Starting phenix.real_space_refine on Sat Apr 13 09:21:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6x_13233/04_2024/7p6x_13233_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6x_13233/04_2024/7p6x_13233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6x_13233/04_2024/7p6x_13233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6x_13233/04_2024/7p6x_13233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6x_13233/04_2024/7p6x_13233_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p6x_13233/04_2024/7p6x_13233_trim_updated.pdb" } resolution = 4.1 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= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 71 5.16 5 C 8826 2.51 5 N 2451 2.21 5 O 2725 1.98 5 H 14395 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 342": "OE1" <-> "OE2" Residue "D ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 400": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 271": "OE1" <-> "OE2" Residue "E ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 353": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E ARG 400": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 400": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 28474 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5006 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 4877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4877 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 2 Chain: "C" Number of atoms: 5034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5034 Classifications: {'peptide': 322} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 311} Chain breaks: 2 Chain: "D" Number of atoms: 4430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4430 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 8, 'TRANS': 273} Chain breaks: 2 Chain: "E" Number of atoms: 4537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 4537 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain breaks: 2 Chain: "F" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 4509 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.40, per 1000 atoms: 0.44 Number of scatterers: 28474 At special positions: 0 Unit cell: (82.005, 127.8, 136.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 6 15.00 O 2725 8.00 N 2451 7.00 C 8826 6.00 H 14395 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 22.20 Conformation dependent library (CDL) restraints added in 3.0 seconds 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3376 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 16 sheets defined 51.3% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 15 through 18 Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.638A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.589A pdb=" N TYR A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.705A pdb=" N THR A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 352 through 357 removed outlier: 4.898A pdb=" N ARG A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.735A pdb=" N GLN A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 400 removed outlier: 3.529A pdb=" N ILE A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.010A pdb=" N LEU A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 427 through 436 removed outlier: 3.845A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 454 removed outlier: 4.446A pdb=" N LYS A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 18 removed outlier: 5.222A pdb=" N SER B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N HIS B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 57 removed outlier: 3.608A pdb=" N GLU B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 242 through 245 No H-bonds generated for 'chain 'B' and resid 242 through 245' Processing helix chain 'B' and resid 273 through 289 removed outlier: 3.574A pdb=" N GLU B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 309 through 318 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 368 through 382 removed outlier: 3.817A pdb=" N GLN B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 400 removed outlier: 3.840A pdb=" N ASN B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 3.786A pdb=" N LEU B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Proline residue: B 412 - end of helix Processing helix chain 'B' and resid 427 through 436 removed outlier: 3.823A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'C' and resid 12 through 18 removed outlier: 3.857A pdb=" N SER C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N HIS C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 57 Processing helix chain 'C' and resid 77 through 87 removed outlier: 3.548A pdb=" N ALA C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.633A pdb=" N ARG C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.858A pdb=" N GLY C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.999A pdb=" N GLU C 320 " --> pdb=" O HIS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 352 through 357 removed outlier: 4.683A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 382 removed outlier: 3.574A pdb=" N ILE C 377 " --> pdb=" O GLN C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 400 removed outlier: 3.542A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 419 removed outlier: 3.909A pdb=" N LEU C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Proline residue: C 412 - end of helix Processing helix chain 'C' and resid 427 through 436 Processing helix chain 'C' and resid 440 through 450 removed outlier: 4.357A pdb=" N LYS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 64 removed outlier: 3.675A pdb=" N ARG D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.588A pdb=" N ALA D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.977A pdb=" N ILE D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 286 removed outlier: 3.798A pdb=" N GLU D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 306 through 317 removed outlier: 4.071A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 348 through 351 No H-bonds generated for 'chain 'D' and resid 348 through 351' Processing helix chain 'D' and resid 364 through 378 removed outlier: 3.565A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 396 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.724A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 432 Processing helix chain 'D' and resid 436 through 448 removed outlier: 5.134A pdb=" N TYR D 446 " --> pdb=" O TYR D 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 removed outlier: 3.563A pdb=" N ARG E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 115 through 125 Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.927A pdb=" N VAL E 249 " --> pdb=" O HIS E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 286 removed outlier: 3.538A pdb=" N GLU E 285 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 303 No H-bonds generated for 'chain 'E' and resid 301 through 303' Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.939A pdb=" N PHE E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'E' and resid 348 through 353 removed outlier: 3.661A pdb=" N ASP E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG E 353 " --> pdb=" O ASP E 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 348 through 353' Processing helix chain 'E' and resid 364 through 377 removed outlier: 3.555A pdb=" N GLU E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 396 removed outlier: 3.523A pdb=" N ARG E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 416 removed outlier: 3.950A pdb=" N GLN E 404 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 432 Processing helix chain 'E' and resid 436 through 449 removed outlier: 3.559A pdb=" N ALA E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 64 removed outlier: 3.660A pdb=" N GLU F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 115 through 125 Processing helix chain 'F' and resid 244 through 250 removed outlier: 3.574A pdb=" N VAL F 249 " --> pdb=" O HIS F 245 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE F 250 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 306 through 315 removed outlier: 3.958A pdb=" N PHE F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 345 No H-bonds generated for 'chain 'F' and resid 343 through 345' Processing helix chain 'F' and resid 348 through 353 removed outlier: 3.689A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ARG F 353 " --> pdb=" O ASP F 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 348 through 353' Processing helix chain 'F' and resid 364 through 377 removed outlier: 3.605A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 396 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.544A pdb=" N GLN F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 432 removed outlier: 3.531A pdb=" N SER F 431 " --> pdb=" O LYS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 451 Processing sheet with id= A, first strand: chain 'A' and resid 358 through 363 removed outlier: 6.887A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 363 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ALA A 69 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 331 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 293 through 296 Processing sheet with id= C, first strand: chain 'A' and resid 335 through 337 Processing sheet with id= D, first strand: chain 'B' and resid 358 through 363 removed outlier: 6.732A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR B 363 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA B 69 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 331 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 120 through 122 Processing sheet with id= F, first strand: chain 'B' and resid 335 through 337 Processing sheet with id= G, first strand: chain 'C' and resid 358 through 362 removed outlier: 6.689A pdb=" N ALA C 65 " --> pdb=" O MET C 359 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE C 361 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU C 67 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 294 through 296 Processing sheet with id= I, first strand: chain 'C' and resid 335 through 337 Processing sheet with id= J, first strand: chain 'D' and resid 354 through 359 removed outlier: 6.622A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR D 359 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA D 76 " --> pdb=" O THR D 359 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 332 through 334 Processing sheet with id= L, first strand: chain 'E' and resid 354 through 358 removed outlier: 6.525A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR E 328 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 127 through 130 Processing sheet with id= N, first strand: chain 'E' and resid 332 through 334 Processing sheet with id= O, first strand: chain 'F' and resid 354 through 358 removed outlier: 6.429A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 332 through 334 597 hydrogen bonds defined for protein. 1779 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: 10.30 Time building geometry restraints manager: 23.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 14377 1.05 - 1.27: 2144 1.27 - 1.48: 5185 1.48 - 1.70: 6810 1.70 - 1.91: 124 Bond restraints: 28640 Sorted by residual: bond pdb=" C ARG E 273 " pdb=" O ARG E 273 " ideal model delta sigma weight residual 1.236 1.145 0.092 1.16e-02 7.43e+03 6.27e+01 bond pdb=" C SER B 89 " pdb=" O SER B 89 " ideal model delta sigma weight residual 1.236 1.319 -0.084 1.21e-02 6.83e+03 4.79e+01 bond pdb=" O3B ADP A 501 " pdb=" PB ADP A 501 " ideal model delta sigma weight residual 1.510 1.373 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C PRO D 322 " pdb=" O PRO D 322 " ideal model delta sigma weight residual 1.235 1.152 0.083 1.30e-02 5.92e+03 4.07e+01 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.364 0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 28635 not shown) Histogram of bond angle deviations from ideal: 95.47 - 103.31: 202 103.31 - 111.15: 31428 111.15 - 118.99: 10418 118.99 - 126.82: 9812 126.82 - 134.66: 129 Bond angle restraints: 51989 Sorted by residual: angle pdb=" N TYR D 442 " pdb=" CA TYR D 442 " pdb=" C TYR D 442 " ideal model delta sigma weight residual 113.02 102.88 10.14 1.20e+00 6.94e-01 7.14e+01 angle pdb=" CA ASP E 385 " pdb=" CB ASP E 385 " pdb=" CG ASP E 385 " ideal model delta sigma weight residual 112.60 105.26 7.34 1.00e+00 1.00e+00 5.39e+01 angle pdb=" C ALA F 281 " pdb=" N GLU F 282 " pdb=" CA GLU F 282 " ideal model delta sigma weight residual 120.63 130.38 -9.75 1.36e+00 5.41e-01 5.14e+01 angle pdb=" C ALA E 281 " pdb=" N GLU E 282 " pdb=" CA GLU E 282 " ideal model delta sigma weight residual 120.63 129.72 -9.09 1.36e+00 5.41e-01 4.47e+01 angle pdb=" C LYS C 285 " pdb=" N TYR C 286 " pdb=" CA TYR C 286 " ideal model delta sigma weight residual 120.44 129.50 -9.06 1.36e+00 5.41e-01 4.43e+01 ... (remaining 51984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.73: 12782 31.73 - 63.46: 410 63.46 - 95.18: 24 95.18 - 126.91: 3 126.91 - 158.64: 2 Dihedral angle restraints: 13221 sinusoidal: 7512 harmonic: 5709 Sorted by residual: dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 141.36 158.64 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 146.27 153.74 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual 300.00 177.81 122.19 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 13218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1417 0.093 - 0.186: 722 0.186 - 0.279: 131 0.279 - 0.372: 14 0.372 - 0.465: 4 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA ARG B 14 " pdb=" N ARG B 14 " pdb=" C ARG B 14 " pdb=" CB ARG B 14 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CA GLU A 86 " pdb=" N GLU A 86 " pdb=" C GLU A 86 " pdb=" CB GLU A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB THR D 241 " pdb=" CA THR D 241 " pdb=" OG1 THR D 241 " pdb=" CG2 THR D 241 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 2285 not shown) Planarity restraints: 4185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 369 " 0.211 2.00e-02 2.50e+03 3.87e-01 2.25e+03 pdb=" CD GLN A 369 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 369 " -0.204 2.00e-02 2.50e+03 pdb=" NE2 GLN A 369 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 369 " 0.641 2.00e-02 2.50e+03 pdb="HE22 GLN A 369 " -0.635 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 447 " -0.138 2.00e-02 2.50e+03 1.54e-01 3.55e+02 pdb=" CD GLN E 447 " 0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN E 447 " 0.134 2.00e-02 2.50e+03 pdb=" NE2 GLN E 447 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN E 447 " 0.228 2.00e-02 2.50e+03 pdb="HE22 GLN E 447 " -0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 447 " -0.127 2.00e-02 2.50e+03 1.41e-01 2.98e+02 pdb=" CD GLN D 447 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN D 447 " 0.123 2.00e-02 2.50e+03 pdb=" NE2 GLN D 447 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN D 447 " 0.209 2.00e-02 2.50e+03 pdb="HE22 GLN D 447 " -0.210 2.00e-02 2.50e+03 ... (remaining 4182 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1580 2.17 - 2.78: 58731 2.78 - 3.39: 76483 3.39 - 3.99: 99819 3.99 - 4.60: 157258 Nonbonded interactions: 393871 Sorted by model distance: nonbonded pdb="HD21 LEU E 324 " pdb=" HE3 MET E 326 " model vdw 1.564 2.440 nonbonded pdb=" HZ3 LYS B 108 " pdb=" OD2 ASP B 308 " model vdw 1.602 1.850 nonbonded pdb=" HG1 THR D 397 " pdb=" OD2 ASP D 435 " model vdw 1.635 1.850 nonbonded pdb=" HG1 THR D 101 " pdb="HD12 LEU D 296 " model vdw 1.639 2.270 nonbonded pdb=" O THR E 116 " pdb=" HG1 THR E 120 " model vdw 1.659 1.850 ... (remaining 393866 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 6 through 123 or (resid 238 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG \ 11 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 2 \ 39 through 247 or (resid 271 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or nam \ e HG13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name \ HD13)) or resid 272 through 452 or resid 501)) selection = (chain 'B' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 7 through 247 or resid 271 \ through 452 or resid 501)) selection = (chain 'C' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 7 through 123 or (resid 23 \ 8 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 \ or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or nam \ e HG22 or name HG23)) or resid 239 through 247 or (resid 271 and (name N or name \ CA or name C or name O or name CB or name CG1 or name CG2 or name CD1 or name H \ A or name HB or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or \ name HD11 or name HD12 or name HD13)) or resid 272 through 452 or resid 501)) } ncs_group { reference = (chain 'D' and (resid 43 through 127 or resid 243 through 283 or (resid 284 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 285 through 449)) selection = (chain 'E' and (resid 43 through 127 or resid 243 through 253 or resid 267 throu \ gh 283 or (resid 284 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 285 through 449)) selection = (chain 'F' and (resid 43 through 127 or resid 243 through 449)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.410 Extract box with map and model: 11.070 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 91.030 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.100 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.017 0.137 14245 Z= 1.145 Angle : 1.825 14.728 19216 Z= 1.234 Chirality : 0.104 0.465 2288 Planarity : 0.010 0.055 2444 Dihedral : 12.652 158.638 5423 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.92 % Allowed : 3.92 % Favored : 95.16 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % 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: -3.80 (0.16), residues: 1777 helix: -2.99 (0.12), residues: 987 sheet: -1.05 (0.37), residues: 180 loop : -1.72 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 283 HIS 0.039 0.008 HIS A 348 PHE 0.059 0.011 PHE F 123 TYR 0.065 0.013 TYR E 387 ARG 0.042 0.004 ARG D 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 337 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 LEU cc_start: 0.9544 (mt) cc_final: 0.9109 (mt) REVERT: C 1 MET cc_start: 0.2636 (ptp) cc_final: 0.1650 (ppp) REVERT: C 52 ILE cc_start: 0.9592 (mm) cc_final: 0.9385 (tp) REVERT: C 56 ILE cc_start: 0.9552 (mt) cc_final: 0.9301 (tp) REVERT: C 61 MET cc_start: 0.8630 (mmm) cc_final: 0.8376 (tmm) REVERT: C 307 LEU cc_start: 0.8665 (mt) cc_final: 0.8443 (mm) REVERT: E 109 PHE cc_start: 0.9178 (m-80) cc_final: 0.8855 (m-10) REVERT: F 108 ILE cc_start: 0.9515 (pt) cc_final: 0.9241 (mm) REVERT: F 243 SER cc_start: 0.7987 (OUTLIER) cc_final: 0.7778 (t) REVERT: F 452 PHE cc_start: 0.8917 (t80) cc_final: 0.8646 (t80) outliers start: 14 outliers final: 3 residues processed: 350 average time/residue: 0.6634 time to fit residues: 326.7304 Evaluate side-chains 223 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 219 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN F 49 GLN F 422 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14245 Z= 0.205 Angle : 0.639 6.159 19216 Z= 0.337 Chirality : 0.042 0.144 2288 Planarity : 0.004 0.041 2444 Dihedral : 7.743 132.173 1977 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.90 (0.18), residues: 1777 helix: -1.20 (0.15), residues: 1019 sheet: -0.59 (0.36), residues: 187 loop : -1.22 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 283 HIS 0.006 0.001 HIS B 241 PHE 0.024 0.002 PHE C 116 TYR 0.013 0.002 TYR F 446 ARG 0.005 0.001 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.2102 (ptp) cc_final: 0.1487 (ppp) REVERT: C 21 VAL cc_start: 0.9206 (t) cc_final: 0.8987 (p) REVERT: C 56 ILE cc_start: 0.9566 (mt) cc_final: 0.9363 (tp) REVERT: D 299 ASP cc_start: 0.8709 (t0) cc_final: 0.8489 (t0) REVERT: D 355 LEU cc_start: 0.8932 (mt) cc_final: 0.8707 (mp) REVERT: E 67 LYS cc_start: 0.9157 (mttt) cc_final: 0.8597 (mttt) REVERT: E 100 PHE cc_start: 0.8686 (t80) cc_final: 0.8356 (t80) REVERT: F 62 MET cc_start: 0.8824 (ttm) cc_final: 0.8543 (tpp) REVERT: F 452 PHE cc_start: 0.8771 (t80) cc_final: 0.8516 (t80) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.6463 time to fit residues: 243.9929 Evaluate side-chains 197 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14245 Z= 0.288 Angle : 0.620 5.939 19216 Z= 0.332 Chirality : 0.039 0.150 2288 Planarity : 0.003 0.028 2444 Dihedral : 7.246 116.624 1977 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 1777 helix: -0.31 (0.16), residues: 1007 sheet: -0.32 (0.36), residues: 193 loop : -0.91 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 283 HIS 0.006 0.001 HIS A 348 PHE 0.021 0.002 PHE C 312 TYR 0.018 0.001 TYR F 446 ARG 0.004 0.000 ARG F 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 273 ASP cc_start: 0.8401 (t0) cc_final: 0.8192 (t0) REVERT: D 299 ASP cc_start: 0.8644 (t0) cc_final: 0.8336 (t0) REVERT: D 355 LEU cc_start: 0.9021 (mt) cc_final: 0.8803 (mp) REVERT: E 443 MET cc_start: 0.9070 (tpp) cc_final: 0.8614 (tpp) REVERT: F 62 MET cc_start: 0.9015 (ttm) cc_final: 0.8740 (tpp) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.7228 time to fit residues: 215.3443 Evaluate side-chains 165 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14245 Z= 0.208 Angle : 0.549 5.993 19216 Z= 0.285 Chirality : 0.039 0.132 2288 Planarity : 0.003 0.029 2444 Dihedral : 6.982 118.363 1977 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.19), residues: 1777 helix: 0.08 (0.16), residues: 1015 sheet: -0.13 (0.36), residues: 194 loop : -0.79 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 283 HIS 0.004 0.001 HIS B 429 PHE 0.026 0.002 PHE B 312 TYR 0.018 0.001 TYR F 442 ARG 0.006 0.000 ARG C 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 PHE cc_start: 0.8818 (m-80) cc_final: 0.8545 (m-80) REVERT: C 273 ASP cc_start: 0.8381 (t0) cc_final: 0.8137 (t0) REVERT: D 299 ASP cc_start: 0.8595 (t0) cc_final: 0.8268 (t0) REVERT: D 355 LEU cc_start: 0.9009 (mt) cc_final: 0.8796 (mp) REVERT: E 443 MET cc_start: 0.9080 (tpp) cc_final: 0.8705 (tpp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.6687 time to fit residues: 187.6937 Evaluate side-chains 159 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 128 optimal weight: 0.0980 chunk 71 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14245 Z= 0.174 Angle : 0.514 6.149 19216 Z= 0.264 Chirality : 0.038 0.142 2288 Planarity : 0.003 0.027 2444 Dihedral : 6.707 113.013 1977 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.19), residues: 1777 helix: 0.40 (0.16), residues: 1018 sheet: 0.04 (0.36), residues: 195 loop : -0.62 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 283 HIS 0.004 0.001 HIS B 429 PHE 0.024 0.002 PHE B 312 TYR 0.010 0.001 TYR C 314 ARG 0.006 0.000 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 PHE cc_start: 0.8820 (m-80) cc_final: 0.8516 (m-80) REVERT: C 273 ASP cc_start: 0.8313 (t0) cc_final: 0.8093 (t0) REVERT: D 299 ASP cc_start: 0.8558 (t0) cc_final: 0.8239 (t0) REVERT: D 355 LEU cc_start: 0.9028 (mt) cc_final: 0.8823 (mp) REVERT: E 443 MET cc_start: 0.9066 (tpp) cc_final: 0.8687 (tpp) REVERT: F 311 PHE cc_start: 0.8978 (t80) cc_final: 0.8733 (t80) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.6638 time to fit residues: 187.8009 Evaluate side-chains 163 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14245 Z= 0.238 Angle : 0.549 6.335 19216 Z= 0.287 Chirality : 0.038 0.127 2288 Planarity : 0.003 0.031 2444 Dihedral : 6.452 113.284 1977 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.19), residues: 1777 helix: 0.26 (0.16), residues: 1031 sheet: 0.13 (0.35), residues: 204 loop : -0.78 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 283 HIS 0.004 0.001 HIS C 18 PHE 0.021 0.002 PHE B 116 TYR 0.013 0.001 TYR C 314 ARG 0.003 0.000 ARG C 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.7955 (mmtm) cc_final: 0.7373 (mtmt) REVERT: B 81 LEU cc_start: 0.9364 (tp) cc_final: 0.9038 (tt) REVERT: C 273 ASP cc_start: 0.8472 (t0) cc_final: 0.8252 (t0) REVERT: D 299 ASP cc_start: 0.8559 (t0) cc_final: 0.8273 (t0) REVERT: F 62 MET cc_start: 0.8581 (tpp) cc_final: 0.8378 (tpp) REVERT: F 311 PHE cc_start: 0.9023 (t80) cc_final: 0.8774 (t80) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.6936 time to fit residues: 183.6090 Evaluate side-chains 151 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 0.0040 chunk 19 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14245 Z= 0.227 Angle : 0.534 6.121 19216 Z= 0.280 Chirality : 0.038 0.122 2288 Planarity : 0.003 0.033 2444 Dihedral : 6.251 106.220 1977 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.19), residues: 1777 helix: 0.35 (0.16), residues: 1026 sheet: 0.09 (0.36), residues: 200 loop : -0.68 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 283 HIS 0.004 0.001 HIS C 316 PHE 0.023 0.002 PHE C 312 TYR 0.011 0.001 TYR C 314 ARG 0.005 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LEU cc_start: 0.9403 (tp) cc_final: 0.9110 (tt) REVERT: B 303 GLU cc_start: 0.8407 (pt0) cc_final: 0.8063 (pt0) REVERT: C 1 MET cc_start: 0.3194 (ppp) cc_final: 0.2938 (ppp) REVERT: C 273 ASP cc_start: 0.8469 (t0) cc_final: 0.8248 (t0) REVERT: D 299 ASP cc_start: 0.8515 (t0) cc_final: 0.8238 (t0) REVERT: E 443 MET cc_start: 0.8946 (tpp) cc_final: 0.8617 (tpp) REVERT: E 446 TYR cc_start: 0.8702 (t80) cc_final: 0.8393 (t80) REVERT: F 62 MET cc_start: 0.8628 (tpp) cc_final: 0.8404 (tpp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.7015 time to fit residues: 186.2450 Evaluate side-chains 148 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 135 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 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: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14245 Z= 0.140 Angle : 0.491 6.146 19216 Z= 0.248 Chirality : 0.038 0.130 2288 Planarity : 0.003 0.034 2444 Dihedral : 5.995 105.093 1977 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.20), residues: 1777 helix: 0.86 (0.16), residues: 1025 sheet: 0.21 (0.36), residues: 207 loop : -0.46 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 283 HIS 0.003 0.001 HIS B 429 PHE 0.012 0.001 PHE C 116 TYR 0.011 0.001 TYR C 314 ARG 0.004 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.8193 (mmtm) cc_final: 0.7635 (mtmt) REVERT: B 81 LEU cc_start: 0.9358 (tp) cc_final: 0.9090 (tt) REVERT: B 303 GLU cc_start: 0.8141 (pt0) cc_final: 0.7923 (pt0) REVERT: C 1 MET cc_start: 0.3234 (ppp) cc_final: 0.3011 (ppp) REVERT: C 273 ASP cc_start: 0.8446 (t0) cc_final: 0.8219 (t0) REVERT: D 299 ASP cc_start: 0.8496 (t0) cc_final: 0.8177 (t0) REVERT: E 443 MET cc_start: 0.8923 (tpp) cc_final: 0.8566 (tpp) REVERT: E 446 TYR cc_start: 0.8698 (t80) cc_final: 0.8416 (t80) REVERT: F 62 MET cc_start: 0.8661 (tpp) cc_final: 0.8439 (tpp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.6096 time to fit residues: 163.4786 Evaluate side-chains 154 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14245 Z= 0.192 Angle : 0.513 5.839 19216 Z= 0.264 Chirality : 0.038 0.129 2288 Planarity : 0.003 0.033 2444 Dihedral : 5.932 103.225 1977 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.20), residues: 1777 helix: 0.81 (0.16), residues: 1032 sheet: 0.18 (0.36), residues: 199 loop : -0.50 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 283 HIS 0.004 0.001 HIS D 302 PHE 0.015 0.001 PHE D 123 TYR 0.010 0.001 TYR C 314 ARG 0.004 0.000 ARG C 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LEU cc_start: 0.9394 (tp) cc_final: 0.9148 (tt) REVERT: B 303 GLU cc_start: 0.8251 (pt0) cc_final: 0.8029 (pt0) REVERT: C 273 ASP cc_start: 0.8444 (t0) cc_final: 0.8211 (t0) REVERT: D 299 ASP cc_start: 0.8529 (t0) cc_final: 0.8251 (t0) REVERT: E 443 MET cc_start: 0.8912 (tpp) cc_final: 0.8520 (tpp) REVERT: E 446 TYR cc_start: 0.8731 (t80) cc_final: 0.8359 (t80) REVERT: F 62 MET cc_start: 0.8699 (tpp) cc_final: 0.8480 (tpp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.6147 time to fit residues: 162.4278 Evaluate side-chains 149 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 142 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14245 Z= 0.283 Angle : 0.563 6.143 19216 Z= 0.299 Chirality : 0.038 0.122 2288 Planarity : 0.003 0.033 2444 Dihedral : 6.065 101.126 1977 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.20), residues: 1777 helix: 0.46 (0.16), residues: 1018 sheet: 0.20 (0.37), residues: 199 loop : -0.61 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 283 HIS 0.005 0.002 HIS A 18 PHE 0.017 0.002 PHE C 437 TYR 0.012 0.001 TYR C 314 ARG 0.005 0.001 ARG C 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LEU cc_start: 0.9402 (tp) cc_final: 0.9173 (tt) REVERT: C 273 ASP cc_start: 0.8418 (t0) cc_final: 0.8217 (t0) REVERT: D 299 ASP cc_start: 0.8553 (t0) cc_final: 0.8271 (t0) REVERT: E 443 MET cc_start: 0.8904 (tpp) cc_final: 0.8591 (tpp) REVERT: F 62 MET cc_start: 0.8753 (tpp) cc_final: 0.8528 (tpp) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.6246 time to fit residues: 154.6999 Evaluate side-chains 137 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 0.0060 chunk 26 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 GLN ** 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 = 0.2918 r_free = 0.2918 target = 0.045542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.033846 restraints weight = 238366.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.035828 restraints weight = 107445.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.037269 restraints weight = 63937.852| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14245 Z= 0.128 Angle : 0.487 6.126 19216 Z= 0.241 Chirality : 0.038 0.130 2288 Planarity : 0.003 0.035 2444 Dihedral : 5.839 107.450 1977 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.20), residues: 1777 helix: 1.09 (0.17), residues: 1020 sheet: 0.30 (0.37), residues: 199 loop : -0.28 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 283 HIS 0.006 0.001 HIS B 305 PHE 0.017 0.001 PHE E 311 TYR 0.009 0.001 TYR E 401 ARG 0.004 0.000 ARG C 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5909.52 seconds wall clock time: 107 minutes 18.04 seconds (6438.04 seconds total)