Starting phenix.real_space_refine on Wed Feb 14 20:02:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ran_4781/02_2024/6ran_4781.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ran_4781/02_2024/6ran_4781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ran_4781/02_2024/6ran_4781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ran_4781/02_2024/6ran_4781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ran_4781/02_2024/6ran_4781.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ran_4781/02_2024/6ran_4781.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 25 5.16 5 C 6579 2.51 5 N 1795 2.21 5 O 1774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 332": "OD1" <-> "OD2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 516": "OD1" <-> "OD2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 108": "OD1" <-> "OD2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 326": "OD1" <-> "OD2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "B ASP 440": "OD1" <-> "OD2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B ASP 540": "OD1" <-> "OD2" Residue "B GLU 552": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B GLU 568": "OE1" <-> "OE2" Residue "B ASP 570": "OD1" <-> "OD2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10173 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4741 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 24, 'TRANS': 567} Chain: "B" Number of atoms: 4535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4535 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 18, 'TRANS': 555} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Time building chain proxies: 5.54, per 1000 atoms: 0.54 Number of scatterers: 10173 At special positions: 0 Unit cell: (104.469, 91.545, 159.396, 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 25 16.00 O 1774 8.00 N 1795 7.00 C 6579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.06 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: 3.77 Conformation dependent library (CDL) restraints added in 1.8 seconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 66.7% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 removed outlier: 3.587A pdb=" N ARG A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 24 Proline residue: A 24 - end of helix No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 25 through 45 removed outlier: 3.603A pdb=" N PHE A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 72 through 120 Processing helix chain 'A' and resid 121 through 128 removed outlier: 4.313A pdb=" N TYR A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 3.519A pdb=" N LEU A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.592A pdb=" N ILE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 173 removed outlier: 3.848A pdb=" N VAL A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 removed outlier: 4.337A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 222 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 231 through 285 removed outlier: 3.897A pdb=" N ARG A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 260 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.654A pdb=" N VAL A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 314 removed outlier: 3.739A pdb=" N PHE A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Proline residue: A 306 - end of helix removed outlier: 3.865A pdb=" N ASP A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 332 removed outlier: 4.092A pdb=" N GLY A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 407 removed outlier: 3.995A pdb=" N VAL A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.797A pdb=" N VAL A 466 " --> pdb=" O PRO A 462 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.829A pdb=" N THR A 488 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 578 through 586 removed outlier: 3.822A pdb=" N GLY A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 removed outlier: 3.685A pdb=" N ALA A 590 " --> pdb=" O GLY A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 19 removed outlier: 3.993A pdb=" N LEU B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Proline residue: B 15 - end of helix Processing helix chain 'B' and resid 20 through 54 removed outlier: 3.896A pdb=" N TYR B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 57 through 103 removed outlier: 4.521A pdb=" N TYR B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 removed outlier: 4.155A pdb=" N TYR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 133 removed outlier: 3.643A pdb=" N ASN B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 removed outlier: 4.050A pdb=" N LEU B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 207 removed outlier: 3.814A pdb=" N ALA B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.665A pdb=" N LEU B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 216 through 243 removed outlier: 4.091A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 271 removed outlier: 3.849A pdb=" N PHE B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 288 through 318 removed outlier: 4.204A pdb=" N ILE B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.540A pdb=" N LEU B 335 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.708A pdb=" N ALA B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 440 through 451 removed outlier: 3.751A pdb=" N VAL B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 460 removed outlier: 3.802A pdb=" N PHE B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 466 removed outlier: 3.719A pdb=" N THR B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 3.727A pdb=" N LYS B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 521 Processing helix chain 'B' and resid 532 through 538 removed outlier: 4.212A pdb=" N HIS B 538 " --> pdb=" O ALA B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 563 Processing helix chain 'B' and resid 564 through 574 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.924A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 383 removed outlier: 5.563A pdb=" N LYS A 377 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU A 360 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE A 381 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ARG A 356 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL A 383 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLU A 354 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 358 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG A 414 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 6.483A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS A 388 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU A 566 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ALA A 390 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE A 568 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL A 392 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 565 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU A 576 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 567 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 351 through 361 removed outlier: 6.999A pdb=" N LEU B 353 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LYS B 347 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG B 355 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLY B 345 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU B 357 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL B 344 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU B 392 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.172A pdb=" N GLY B 415 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASP B 499 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 417 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU B 367 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR B 366 " --> pdb=" O TRP B 541 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE B 543 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY B 368 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU B 545 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N THR B 370 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.659A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.529A pdb=" N ALA C 92 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1620 1.31 - 1.44: 3197 1.44 - 1.57: 5520 1.57 - 1.70: 2 1.70 - 1.83: 45 Bond restraints: 10384 Sorted by residual: bond pdb=" N PRO A 340 " pdb=" CD PRO A 340 " ideal model delta sigma weight residual 1.473 1.572 -0.099 1.40e-02 5.10e+03 4.96e+01 bond pdb=" N PRO B 291 " pdb=" CD PRO B 291 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.21e+01 bond pdb=" CA GLY B 345 " pdb=" C GLY B 345 " ideal model delta sigma weight residual 1.516 1.481 0.035 8.20e-03 1.49e+04 1.87e+01 bond pdb=" CA GLY B 415 " pdb=" C GLY B 415 " ideal model delta sigma weight residual 1.520 1.489 0.031 7.30e-03 1.88e+04 1.79e+01 bond pdb=" N ILE C 51 " pdb=" CA ILE C 51 " ideal model delta sigma weight residual 1.456 1.504 -0.048 1.15e-02 7.56e+03 1.76e+01 ... (remaining 10379 not shown) Histogram of bond angle deviations from ideal: 95.06 - 102.90: 101 102.90 - 110.74: 2749 110.74 - 118.59: 5461 118.59 - 126.43: 5604 126.43 - 134.27: 159 Bond angle restraints: 14074 Sorted by residual: angle pdb=" N VAL B 210 " pdb=" CA VAL B 210 " pdb=" C VAL B 210 " ideal model delta sigma weight residual 111.81 103.51 8.30 8.60e-01 1.35e+00 9.31e+01 angle pdb=" N GLU B 442 " pdb=" CA GLU B 442 " pdb=" C GLU B 442 " ideal model delta sigma weight residual 111.07 120.93 -9.86 1.07e+00 8.73e-01 8.49e+01 angle pdb=" N VAL A 186 " pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 110.42 119.00 -8.58 9.60e-01 1.09e+00 7.98e+01 angle pdb=" N VAL B 444 " pdb=" CA VAL B 444 " pdb=" CB VAL B 444 " ideal model delta sigma weight residual 110.55 120.47 -9.92 1.17e+00 7.31e-01 7.19e+01 angle pdb=" N VAL B 576 " pdb=" CA VAL B 576 " pdb=" C VAL B 576 " ideal model delta sigma weight residual 107.80 119.82 -12.02 1.45e+00 4.76e-01 6.88e+01 ... (remaining 14069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 5849 17.38 - 34.75: 218 34.75 - 52.13: 52 52.13 - 69.50: 42 69.50 - 86.88: 14 Dihedral angle restraints: 6175 sinusoidal: 2495 harmonic: 3680 Sorted by residual: dihedral pdb=" N THR A 135 " pdb=" C THR A 135 " pdb=" CA THR A 135 " pdb=" CB THR A 135 " ideal model delta harmonic sigma weight residual 123.40 135.75 -12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" N VAL B 90 " pdb=" C VAL B 90 " pdb=" CA VAL B 90 " pdb=" CB VAL B 90 " ideal model delta harmonic sigma weight residual 123.40 135.67 -12.27 0 2.50e+00 1.60e-01 2.41e+01 dihedral pdb=" C VAL B 483 " pdb=" N VAL B 483 " pdb=" CA VAL B 483 " pdb=" CB VAL B 483 " ideal model delta harmonic sigma weight residual -122.00 -134.14 12.14 0 2.50e+00 1.60e-01 2.36e+01 ... (remaining 6172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1010 0.106 - 0.211: 397 0.211 - 0.316: 137 0.316 - 0.421: 39 0.421 - 0.527: 24 Chirality restraints: 1607 Sorted by residual: chirality pdb=" CA LEU A 33 " pdb=" N LEU A 33 " pdb=" C LEU A 33 " pdb=" CB LEU A 33 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" CA GLU B 442 " pdb=" N GLU B 442 " pdb=" C GLU B 442 " pdb=" CB GLU B 442 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CA VAL B 90 " pdb=" N VAL B 90 " pdb=" C VAL B 90 " pdb=" CB VAL B 90 " both_signs ideal model delta sigma weight residual False 2.44 1.94 0.50 2.00e-01 2.50e+01 6.30e+00 ... (remaining 1604 not shown) Planarity restraints: 1790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 172 " 0.030 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C LEU A 172 " -0.105 2.00e-02 2.50e+03 pdb=" O LEU A 172 " 0.040 2.00e-02 2.50e+03 pdb=" N SER A 173 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 75 " -0.059 2.00e-02 2.50e+03 2.86e-02 2.04e+01 pdb=" CG TRP A 75 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 75 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 75 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP A 75 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 75 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 75 " 0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 75 " -0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 75 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 75 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 22 " -0.060 2.00e-02 2.50e+03 2.78e-02 1.94e+01 pdb=" CG TRP B 22 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 22 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 22 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP B 22 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 22 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 22 " 0.034 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 22 " -0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 22 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 22 " -0.026 2.00e-02 2.50e+03 ... (remaining 1787 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 3616 2.92 - 3.41: 10205 3.41 - 3.91: 16524 3.91 - 4.40: 18254 4.40 - 4.90: 30613 Nonbonded interactions: 79212 Sorted by model distance: nonbonded pdb=" NH1 ARG C 19 " pdb=" OE1 GLN C 82 " model vdw 2.421 2.520 nonbonded pdb=" O SER C 85 " pdb=" OG SER C 85 " model vdw 2.450 2.440 nonbonded pdb=" O PRO A 47 " pdb=" N PHE A 50 " model vdw 2.451 2.520 nonbonded pdb=" N LEU B 468 " pdb=" O LEU B 468 " model vdw 2.481 2.496 nonbonded pdb=" N LEU B 388 " pdb=" O LEU B 388 " model vdw 2.485 2.496 ... (remaining 79207 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.040 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.570 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 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 0.099 10384 Z= 1.106 Angle : 2.079 12.069 14074 Z= 1.489 Chirality : 0.140 0.527 1607 Planarity : 0.012 0.092 1790 Dihedral : 12.459 86.879 3813 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.44 % Cbeta Deviations : 1.61 % 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: 0.16 (0.22), residues: 1281 helix: 1.09 (0.18), residues: 784 sheet: 0.14 (0.44), residues: 131 loop : -2.07 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.009 TRP B 22 HIS 0.007 0.001 HIS A 435 PHE 0.049 0.009 PHE A 270 TYR 0.058 0.006 TYR B 284 ARG 0.004 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 333 time to evaluate : 1.119 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: A 25 TYR cc_start: 0.7813 (m-80) cc_final: 0.7140 (m-80) REVERT: A 40 THR cc_start: 0.8383 (p) cc_final: 0.8134 (t) REVERT: A 205 MET cc_start: 0.8764 (tmm) cc_final: 0.8363 (tmm) REVERT: A 359 TRP cc_start: 0.7247 (m100) cc_final: 0.6989 (m100) REVERT: A 365 LYS cc_start: 0.6656 (mmtm) cc_final: 0.5315 (tptt) REVERT: B 32 LEU cc_start: 0.9263 (mt) cc_final: 0.8881 (mt) REVERT: B 102 LEU cc_start: 0.9222 (mt) cc_final: 0.8925 (mt) REVERT: B 130 ARG cc_start: 0.8858 (ttp80) cc_final: 0.8392 (tmm160) REVERT: B 132 MET cc_start: 0.8394 (ttp) cc_final: 0.7765 (tmm) REVERT: B 145 PHE cc_start: 0.8508 (t80) cc_final: 0.8159 (t80) REVERT: B 161 LEU cc_start: 0.8271 (tp) cc_final: 0.8051 (tp) REVERT: B 173 PHE cc_start: 0.6584 (t80) cc_final: 0.6322 (t80) REVERT: B 255 PHE cc_start: 0.6998 (m-10) cc_final: 0.6582 (m-10) REVERT: B 258 LEU cc_start: 0.8111 (tt) cc_final: 0.7527 (tp) REVERT: B 289 THR cc_start: 0.6625 (p) cc_final: 0.6383 (p) REVERT: B 365 MET cc_start: 0.9128 (ppp) cc_final: 0.8798 (ppp) REVERT: C 6 GLU cc_start: 0.5873 (mp0) cc_final: 0.5667 (mp0) outliers start: 1 outliers final: 0 residues processed: 334 average time/residue: 0.2748 time to fit residues: 120.5852 Evaluate side-chains 187 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 111 HIS B 515 GLN C 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10384 Z= 0.215 Angle : 0.645 7.299 14074 Z= 0.349 Chirality : 0.041 0.179 1607 Planarity : 0.006 0.074 1790 Dihedral : 4.960 26.833 1442 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.19 % Allowed : 2.37 % Favored : 97.44 % 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 (0.23), residues: 1281 helix: 2.02 (0.18), residues: 786 sheet: 0.03 (0.40), residues: 137 loop : -1.48 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 262 HIS 0.006 0.001 HIS B 111 PHE 0.020 0.002 PHE A 472 TYR 0.024 0.002 TYR A 299 ARG 0.008 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 1.134 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: A 25 TYR cc_start: 0.7763 (m-80) cc_final: 0.6904 (m-10) REVERT: A 205 MET cc_start: 0.8748 (tmm) cc_final: 0.8463 (tmm) REVERT: B 32 LEU cc_start: 0.8990 (mt) cc_final: 0.8768 (mt) REVERT: B 109 PHE cc_start: 0.7941 (t80) cc_final: 0.7681 (t80) REVERT: B 132 MET cc_start: 0.8644 (ttp) cc_final: 0.7602 (tmm) REVERT: B 161 LEU cc_start: 0.8361 (tp) cc_final: 0.8124 (tp) REVERT: B 309 LEU cc_start: 0.7639 (tp) cc_final: 0.7426 (tp) REVERT: B 365 MET cc_start: 0.9160 (ppp) cc_final: 0.8832 (ppp) REVERT: B 373 THR cc_start: 0.8730 (m) cc_final: 0.8446 (p) REVERT: B 388 LEU cc_start: 0.8533 (mt) cc_final: 0.8311 (mt) REVERT: B 465 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8155 (mp0) outliers start: 2 outliers final: 0 residues processed: 232 average time/residue: 0.2251 time to fit residues: 73.6765 Evaluate side-chains 164 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 96 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 93 optimal weight: 0.0670 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 243 ASN A 503 GLN B 419 GLN C 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10384 Z= 0.209 Angle : 0.597 7.052 14074 Z= 0.315 Chirality : 0.041 0.161 1607 Planarity : 0.005 0.052 1790 Dihedral : 4.695 27.337 1442 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 1.45 (0.23), residues: 1281 helix: 2.01 (0.18), residues: 787 sheet: 0.33 (0.43), residues: 130 loop : -1.17 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 262 HIS 0.004 0.001 HIS B 111 PHE 0.016 0.002 PHE B 151 TYR 0.020 0.002 TYR B 302 ARG 0.010 0.001 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.132 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: A 139 SER cc_start: 0.7602 (m) cc_final: 0.7398 (t) REVERT: A 205 MET cc_start: 0.8825 (tmm) cc_final: 0.8443 (tmm) REVERT: A 519 LEU cc_start: 0.8949 (tp) cc_final: 0.8048 (tp) REVERT: B 32 LEU cc_start: 0.8938 (mt) cc_final: 0.8591 (mt) REVERT: B 43 TYR cc_start: 0.8014 (t80) cc_final: 0.7722 (t80) REVERT: B 60 VAL cc_start: 0.8624 (m) cc_final: 0.8388 (p) REVERT: B 111 HIS cc_start: 0.7397 (m-70) cc_final: 0.7196 (m-70) REVERT: B 132 MET cc_start: 0.8747 (ttp) cc_final: 0.7638 (tmm) REVERT: B 142 ARG cc_start: 0.7161 (tmm-80) cc_final: 0.6764 (tmm-80) REVERT: B 145 PHE cc_start: 0.8290 (t80) cc_final: 0.8050 (t80) REVERT: B 465 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8190 (mp0) REVERT: B 499 ASP cc_start: 0.7418 (t0) cc_final: 0.6969 (p0) REVERT: B 546 ASP cc_start: 0.6534 (t0) cc_final: 0.6038 (m-30) REVERT: C 20 LEU cc_start: 0.5935 (tp) cc_final: 0.5251 (tp) REVERT: C 31 TYR cc_start: 0.8056 (p90) cc_final: 0.7661 (p90) REVERT: C 36 TRP cc_start: 0.6094 (m100) cc_final: 0.5715 (m100) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2196 time to fit residues: 66.7735 Evaluate side-chains 170 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 0.0770 chunk 12 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 123 optimal weight: 0.0870 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN B 400 HIS B 419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10384 Z= 0.161 Angle : 0.546 8.073 14074 Z= 0.284 Chirality : 0.040 0.179 1607 Planarity : 0.004 0.049 1790 Dihedral : 4.451 25.079 1442 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: 1.59 (0.23), residues: 1281 helix: 2.13 (0.18), residues: 787 sheet: 0.14 (0.43), residues: 131 loop : -1.04 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 262 HIS 0.002 0.001 HIS B 538 PHE 0.023 0.001 PHE A 472 TYR 0.016 0.001 TYR B 302 ARG 0.004 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.133 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: A 25 TYR cc_start: 0.7643 (m-80) cc_final: 0.7316 (m-80) REVERT: A 205 MET cc_start: 0.8825 (tmm) cc_final: 0.8515 (tmm) REVERT: A 328 PHE cc_start: 0.8094 (m-10) cc_final: 0.7323 (m-10) REVERT: A 544 MET cc_start: 0.8308 (mmp) cc_final: 0.7006 (ptm) REVERT: B 32 LEU cc_start: 0.8795 (mt) cc_final: 0.8575 (mt) REVERT: B 40 LEU cc_start: 0.8853 (tp) cc_final: 0.8184 (tt) REVERT: B 43 TYR cc_start: 0.7994 (t80) cc_final: 0.7725 (t80) REVERT: B 111 HIS cc_start: 0.7291 (m-70) cc_final: 0.7013 (m-70) REVERT: B 132 MET cc_start: 0.8739 (ttp) cc_final: 0.7631 (tmm) REVERT: B 217 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7698 (tm-30) REVERT: B 255 PHE cc_start: 0.7361 (m-10) cc_final: 0.7118 (m-80) REVERT: B 465 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8193 (mp0) REVERT: B 546 ASP cc_start: 0.6492 (t0) cc_final: 0.6139 (m-30) REVERT: C 6 GLU cc_start: 0.5362 (mp0) cc_final: 0.4166 (mt-10) REVERT: C 31 TYR cc_start: 0.8054 (p90) cc_final: 0.7707 (p90) REVERT: C 36 TRP cc_start: 0.6019 (m100) cc_final: 0.5158 (m100) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2063 time to fit residues: 62.2964 Evaluate side-chains 161 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 308 GLN A 554 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10384 Z= 0.328 Angle : 0.735 8.813 14074 Z= 0.373 Chirality : 0.044 0.173 1607 Planarity : 0.006 0.068 1790 Dihedral : 5.023 25.527 1442 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: 0.65 (0.22), residues: 1281 helix: 1.25 (0.17), residues: 785 sheet: -0.06 (0.43), residues: 137 loop : -1.12 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 374 HIS 0.006 0.002 HIS B 400 PHE 0.030 0.002 PHE B 151 TYR 0.028 0.002 TYR B 92 ARG 0.005 0.001 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.8220 (mt) cc_final: 0.7658 (tt) REVERT: A 205 MET cc_start: 0.8587 (tmm) cc_final: 0.8319 (tmm) REVERT: A 328 PHE cc_start: 0.8222 (m-10) cc_final: 0.7479 (m-10) REVERT: A 544 MET cc_start: 0.8128 (mmp) cc_final: 0.7164 (ppp) REVERT: A 593 TYR cc_start: 0.6368 (t80) cc_final: 0.5770 (t80) REVERT: B 32 LEU cc_start: 0.9016 (mt) cc_final: 0.8500 (mt) REVERT: B 132 MET cc_start: 0.8542 (ttp) cc_final: 0.7473 (tmm) REVERT: B 145 PHE cc_start: 0.8260 (t80) cc_final: 0.7955 (t80) REVERT: B 255 PHE cc_start: 0.7474 (m-10) cc_final: 0.7220 (m-80) REVERT: B 301 LEU cc_start: 0.8739 (tp) cc_final: 0.8525 (tp) REVERT: C 18 LEU cc_start: 0.8191 (tt) cc_final: 0.7836 (mt) REVERT: C 31 TYR cc_start: 0.8190 (p90) cc_final: 0.7692 (p90) REVERT: C 36 TRP cc_start: 0.6123 (m100) cc_final: 0.5021 (m100) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2035 time to fit residues: 57.1753 Evaluate side-chains 148 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN B 419 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10384 Z= 0.178 Angle : 0.572 8.576 14074 Z= 0.294 Chirality : 0.040 0.173 1607 Planarity : 0.004 0.048 1790 Dihedral : 4.586 24.544 1442 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 1.12 (0.23), residues: 1281 helix: 1.64 (0.18), residues: 788 sheet: 0.09 (0.44), residues: 130 loop : -0.96 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 223 HIS 0.003 0.001 HIS B 111 PHE 0.014 0.001 PHE A 296 TYR 0.015 0.001 TYR B 155 ARG 0.014 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.174 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: A 205 MET cc_start: 0.8635 (tmm) cc_final: 0.8223 (tmm) REVERT: A 544 MET cc_start: 0.7774 (mmp) cc_final: 0.6991 (ptm) REVERT: A 593 TYR cc_start: 0.6371 (t80) cc_final: 0.5787 (t80) REVERT: B 32 LEU cc_start: 0.8665 (mt) cc_final: 0.8386 (mt) REVERT: B 40 LEU cc_start: 0.8921 (tp) cc_final: 0.8457 (tt) REVERT: B 63 LEU cc_start: 0.8786 (mm) cc_final: 0.8455 (tp) REVERT: B 132 MET cc_start: 0.8544 (ttp) cc_final: 0.7373 (tmm) REVERT: B 255 PHE cc_start: 0.7239 (m-10) cc_final: 0.7021 (m-80) REVERT: B 365 MET cc_start: 0.8924 (ppp) cc_final: 0.8721 (ppp) REVERT: B 465 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8134 (mp0) REVERT: B 473 ILE cc_start: 0.8266 (mm) cc_final: 0.8062 (mm) REVERT: C 6 GLU cc_start: 0.5826 (mp0) cc_final: 0.5418 (mp0) REVERT: C 18 LEU cc_start: 0.8027 (tt) cc_final: 0.7657 (mt) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1907 time to fit residues: 58.4278 Evaluate side-chains 152 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 69 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN B 280 GLN B 400 HIS B 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10384 Z= 0.166 Angle : 0.564 8.158 14074 Z= 0.286 Chirality : 0.039 0.166 1607 Planarity : 0.004 0.048 1790 Dihedral : 4.393 22.459 1442 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 1.39 (0.23), residues: 1281 helix: 1.90 (0.18), residues: 788 sheet: 0.07 (0.43), residues: 131 loop : -0.92 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 223 HIS 0.005 0.001 HIS B 111 PHE 0.023 0.002 PHE B 38 TYR 0.021 0.001 TYR B 92 ARG 0.004 0.000 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.108 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: A 169 MET cc_start: 0.7879 (mtp) cc_final: 0.7351 (mpp) REVERT: A 205 MET cc_start: 0.8765 (tmm) cc_final: 0.8315 (tmm) REVERT: A 544 MET cc_start: 0.7763 (mmp) cc_final: 0.6919 (ptm) REVERT: A 593 TYR cc_start: 0.6326 (t80) cc_final: 0.5785 (t80) REVERT: B 40 LEU cc_start: 0.8943 (tp) cc_final: 0.8474 (tt) REVERT: B 43 TYR cc_start: 0.7953 (t80) cc_final: 0.7649 (t80) REVERT: B 132 MET cc_start: 0.8588 (ttp) cc_final: 0.7377 (tmm) REVERT: B 465 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8065 (mp0) REVERT: B 499 ASP cc_start: 0.7960 (t0) cc_final: 0.6580 (p0) REVERT: B 546 ASP cc_start: 0.6474 (t0) cc_final: 0.6056 (m-30) REVERT: C 6 GLU cc_start: 0.5690 (mp0) cc_final: 0.4828 (mt-10) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1971 time to fit residues: 56.9764 Evaluate side-chains 150 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN B 419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10384 Z= 0.169 Angle : 0.559 7.367 14074 Z= 0.285 Chirality : 0.040 0.166 1607 Planarity : 0.004 0.047 1790 Dihedral : 4.320 21.472 1442 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.09 % Allowed : 0.85 % Favored : 99.05 % 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: 1.45 (0.23), residues: 1281 helix: 1.97 (0.18), residues: 788 sheet: -0.06 (0.42), residues: 136 loop : -0.90 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 446 HIS 0.005 0.001 HIS A 435 PHE 0.017 0.002 PHE B 38 TYR 0.019 0.001 TYR B 155 ARG 0.003 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8785 (tmm) cc_final: 0.8324 (tmm) REVERT: A 353 VAL cc_start: 0.7761 (t) cc_final: 0.7550 (p) REVERT: A 544 MET cc_start: 0.7747 (mmp) cc_final: 0.6890 (ptm) REVERT: A 593 TYR cc_start: 0.6290 (t80) cc_final: 0.5742 (t80) REVERT: B 40 LEU cc_start: 0.8932 (tp) cc_final: 0.8487 (tt) REVERT: B 43 TYR cc_start: 0.7983 (t80) cc_final: 0.7659 (t80) REVERT: B 132 MET cc_start: 0.8518 (ttp) cc_final: 0.7258 (tmm) REVERT: B 220 MET cc_start: 0.8317 (mmp) cc_final: 0.8094 (mmp) REVERT: B 465 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8112 (mp0) REVERT: B 473 ILE cc_start: 0.8192 (mm) cc_final: 0.7988 (mm) REVERT: B 546 ASP cc_start: 0.6404 (t0) cc_final: 0.6010 (m-30) REVERT: C 6 GLU cc_start: 0.5619 (mp0) cc_final: 0.4558 (mt-10) REVERT: C 36 TRP cc_start: 0.6319 (m100) cc_final: 0.5435 (m100) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.1879 time to fit residues: 53.8183 Evaluate side-chains 154 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.0030 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN B 419 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10384 Z= 0.160 Angle : 0.558 9.214 14074 Z= 0.281 Chirality : 0.039 0.159 1607 Planarity : 0.004 0.047 1790 Dihedral : 4.209 20.844 1442 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 1.57 (0.23), residues: 1281 helix: 2.07 (0.18), residues: 791 sheet: -0.06 (0.43), residues: 135 loop : -0.85 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 446 HIS 0.004 0.001 HIS B 111 PHE 0.036 0.002 PHE B 145 TYR 0.022 0.001 TYR B 92 ARG 0.005 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.8564 (mtm) cc_final: 0.7536 (mpp) REVERT: A 205 MET cc_start: 0.8792 (tmm) cc_final: 0.8327 (tmm) REVERT: A 353 VAL cc_start: 0.7555 (t) cc_final: 0.7335 (p) REVERT: A 544 MET cc_start: 0.7766 (mmp) cc_final: 0.6933 (ptm) REVERT: A 593 TYR cc_start: 0.6294 (t80) cc_final: 0.5795 (t80) REVERT: B 40 LEU cc_start: 0.8936 (tp) cc_final: 0.8521 (tt) REVERT: B 43 TYR cc_start: 0.7911 (t80) cc_final: 0.7658 (t80) REVERT: B 132 MET cc_start: 0.8505 (ttp) cc_final: 0.7216 (tmm) REVERT: B 299 MET cc_start: 0.5980 (ttt) cc_final: 0.5757 (ttt) REVERT: B 465 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8047 (mp0) REVERT: B 473 ILE cc_start: 0.8180 (mm) cc_final: 0.7967 (mm) REVERT: B 546 ASP cc_start: 0.6472 (t0) cc_final: 0.6090 (m-30) REVERT: C 6 GLU cc_start: 0.5483 (mp0) cc_final: 0.4398 (mt-10) REVERT: C 36 TRP cc_start: 0.6346 (m100) cc_final: 0.5299 (m100) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1814 time to fit residues: 53.2677 Evaluate side-chains 152 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS B 228 ASN B 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10384 Z= 0.157 Angle : 0.555 8.684 14074 Z= 0.280 Chirality : 0.039 0.167 1607 Planarity : 0.004 0.047 1790 Dihedral : 4.150 19.477 1442 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.09 % Allowed : 0.38 % Favored : 99.53 % 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: 1.70 (0.23), residues: 1281 helix: 2.16 (0.18), residues: 795 sheet: -0.08 (0.43), residues: 136 loop : -0.78 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 446 HIS 0.010 0.001 HIS B 111 PHE 0.024 0.001 PHE B 38 TYR 0.025 0.001 TYR B 155 ARG 0.003 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.092 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: A 169 MET cc_start: 0.8659 (mtm) cc_final: 0.7537 (mpp) REVERT: A 205 MET cc_start: 0.8805 (tmm) cc_final: 0.8349 (tmm) REVERT: A 353 VAL cc_start: 0.7511 (t) cc_final: 0.7276 (p) REVERT: A 430 GLU cc_start: 0.8036 (tp30) cc_final: 0.6719 (mt-10) REVERT: A 593 TYR cc_start: 0.6260 (t80) cc_final: 0.5762 (t80) REVERT: B 40 LEU cc_start: 0.8925 (tp) cc_final: 0.8546 (tt) REVERT: B 43 TYR cc_start: 0.7910 (t80) cc_final: 0.7539 (t80) REVERT: B 63 LEU cc_start: 0.8768 (mm) cc_final: 0.8372 (tt) REVERT: B 132 MET cc_start: 0.8552 (ttp) cc_final: 0.7317 (tmm) REVERT: B 173 PHE cc_start: 0.6553 (t80) cc_final: 0.6268 (t80) REVERT: B 282 ASN cc_start: 0.8603 (t0) cc_final: 0.8140 (t0) REVERT: B 465 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8039 (mp0) REVERT: B 546 ASP cc_start: 0.6466 (t0) cc_final: 0.6072 (m-30) REVERT: C 6 GLU cc_start: 0.5391 (mp0) cc_final: 0.4146 (mt-10) REVERT: C 36 TRP cc_start: 0.6374 (m100) cc_final: 0.5278 (m100) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1773 time to fit residues: 50.9540 Evaluate side-chains 152 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 0.0270 chunk 14 optimal weight: 0.0670 chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN B 228 ASN B 419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.119103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.099145 restraints weight = 27833.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.100938 restraints weight = 16528.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.102198 restraints weight = 11005.554| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10384 Z= 0.145 Angle : 0.552 9.703 14074 Z= 0.273 Chirality : 0.039 0.166 1607 Planarity : 0.004 0.046 1790 Dihedral : 4.020 18.403 1442 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.09 % Allowed : 0.57 % Favored : 99.34 % 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: 1.84 (0.24), residues: 1281 helix: 2.26 (0.18), residues: 795 sheet: -0.04 (0.43), residues: 136 loop : -0.71 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 446 HIS 0.002 0.000 HIS B 454 PHE 0.025 0.001 PHE B 38 TYR 0.015 0.001 TYR A 202 ARG 0.004 0.000 ARG A 547 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2255.78 seconds wall clock time: 41 minutes 24.70 seconds (2484.70 seconds total)