral : 4.374 28.379 1879 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.64 % Favored : 93.06 % Rotamer: Outliers : 1.08 % Allowed : 13.80 % Favored : 85.11 % 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: -1.03 (0.21), residues: 1686 helix: -0.13 (0.37), residues: 212 sheet: -0.24 (0.29), residues: 365 loop : -0.97 (0.20), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 414 HIS 0.003 0.001 HIS B 829 PHE 0.027 0.001 PHE B 572 TYR 0.013 0.001 TYR B 708 ARG 0.002 0.000 ARG B 702 *********************** 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 64 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 1.699 Fit side-chains REVERT: A 32 HIS cc_start: 0.9162 (p90) cc_final: 0.8785 (p-80) REVERT: A 69 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8289 (mm) REVERT: B 442 MET cc_start: 0.9195 (tpp) cc_final: 0.8988 (tpp) outliers start: 17 outliers final: 13 residues processed: 56 average time/residue: 0.2094 time to fit residues: 20.9208 Evaluate side-chains 58 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 133 TRP 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 806 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 165 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1632 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= 0.206 Angle : 0.560 9.883 19300 Z= 0.281 Chirality : 0.043 0.174 2095 Planarity : 0.003 0.041 2493 Dihedral : 4.327 28.439 1879 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.30 % Favored : 92.41 % Rotamer: Outliers : 1.40 % Allowed : 14.89 % Favored : 83.72 % 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: -1.01 (0.21), residues: 1686 helix: -0.15 (0.37), residues: 212 sheet: -0.24 (0.28), residues: 367 loop : -0.93 (0.20), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 414 HIS 0.003 0.001 HIS B 829 PHE 0.021 0.001 PHE A 88 TYR 0.018 0.001 TYR C 69 ARG 0.004 0.000 ARG A 114 *********************** 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 70 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 1.673 Fit side-chains REVERT: A 11 MET cc_start: 0.7850 (ppp) cc_final: 0.7545 (ppp) REVERT: A 69 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8190 (mm) outliers start: 22 outliers final: 17 residues processed: 62 average time/residue: 0.2006 time to fit residues: 22.0153 Evaluate side-chains 65 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 47 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 782 GLU 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 130 THR 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 Chi-restraints excluded: chain D residue 10 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 93 optimal weight: 0.0270 chunk 139 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- 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 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14246 Z= 0.170 Angle : 0.550 9.405 19300 Z= 0.276 Chirality : 0.043 0.173 2095 Planarity : 0.003 0.041 2493 Dihedral : 4.268 28.222 1879 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.88 % Favored : 92.82 % Rotamer: Outliers : 1.34 % Allowed : 15.52 % Favored : 83.14 % 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: -0.94 (0.21), residues: 1686 helix: -0.07 (0.37), residues: 209 sheet: -0.16 (0.28), residues: 366 loop : -0.91 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 414 HIS 0.008 0.001 HIS B 21 PHE 0.014 0.001 PHE A 76 TYR 0.015 0.001 TYR B 708 ARG 0.002 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 70 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 49 time to evaluate : 1.604 Fit side-chains revert: symmetry clash REVERT: A 11 MET cc_start: 0.7836 (ppp) cc_final: 0.7485 (ppp) REVERT: A 69 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8339 (mm) REVERT: A 469 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7963 (mt-10) outliers start: 21 outliers final: 18 residues processed: 61 average time/residue: 0.2016 time to fit residues: 21.5067 Evaluate side-chains 67 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 469 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 782 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14246 Z= 0.173 Angle : 0.539 9.343 19300 Z= 0.272 Chirality : 0.043 0.171 2095 Planarity : 0.003 0.041 2493 Dihedral : 4.213 27.958 1879 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.00 % Favored : 92.70 % Rotamer: Outliers : 1.27 % Allowed : 16.16 % Favored : 82.57 % 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: -0.90 (0.21), residues: 1686 helix: -0.00 (0.38), residues: 209 sheet: -0.15 (0.28), residues: 364 loop : -0.89 (0.20), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 414 HIS 0.002 0.001 HIS A 440 PHE 0.024 0.001 PHE A 88 TYR 0.021 0.001 TYR C 69 ARG 0.003 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 69 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 49 time to evaluate : 1.753 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6908 (mt) REVERT: A 69 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8331 (mm) REVERT: A 469 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7911 (mt-10) outliers start: 20 outliers final: 16 residues processed: 62 average time/residue: 0.1996 time to fit residues: 21.4439 Evaluate side-chains 65 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 46 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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 311 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 782 GLU 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 C residue 7 CYS 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: 8.9990 chunk 157 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 47 optimal weight: 0.0170 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 overall best weight: 2.3222 ------------------------------------------------------------------------------- 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 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14246 Z= 0.257 Angle : 0.577 9.956 19300 Z= 0.289 Chirality : 0.043 0.164 2095 Planarity : 0.003 0.041 2493 Dihedral : 4.348 28.199 1879 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.35 % Favored : 92.35 % Rotamer: Outliers : 1.40 % Allowed : 16.28 % Favored : 82.32 % 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: -0.07 (0.37), residues: 209 sheet: -0.23 (0.28), residues: 367 loop : -0.89 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 414 HIS 0.004 0.001 HIS B 32 PHE 0.012 0.001 PHE A 76 TYR 0.015 0.001 TYR B 708 ARG 0.005 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 68 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 46 time to evaluate : 1.699 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7006 (mt) REVERT: A 69 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8229 (mm) REVERT: A 469 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7948 (mt-10) outliers start: 22 outliers final: 18 residues processed: 61 average time/residue: 0.2031 time to fit residues: 21.7072 Evaluate side-chains 65 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 44 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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 311 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 591 ASP Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 130 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 0.0020 chunk 83 optimal weight: 0.1980 chunk 107 optimal weight: 0.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 148 ASN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2002 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= 0.134 Angle : 0.556 9.868 19300 Z= 0.276 Chirality : 0.043 0.176 2095 Planarity : 0.003 0.041 2493 Dihedral : 4.155 27.794 1879 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.29 % Favored : 93.42 % Rotamer: Outliers : 1.02 % Allowed : 16.67 % Favored : 82.32 % 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: -0.81 (0.22), residues: 1686 helix: 0.17 (0.39), residues: 200 sheet: -0.14 (0.29), residues: 364 loop : -0.81 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 414 HIS 0.003 0.000 HIS A 440 PHE 0.030 0.001 PHE A 88 TYR 0.021 0.001 TYR C 69 ARG 0.002 0.000 ARG B 702 ********************** 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 66 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6934 (mt) REVERT: A 69 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8464 (mm) REVERT: B 401 TYR cc_start: 0.8814 (t80) cc_final: 0.8293 (t80) outliers start: 16 outliers final: 12 residues processed: 61 average time/residue: 0.2188 time to fit residues: 22.7039 Evaluate side-chains 62 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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 311 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 806 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 C residue 7 CYS Chi-restraints excluded: chain C residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.068898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.044813 restraints weight = 79455.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.045468 restraints weight = 54867.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.045506 restraints weight = 38330.281| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14246 Z= 0.276 Angle : 0.586 9.770 19300 Z= 0.295 Chirality : 0.043 0.177 2095 Planarity : 0.003 0.041 2493 Dihedral : 4.294 27.991 1879 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.30 % Favored : 92.35 % Rotamer: Outliers : 1.02 % Allowed : 16.79 % Favored : 82.19 % 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: -0.85 (0.22), residues: 1686 helix: 0.12 (0.39), residues: 200 sheet: -0.21 (0.28), residues: 366 loop : -0.83 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 414 HIS 0.003 0.001 HIS B 32 PHE 0.018 0.001 PHE A 76 TYR 0.018 0.001 TYR A 631 ARG 0.005 0.000 ARG A 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2202.27 seconds wall clock time: 41 minutes 12.07 seconds (2472.07 seconds total)