Starting phenix.real_space_refine on Thu Feb 15 23:39:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z5c_14517/02_2024/7z5c_14517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z5c_14517/02_2024/7z5c_14517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z5c_14517/02_2024/7z5c_14517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z5c_14517/02_2024/7z5c_14517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z5c_14517/02_2024/7z5c_14517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z5c_14517/02_2024/7z5c_14517.pdb" } resolution = 4.16 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= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8767 2.51 5 N 2336 2.21 5 O 2532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 142": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A ASP 391": "OD1" <-> "OD2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ASP 573": "OD1" <-> "OD2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 271": "OE1" <-> "OE2" Residue "M GLU 348": "OE1" <-> "OE2" Residue "M PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 27": "OE1" <-> "OE2" Residue "S TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13707 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4737 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 22, 'TRANS': 577} Chain: "B" Number of atoms: 4578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4578 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 26, 'TRANS': 552} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3192 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 378} Chain breaks: 3 Chain: "S" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1200 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'TRANS': 141} Time building chain proxies: 7.56, per 1000 atoms: 0.55 Number of scatterers: 13707 At special positions: 0 Unit cell: (104.32, 112.796, 128.444, 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 72 16.00 O 2532 8.00 N 2336 7.00 C 8767 6.00 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: 5.53 Conformation dependent library (CDL) restraints added in 2.5 seconds 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 7 sheets defined 61.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 25 through 46 Processing helix chain 'A' and resid 51 through 68 removed outlier: 3.657A pdb=" N LYS A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.611A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.584A pdb=" N VAL A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 215 Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.085A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.777A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.508A pdb=" N LEU A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 357 Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.796A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 401 through 415 removed outlier: 3.869A pdb=" N THR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 435 Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.981A pdb=" N TRP A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.583A pdb=" N GLN A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.822A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 Processing helix chain 'A' and resid 552 through 563 removed outlier: 4.286A pdb=" N ALA A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 589 Processing helix chain 'A' and resid 591 through 599 removed outlier: 3.935A pdb=" N LEU A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 23 Processing helix chain 'B' and resid 26 through 43 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 62 through 80 removed outlier: 3.833A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 removed outlier: 3.685A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 100 through 113 Processing helix chain 'B' and resid 117 through 131 removed outlier: 4.641A pdb=" N TYR B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 4.420A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.531A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.772A pdb=" N ASN B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 284 through 291 removed outlier: 3.813A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.680A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 350 through 361 removed outlier: 4.222A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 403 through 421 removed outlier: 4.196A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 433 removed outlier: 4.517A pdb=" N THR B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 461 through 472 removed outlier: 4.577A pdb=" N GLY B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 499 through 508 removed outlier: 3.815A pdb=" N VAL B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 533 Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.671A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 566 Processing helix chain 'B' and resid 569 through 575 removed outlier: 3.878A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 36 removed outlier: 4.035A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 128 through 133 removed outlier: 4.041A pdb=" N PHE M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.760A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 95 removed outlier: 3.611A pdb=" N TYR S 80 " --> pdb=" O ASN S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 106 removed outlier: 3.630A pdb=" N ASN S 106 " --> pdb=" O ASP S 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 127 through 141 Processing sheet with id=AA1, first strand: chain 'M' and resid 14 through 19 Processing sheet with id=AA2, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=AA3, first strand: chain 'M' and resid 245 through 248 removed outlier: 6.555A pdb=" N VAL M 200 " --> pdb=" O LEU M 274 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG M 276 " --> pdb=" O GLY M 198 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY M 198 " --> pdb=" O ARG M 276 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG M 278 " --> pdb=" O VAL M 196 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL M 196 " --> pdb=" O ARG M 278 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LYS M 356 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU M 321 " --> pdb=" O LYS M 354 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS M 354 " --> pdb=" O GLU M 321 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG M 323 " --> pdb=" O VAL M 352 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL M 352 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA M 350 " --> pdb=" O PRO M 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 253 through 254 Processing sheet with id=AA5, first strand: chain 'M' and resid 287 through 294 removed outlier: 3.512A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 16 through 19 removed outlier: 3.700A pdb=" N PHE S 4 " --> pdb=" O CYS S 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 118 through 119 798 hydrogen bonds defined for protein. 2334 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: 3.97 Time building geometry restraints manager: 6.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4485 1.34 - 1.46: 2863 1.46 - 1.58: 6492 1.58 - 1.70: 0 1.70 - 1.81: 111 Bond restraints: 13951 Sorted by residual: bond pdb=" N ASP A 474 " pdb=" CA ASP A 474 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.25e+00 bond pdb=" CA ILE M 430 " pdb=" CB ILE M 430 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.20e+00 bond pdb=" C ASN B 200 " pdb=" N PRO B 201 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.19e-01 bond pdb=" CA ASP A 474 " pdb=" CB ASP A 474 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.90e-01 bond pdb=" CB PRO B 231 " pdb=" CG PRO B 231 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.72e-01 ... (remaining 13946 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.59: 337 106.59 - 113.44: 7814 113.44 - 120.29: 4998 120.29 - 127.14: 5623 127.14 - 133.99: 114 Bond angle restraints: 18886 Sorted by residual: angle pdb=" C ALA A 590 " pdb=" CA ALA A 590 " pdb=" CB ALA A 590 " ideal model delta sigma weight residual 115.89 110.72 5.17 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CA MET B 155 " pdb=" CB MET B 155 " pdb=" CG MET B 155 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 angle pdb=" N GLU B 498 " pdb=" CA GLU B 498 " pdb=" C GLU B 498 " ideal model delta sigma weight residual 114.04 109.98 4.06 1.24e+00 6.50e-01 1.07e+01 angle pdb=" C ASP A 473 " pdb=" N ASP A 474 " pdb=" CA ASP A 474 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.29e+00 angle pdb=" CB MET B 58 " pdb=" CG MET B 58 " pdb=" SD MET B 58 " ideal model delta sigma weight residual 112.70 121.30 -8.60 3.00e+00 1.11e-01 8.21e+00 ... (remaining 18881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 7661 17.38 - 34.76: 735 34.76 - 52.14: 154 52.14 - 69.52: 15 69.52 - 86.90: 15 Dihedral angle restraints: 8580 sinusoidal: 3488 harmonic: 5092 Sorted by residual: dihedral pdb=" CA HIS A 493 " pdb=" C HIS A 493 " pdb=" N GLU A 494 " pdb=" CA GLU A 494 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA TRP A 462 " pdb=" C TRP A 462 " pdb=" N TYR A 463 " pdb=" CA TYR A 463 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA MET B 155 " pdb=" C MET B 155 " pdb=" N VAL B 156 " pdb=" CA VAL B 156 " ideal model delta harmonic sigma weight residual -180.00 -163.57 -16.43 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 8577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1667 0.043 - 0.085: 410 0.085 - 0.128: 107 0.128 - 0.171: 13 0.171 - 0.214: 1 Chirality restraints: 2198 Sorted by residual: chirality pdb=" CB VAL A 475 " pdb=" CA VAL A 475 " pdb=" CG1 VAL A 475 " pdb=" CG2 VAL A 475 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASP A 474 " pdb=" N ASP A 474 " pdb=" C ASP A 474 " pdb=" CB ASP A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 2195 not shown) Planarity restraints: 2403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 473 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.44e+00 pdb=" C ASP A 473 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A 473 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A 474 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 76 " 0.012 2.00e-02 2.50e+03 1.10e-02 2.41e+00 pdb=" CG TYR B 76 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 76 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 76 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 76 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 76 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 76 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 76 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 191 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO B 192 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " -0.019 5.00e-02 4.00e+02 ... (remaining 2400 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 361 2.71 - 3.26: 14103 3.26 - 3.81: 22028 3.81 - 4.35: 26783 4.35 - 4.90: 45063 Nonbonded interactions: 108338 Sorted by model distance: nonbonded pdb=" OE1 GLU B 297 " pdb=" OH TYR M 83 " model vdw 2.167 2.440 nonbonded pdb=" NH2 ARG B 108 " pdb=" OH TYR B 136 " model vdw 2.170 2.520 nonbonded pdb=" OE2 GLU S 125 " pdb=" NZ LYS S 130 " model vdw 2.177 2.520 nonbonded pdb=" OE2 GLU M 179 " pdb=" OH TYR M 277 " model vdw 2.192 2.440 nonbonded pdb=" OG SER A 359 " pdb=" OG SER A 362 " model vdw 2.208 2.440 ... (remaining 108333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.690 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 38.270 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13951 Z= 0.166 Angle : 0.549 8.596 18886 Z= 0.305 Chirality : 0.040 0.214 2198 Planarity : 0.003 0.034 2403 Dihedral : 14.207 86.898 5262 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.07 % Allowed : 0.26 % 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: 1.03 (0.21), residues: 1703 helix: 1.64 (0.17), residues: 964 sheet: 0.09 (0.39), residues: 183 loop : -0.75 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 421 HIS 0.004 0.001 HIS S 85 PHE 0.014 0.001 PHE B 581 TYR 0.027 0.001 TYR B 76 ARG 0.007 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 PHE cc_start: 0.7122 (m-80) cc_final: 0.6915 (m-10) REVERT: B 83 MET cc_start: 0.8510 (tpp) cc_final: 0.8063 (tpp) REVERT: B 110 MET cc_start: 0.8472 (mpp) cc_final: 0.7845 (mpp) REVERT: M 35 ASN cc_start: 0.7048 (t0) cc_final: 0.6838 (t0) REVERT: S 1 MET cc_start: 0.6948 (ptm) cc_final: 0.6618 (ptm) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.2918 time to fit residues: 82.4963 Evaluate side-chains 135 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.0030 chunk 68 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 154 optimal weight: 0.3980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13951 Z= 0.156 Angle : 0.488 6.290 18886 Z= 0.259 Chirality : 0.040 0.156 2198 Planarity : 0.003 0.036 2403 Dihedral : 3.853 27.114 1868 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.13 % Allowed : 2.23 % Favored : 97.64 % 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: 1.20 (0.21), residues: 1703 helix: 1.77 (0.17), residues: 983 sheet: 0.30 (0.41), residues: 175 loop : -0.82 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 421 HIS 0.011 0.001 HIS B 149 PHE 0.014 0.001 PHE A 484 TYR 0.021 0.001 TYR B 136 ARG 0.006 0.000 ARG S 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8057 (tttm) cc_final: 0.7444 (tmtt) REVERT: A 546 ILE cc_start: 0.8449 (tt) cc_final: 0.8211 (tt) REVERT: A 568 GLN cc_start: 0.8147 (mp10) cc_final: 0.7801 (mp10) REVERT: M 371 GLU cc_start: 0.7530 (pt0) cc_final: 0.7268 (pm20) REVERT: S 1 MET cc_start: 0.6898 (ptm) cc_final: 0.6536 (ptm) outliers start: 2 outliers final: 1 residues processed: 183 average time/residue: 0.2530 time to fit residues: 69.2253 Evaluate side-chains 140 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13951 Z= 0.217 Angle : 0.503 6.486 18886 Z= 0.262 Chirality : 0.040 0.152 2198 Planarity : 0.004 0.059 2403 Dihedral : 3.840 24.085 1868 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.07 % Allowed : 3.67 % Favored : 96.26 % 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: 1.27 (0.21), residues: 1703 helix: 1.82 (0.17), residues: 975 sheet: 0.17 (0.39), residues: 188 loop : -0.70 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 421 HIS 0.012 0.001 HIS B 149 PHE 0.022 0.001 PHE A 530 TYR 0.014 0.001 TYR B 72 ARG 0.006 0.000 ARG S 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8808 (mt) cc_final: 0.8606 (mt) REVERT: A 546 ILE cc_start: 0.8477 (tt) cc_final: 0.8182 (tt) REVERT: A 568 GLN cc_start: 0.8078 (mp10) cc_final: 0.7738 (mp10) REVERT: B 110 MET cc_start: 0.8651 (mpp) cc_final: 0.8056 (mpp) REVERT: M 371 GLU cc_start: 0.7565 (pt0) cc_final: 0.7300 (pm20) REVERT: S 1 MET cc_start: 0.7086 (ptm) cc_final: 0.6674 (ptm) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.2710 time to fit residues: 72.6044 Evaluate side-chains 138 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.0670 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 155 optimal weight: 0.0970 chunk 164 optimal weight: 0.5980 chunk 81 optimal weight: 0.0870 chunk 147 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13951 Z= 0.138 Angle : 0.479 6.870 18886 Z= 0.251 Chirality : 0.039 0.171 2198 Planarity : 0.003 0.045 2403 Dihedral : 3.790 22.819 1868 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.07 % Allowed : 2.29 % Favored : 97.64 % 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: 1.36 (0.21), residues: 1703 helix: 1.89 (0.17), residues: 977 sheet: 0.33 (0.40), residues: 184 loop : -0.70 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.014 0.001 HIS B 149 PHE 0.020 0.001 PHE A 530 TYR 0.020 0.001 TYR B 136 ARG 0.005 0.000 ARG S 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.904 Fit side-chains REVERT: A 93 ILE cc_start: 0.8689 (mt) cc_final: 0.8450 (tt) REVERT: A 110 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7640 (mtm-85) REVERT: A 128 MET cc_start: 0.7933 (ptp) cc_final: 0.7713 (ptp) REVERT: A 546 ILE cc_start: 0.8370 (tt) cc_final: 0.8117 (tt) REVERT: A 568 GLN cc_start: 0.8097 (mp10) cc_final: 0.7700 (mp10) REVERT: M 327 PRO cc_start: 0.8578 (Cg_exo) cc_final: 0.8318 (Cg_endo) REVERT: M 371 GLU cc_start: 0.7593 (pt0) cc_final: 0.7305 (pm20) REVERT: S 1 MET cc_start: 0.7025 (ptm) cc_final: 0.6688 (ptm) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.2442 time to fit residues: 70.2249 Evaluate side-chains 144 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13951 Z= 0.199 Angle : 0.507 6.791 18886 Z= 0.262 Chirality : 0.040 0.171 2198 Planarity : 0.003 0.039 2403 Dihedral : 3.785 21.044 1868 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.77 % 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: 1.33 (0.21), residues: 1703 helix: 1.85 (0.17), residues: 981 sheet: 0.25 (0.39), residues: 189 loop : -0.69 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 462 HIS 0.018 0.001 HIS B 149 PHE 0.025 0.001 PHE B 581 TYR 0.018 0.001 TYR B 136 ARG 0.006 0.000 ARG M 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.692 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.8735 (mt) cc_final: 0.8521 (tt) REVERT: A 546 ILE cc_start: 0.8354 (tt) cc_final: 0.8130 (tt) REVERT: A 568 GLN cc_start: 0.8122 (mp10) cc_final: 0.7679 (mp10) REVERT: M 327 PRO cc_start: 0.8576 (Cg_exo) cc_final: 0.8321 (Cg_endo) REVERT: M 371 GLU cc_start: 0.7644 (pt0) cc_final: 0.7332 (pm20) REVERT: S 1 MET cc_start: 0.7059 (ptm) cc_final: 0.6721 (ptm) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.2470 time to fit residues: 67.3682 Evaluate side-chains 137 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13951 Z= 0.191 Angle : 0.502 6.965 18886 Z= 0.259 Chirality : 0.040 0.192 2198 Planarity : 0.003 0.037 2403 Dihedral : 3.801 20.405 1868 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.07 % Allowed : 1.77 % Favored : 98.17 % 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: 1.31 (0.21), residues: 1703 helix: 1.83 (0.17), residues: 986 sheet: 0.23 (0.39), residues: 189 loop : -0.72 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 462 HIS 0.016 0.001 HIS B 149 PHE 0.021 0.001 PHE B 581 TYR 0.016 0.001 TYR B 76 ARG 0.005 0.000 ARG M 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.665 Fit side-chains revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8389 (tt) cc_final: 0.8167 (tt) REVERT: A 568 GLN cc_start: 0.8134 (mp10) cc_final: 0.7658 (mp10) REVERT: M 327 PRO cc_start: 0.8583 (Cg_exo) cc_final: 0.8328 (Cg_endo) REVERT: M 371 GLU cc_start: 0.7639 (pt0) cc_final: 0.7308 (pm20) REVERT: S 1 MET cc_start: 0.7100 (ptm) cc_final: 0.6778 (ptm) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.2534 time to fit residues: 69.8462 Evaluate side-chains 137 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13951 Z= 0.165 Angle : 0.504 7.282 18886 Z= 0.261 Chirality : 0.040 0.149 2198 Planarity : 0.003 0.052 2403 Dihedral : 3.783 20.118 1868 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.07 % Allowed : 0.79 % 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: 1.32 (0.21), residues: 1703 helix: 1.85 (0.17), residues: 988 sheet: 0.26 (0.40), residues: 188 loop : -0.73 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 462 HIS 0.014 0.001 HIS B 149 PHE 0.026 0.001 PHE A 530 TYR 0.019 0.001 TYR B 136 ARG 0.009 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8327 (tt) cc_final: 0.8127 (tt) REVERT: A 568 GLN cc_start: 0.8058 (mp10) cc_final: 0.7673 (mp10) REVERT: B 187 ILE cc_start: 0.8080 (mm) cc_final: 0.7788 (mm) REVERT: M 327 PRO cc_start: 0.8559 (Cg_exo) cc_final: 0.8297 (Cg_endo) REVERT: M 371 GLU cc_start: 0.7618 (pt0) cc_final: 0.7292 (pm20) REVERT: S 1 MET cc_start: 0.7132 (ptm) cc_final: 0.6753 (ptm) REVERT: S 61 ARG cc_start: 0.8294 (ttm110) cc_final: 0.8087 (ttm110) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.2340 time to fit residues: 65.3821 Evaluate side-chains 136 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN M 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13951 Z= 0.200 Angle : 0.519 7.454 18886 Z= 0.266 Chirality : 0.040 0.154 2198 Planarity : 0.003 0.037 2403 Dihedral : 3.795 20.898 1868 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.07 % Allowed : 1.25 % Favored : 98.69 % 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: 1.30 (0.21), residues: 1703 helix: 1.84 (0.17), residues: 988 sheet: 0.21 (0.39), residues: 188 loop : -0.74 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 462 HIS 0.018 0.001 HIS B 149 PHE 0.017 0.001 PHE B 581 TYR 0.015 0.001 TYR A 88 ARG 0.006 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 ILE cc_start: 0.8375 (tt) cc_final: 0.8173 (tt) REVERT: A 568 GLN cc_start: 0.8110 (mp10) cc_final: 0.7765 (mp10) REVERT: B 187 ILE cc_start: 0.8074 (mm) cc_final: 0.7742 (mm) REVERT: M 327 PRO cc_start: 0.8590 (Cg_exo) cc_final: 0.8341 (Cg_endo) REVERT: M 371 GLU cc_start: 0.7626 (pt0) cc_final: 0.7302 (pm20) REVERT: S 1 MET cc_start: 0.7157 (ptm) cc_final: 0.6784 (ptm) REVERT: S 61 ARG cc_start: 0.8310 (ttm110) cc_final: 0.8103 (ttm110) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.2393 time to fit residues: 64.5573 Evaluate side-chains 133 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.0470 chunk 143 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13951 Z= 0.151 Angle : 0.505 8.302 18886 Z= 0.260 Chirality : 0.040 0.153 2198 Planarity : 0.003 0.037 2403 Dihedral : 3.772 20.510 1868 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.07 % Allowed : 0.46 % Favored : 99.48 % 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: 1.33 (0.21), residues: 1703 helix: 1.89 (0.17), residues: 987 sheet: 0.22 (0.40), residues: 187 loop : -0.79 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 462 HIS 0.018 0.001 HIS B 149 PHE 0.016 0.001 PHE B 581 TYR 0.020 0.001 TYR A 545 ARG 0.005 0.000 ARG S 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 1.843 Fit side-chains revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.7583 (mtm-85) REVERT: A 546 ILE cc_start: 0.8296 (tt) cc_final: 0.8080 (tt) REVERT: A 568 GLN cc_start: 0.8123 (mp10) cc_final: 0.7777 (mp10) REVERT: B 187 ILE cc_start: 0.8056 (mm) cc_final: 0.7775 (mm) REVERT: M 327 PRO cc_start: 0.8521 (Cg_exo) cc_final: 0.8249 (Cg_endo) REVERT: M 371 GLU cc_start: 0.7667 (pt0) cc_final: 0.7293 (pm20) REVERT: S 1 MET cc_start: 0.7155 (ptm) cc_final: 0.6788 (ptm) REVERT: S 61 ARG cc_start: 0.8275 (ttm110) cc_final: 0.8055 (ttm110) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.2526 time to fit residues: 70.4121 Evaluate side-chains 137 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13951 Z= 0.208 Angle : 0.547 21.280 18886 Z= 0.274 Chirality : 0.041 0.400 2198 Planarity : 0.004 0.037 2403 Dihedral : 3.796 21.233 1868 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.07 % Allowed : 0.13 % 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: 1.28 (0.21), residues: 1703 helix: 1.84 (0.17), residues: 986 sheet: 0.14 (0.40), residues: 189 loop : -0.76 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 462 HIS 0.020 0.001 HIS B 149 PHE 0.016 0.001 PHE B 581 TYR 0.029 0.001 TYR B 136 ARG 0.005 0.000 ARG S 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.683 Fit side-chains revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7564 (mtm-85) REVERT: A 245 GLN cc_start: 0.8083 (mp10) cc_final: 0.7732 (mp10) REVERT: A 568 GLN cc_start: 0.8110 (mp10) cc_final: 0.7805 (mp10) REVERT: B 187 ILE cc_start: 0.8099 (mm) cc_final: 0.7792 (mm) REVERT: M 327 PRO cc_start: 0.8577 (Cg_exo) cc_final: 0.8301 (Cg_endo) REVERT: M 371 GLU cc_start: 0.7683 (pt0) cc_final: 0.7309 (pm20) REVERT: S 1 MET cc_start: 0.7127 (ptm) cc_final: 0.6804 (ptm) REVERT: S 61 ARG cc_start: 0.8288 (ttm110) cc_final: 0.8070 (ttm110) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.2557 time to fit residues: 70.6408 Evaluate side-chains 139 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 0.2980 chunk 17 optimal weight: 0.0170 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118361 restraints weight = 19796.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110510 restraints weight = 26901.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109017 restraints weight = 32713.794| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13951 Z= 0.203 Angle : 0.531 12.990 18886 Z= 0.272 Chirality : 0.041 0.220 2198 Planarity : 0.003 0.038 2403 Dihedral : 3.803 22.232 1868 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.07 % Allowed : 0.26 % 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: 1.27 (0.21), residues: 1703 helix: 1.83 (0.17), residues: 987 sheet: 0.15 (0.40), residues: 188 loop : -0.76 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 462 HIS 0.020 0.001 HIS B 149 PHE 0.016 0.001 PHE B 581 TYR 0.022 0.001 TYR B 136 ARG 0.005 0.000 ARG M 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3053.79 seconds wall clock time: 56 minutes 14.54 seconds (3374.54 seconds total)