Starting phenix.real_space_refine on Mon Apr 8 00:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ram_24369/04_2024/7ram_24369.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ram_24369/04_2024/7ram_24369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ram_24369/04_2024/7ram_24369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ram_24369/04_2024/7ram_24369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ram_24369/04_2024/7ram_24369.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ram_24369/04_2024/7ram_24369.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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 61 5.16 5 C 7659 2.51 5 N 2031 2.21 5 O 2255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 229": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12006 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5403 Classifications: {'peptide': 674} Link IDs: {'PTRANS': 33, 'TRANS': 640} Chain: "B" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1873 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 19, 'TRANS': 217} Chain: "C" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2471 Classifications: {'peptide': 297} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Chain: "D" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2259 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 15, 'TRANS': 273} Time building chain proxies: 6.57, per 1000 atoms: 0.55 Number of scatterers: 12006 At special positions: 0 Unit cell: (98.58, 100.7, 182.32, 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 61 16.00 O 2255 8.00 N 2031 7.00 C 7659 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS B 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 384 " distance=2.03 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 625 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 651 " distance=2.04 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 143 " - pdb=" SG CYS C 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS D 235 " - pdb=" SG CYS D 290 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.31 Conformation dependent library (CDL) restraints added in 2.2 seconds 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2882 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 32.9% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.744A pdb=" N PHE A 98 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.612A pdb=" N GLN A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 Processing helix chain 'A' and resid 128 through 133 removed outlier: 4.093A pdb=" N ASP A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.683A pdb=" N LEU A 287 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.904A pdb=" N ARG A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 removed outlier: 3.715A pdb=" N TYR A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 354 removed outlier: 4.287A pdb=" N ALA A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 363 through 385 removed outlier: 3.747A pdb=" N LEU A 385 " --> pdb=" O MET A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 397 through 410 Processing helix chain 'A' and resid 411 through 414 removed outlier: 3.669A pdb=" N ILE A 414 " --> pdb=" O PRO A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 411 through 414' Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.674A pdb=" N LEU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 437 through 440 removed outlier: 3.670A pdb=" N ALA A 440 " --> pdb=" O PRO A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 437 through 440' Processing helix chain 'A' and resid 441 through 455 Processing helix chain 'A' and resid 463 through 473 removed outlier: 3.528A pdb=" N GLU A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 470 " --> pdb=" O GLN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 495 removed outlier: 3.603A pdb=" N GLU A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 508 Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.751A pdb=" N LEU A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 4.000A pdb=" N ARG A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.803A pdb=" N GLN A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.593A pdb=" N THR A 566 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 567 " --> pdb=" O LEU A 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 567' Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 672 through 679 Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.773A pdb=" N LEU B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 117 through 127 Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.619A pdb=" N VAL B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.500A pdb=" N THR B 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 176 " --> pdb=" O ILE B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 176' Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.939A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 3.598A pdb=" N HIS B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 148 through 162 removed outlier: 3.937A pdb=" N GLU C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 216 removed outlier: 3.506A pdb=" N LEU C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 323 through 338 removed outlier: 3.905A pdb=" N ARG C 338 " --> pdb=" O TYR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 346 removed outlier: 6.697A pdb=" N ASN C 342 " --> pdb=" O TYR C 339 " (cutoff:3.500A) Proline residue: C 343 - end of helix removed outlier: 3.904A pdb=" N GLU C 346 " --> pdb=" O PRO C 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 339 through 346' Processing helix chain 'C' and resid 355 through 360 removed outlier: 3.853A pdb=" N ASN C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 removed outlier: 4.064A pdb=" N LEU C 364 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C 366 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 435 removed outlier: 3.702A pdb=" N TYR C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 421 " --> pdb=" O ASP C 417 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 424 " --> pdb=" O ASP C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 438 No H-bonds generated for 'chain 'C' and resid 436 through 438' Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.775A pdb=" N LEU C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 458 No H-bonds generated for 'chain 'C' and resid 457 through 458' Processing helix chain 'C' and resid 459 through 463 removed outlier: 3.942A pdb=" N LEU C 462 " --> pdb=" O TRP C 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 251 through 255 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 58 removed outlier: 3.520A pdb=" N PHE B 60 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.053A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG B 204 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 137 through 138 removed outlier: 3.610A pdb=" N GLN A 272 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE A 269 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 280 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 277 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 234 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A 225 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AA7, first strand: chain 'A' and resid 592 through 593 removed outlier: 3.575A pdb=" N ILE A 616 " --> pdb=" O TYR A 603 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 668 through 670 removed outlier: 3.519A pdb=" N ALA A 654 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.584A pdb=" N VAL B 99 " --> pdb=" O ARG C 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 155 Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 87 removed outlier: 3.510A pdb=" N MET C 86 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE C 126 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N TYR C 124 " --> pdb=" O PRO C 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AB4, first strand: chain 'C' and resid 186 through 191 removed outlier: 3.713A pdb=" N VAL C 191 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.763A pdb=" N PHE D 45 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D 83 " --> pdb=" O CYS D 49 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY D 51 " --> pdb=" O PHE D 81 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL D 82 " --> pdb=" O GLU D 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 84 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG D 72 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 36 through 38 removed outlier: 6.766A pdb=" N LYS D 37 " --> pdb=" O TYR D 120 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY D 96 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 140 removed outlier: 6.079A pdb=" N VAL D 138 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 205 " --> pdb=" O GLY D 185 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY D 185 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB9, first strand: chain 'D' and resid 171 through 173 Processing sheet with id=AC1, first strand: chain 'D' and resid 216 through 219 Processing sheet with id=AC2, first strand: chain 'D' and resid 224 through 226 removed outlier: 7.008A pdb=" N TYR D 225 " --> pdb=" O HIS D 310 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 303 " --> pdb=" O CYS D 290 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1074 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: 3.76 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3895 1.35 - 1.47: 3010 1.47 - 1.60: 5295 1.60 - 1.72: 0 1.72 - 1.84: 93 Bond restraints: 12293 Sorted by residual: bond pdb=" C PRO C 140 " pdb=" N PRO C 141 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.12e-02 7.97e+03 7.24e+00 bond pdb=" C VAL D 168 " pdb=" N PRO D 169 " ideal model delta sigma weight residual 1.334 1.384 -0.051 2.34e-02 1.83e+03 4.67e+00 bond pdb=" CA ILE A 364 " pdb=" CB ILE A 364 " ideal model delta sigma weight residual 1.534 1.544 -0.009 6.80e-03 2.16e+04 1.80e+00 bond pdb=" CA ILE A 364 " pdb=" C ILE A 364 " ideal model delta sigma weight residual 1.520 1.531 -0.012 8.80e-03 1.29e+04 1.78e+00 bond pdb=" C VAL D 266 " pdb=" N PRO D 267 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.59e+00 ... (remaining 12288 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.17: 441 107.17 - 113.91: 6910 113.91 - 120.66: 4849 120.66 - 127.41: 4410 127.41 - 134.15: 135 Bond angle restraints: 16745 Sorted by residual: angle pdb=" N LEU A 441 " pdb=" CA LEU A 441 " pdb=" C LEU A 441 " ideal model delta sigma weight residual 114.04 108.41 5.63 1.24e+00 6.50e-01 2.06e+01 angle pdb=" N GLN A 332 " pdb=" CA GLN A 332 " pdb=" C GLN A 332 " ideal model delta sigma weight residual 113.72 108.15 5.57 1.52e+00 4.33e-01 1.34e+01 angle pdb=" N THR B 92 " pdb=" CA THR B 92 " pdb=" C THR B 92 " ideal model delta sigma weight residual 109.81 117.55 -7.74 2.21e+00 2.05e-01 1.23e+01 angle pdb=" N GLY D 96 " pdb=" CA GLY D 96 " pdb=" C GLY D 96 " ideal model delta sigma weight residual 110.58 114.92 -4.34 1.35e+00 5.49e-01 1.03e+01 angle pdb=" CA GLN B 237 " pdb=" CB GLN B 237 " pdb=" CG GLN B 237 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.60e+00 ... (remaining 16740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6681 17.86 - 35.71: 603 35.71 - 53.57: 109 53.57 - 71.43: 27 71.43 - 89.29: 17 Dihedral angle restraints: 7437 sinusoidal: 2992 harmonic: 4445 Sorted by residual: dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS B 54 " pdb=" CB CYS B 54 " ideal model delta sinusoidal sigma weight residual -86.00 -150.25 64.25 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CA CYS A 331 " pdb=" C CYS A 331 " pdb=" N GLN A 332 " pdb=" CA GLN A 332 " ideal model delta harmonic sigma weight residual -180.00 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " pdb=" SG CYS A 384 " pdb=" CB CYS A 384 " ideal model delta sinusoidal sigma weight residual -86.00 -128.20 42.20 1 1.00e+01 1.00e-02 2.49e+01 ... (remaining 7434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1416 0.039 - 0.078: 347 0.078 - 0.118: 147 0.118 - 0.157: 7 0.157 - 0.196: 4 Chirality restraints: 1921 Sorted by residual: chirality pdb=" CA THR B 92 " pdb=" N THR B 92 " pdb=" C THR B 92 " pdb=" CB THR B 92 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CB ILE A 364 " pdb=" CA ILE A 364 " pdb=" CG1 ILE A 364 " pdb=" CG2 ILE A 364 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA VAL C 146 " pdb=" N VAL C 146 " pdb=" C VAL C 146 " pdb=" CB VAL C 146 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 1918 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 120 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO C 121 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 168 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO D 169 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 169 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 169 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 436 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO A 437 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 437 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 437 " 0.021 5.00e-02 4.00e+02 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 271 2.70 - 3.25: 11859 3.25 - 3.80: 17715 3.80 - 4.35: 23153 4.35 - 4.90: 38970 Nonbonded interactions: 91968 Sorted by model distance: nonbonded pdb=" O PRO C 183 " pdb=" OG SER C 200 " model vdw 2.154 2.440 nonbonded pdb=" O VAL C 146 " pdb=" ND2 ASN C 233 " model vdw 2.253 2.520 nonbonded pdb=" O VAL A 688 " pdb=" OH TYR A 695 " model vdw 2.256 2.440 nonbonded pdb=" OG SER A 653 " pdb=" O LEU A 698 " model vdw 2.257 2.440 nonbonded pdb=" O THR A 245 " pdb=" NE2 GLN A 286 " model vdw 2.259 2.520 ... (remaining 91963 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 individual isotropic 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: 4.140 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: 0.000 Extract box with map and model: 12.100 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.070 Find NCS groups from input model: 0.310 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 : 0.002 0.051 12293 Z= 0.150 Angle : 0.569 7.744 16745 Z= 0.310 Chirality : 0.041 0.196 1921 Planarity : 0.004 0.051 2142 Dihedral : 14.509 89.286 4513 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -0.56 (0.23), residues: 1485 helix: 0.18 (0.27), residues: 370 sheet: -0.12 (0.33), residues: 297 loop : -0.66 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 459 HIS 0.005 0.001 HIS B 236 PHE 0.020 0.001 PHE C 172 TYR 0.009 0.001 TYR C 339 ARG 0.004 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 387 GLN cc_start: 0.7351 (tp40) cc_final: 0.7059 (tm-30) REVERT: A 402 ASP cc_start: 0.7604 (m-30) cc_final: 0.7141 (t0) REVERT: A 478 MET cc_start: 0.6152 (tpp) cc_final: 0.5914 (tpt) REVERT: A 676 VAL cc_start: 0.8005 (t) cc_final: 0.7690 (t) REVERT: C 445 GLU cc_start: 0.7666 (pp20) cc_final: 0.7396 (pp20) REVERT: D 40 GLN cc_start: 0.8438 (mm110) cc_final: 0.8196 (mm110) REVERT: D 197 LYS cc_start: 0.7781 (mtpp) cc_final: 0.7419 (mttt) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2131 time to fit residues: 47.1236 Evaluate side-chains 104 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.7980 chunk 111 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN B 236 HIS ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12293 Z= 0.203 Angle : 0.585 9.760 16745 Z= 0.300 Chirality : 0.043 0.194 1921 Planarity : 0.004 0.053 2142 Dihedral : 4.471 27.105 1649 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.81 % Allowed : 6.95 % Favored : 92.24 % 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: -0.41 (0.23), residues: 1485 helix: 0.63 (0.28), residues: 383 sheet: -0.08 (0.32), residues: 291 loop : -0.74 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 459 HIS 0.007 0.001 HIS C 446 PHE 0.014 0.001 PHE A 235 TYR 0.010 0.001 TYR C 114 ARG 0.003 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.481 Fit side-chains REVERT: A 387 GLN cc_start: 0.6980 (tp40) cc_final: 0.6671 (tm-30) REVERT: A 402 ASP cc_start: 0.7478 (m-30) cc_final: 0.7196 (t0) outliers start: 11 outliers final: 10 residues processed: 122 average time/residue: 0.2311 time to fit residues: 42.3752 Evaluate side-chains 113 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 244 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12293 Z= 0.202 Angle : 0.555 10.560 16745 Z= 0.282 Chirality : 0.042 0.189 1921 Planarity : 0.004 0.054 2142 Dihedral : 4.448 25.262 1649 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.26 % Allowed : 10.13 % Favored : 88.62 % 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: -0.29 (0.23), residues: 1485 helix: 0.87 (0.28), residues: 381 sheet: 0.09 (0.32), residues: 279 loop : -0.78 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 459 HIS 0.007 0.001 HIS C 446 PHE 0.013 0.001 PHE A 235 TYR 0.009 0.001 TYR A 292 ARG 0.005 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.330 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 126 average time/residue: 0.2218 time to fit residues: 42.3319 Evaluate side-chains 117 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 140 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12293 Z= 0.370 Angle : 0.634 12.379 16745 Z= 0.321 Chirality : 0.045 0.183 1921 Planarity : 0.005 0.057 2142 Dihedral : 4.819 33.390 1649 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.85 % Allowed : 12.34 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.55 (0.22), residues: 1485 helix: 0.63 (0.28), residues: 385 sheet: -0.14 (0.32), residues: 281 loop : -0.91 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 459 HIS 0.011 0.001 HIS C 446 PHE 0.018 0.002 PHE A 235 TYR 0.015 0.002 TYR A 292 ARG 0.006 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.385 Fit side-chains REVERT: A 247 MET cc_start: 0.8341 (ppp) cc_final: 0.8006 (tmm) outliers start: 25 outliers final: 18 residues processed: 125 average time/residue: 0.2242 time to fit residues: 42.5482 Evaluate side-chains 117 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 140 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.0000 chunk 105 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12293 Z= 0.160 Angle : 0.553 11.511 16745 Z= 0.280 Chirality : 0.042 0.203 1921 Planarity : 0.004 0.055 2142 Dihedral : 4.563 32.345 1649 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.70 % Allowed : 13.16 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.32 (0.22), residues: 1485 helix: 0.99 (0.28), residues: 382 sheet: -0.08 (0.32), residues: 285 loop : -0.82 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 439 HIS 0.005 0.001 HIS A 512 PHE 0.013 0.001 PHE A 678 TYR 0.008 0.001 TYR A 603 ARG 0.007 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.360 Fit side-chains REVERT: A 381 MET cc_start: 0.7429 (tpt) cc_final: 0.7099 (tpt) REVERT: A 478 MET cc_start: 0.5831 (tpt) cc_final: 0.5209 (tpt) REVERT: A 559 MET cc_start: 0.7480 (mmt) cc_final: 0.7123 (mmp) REVERT: A 575 LEU cc_start: 0.8271 (mm) cc_final: 0.8070 (mm) REVERT: C 88 MET cc_start: 0.8126 (mtp) cc_final: 0.7892 (mtp) outliers start: 23 outliers final: 13 residues processed: 135 average time/residue: 0.2213 time to fit residues: 45.4895 Evaluate side-chains 121 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 140 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12293 Z= 0.377 Angle : 0.645 14.852 16745 Z= 0.323 Chirality : 0.046 0.177 1921 Planarity : 0.005 0.058 2142 Dihedral : 4.902 34.495 1649 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.92 % Allowed : 14.12 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.56 (0.22), residues: 1485 helix: 0.70 (0.28), residues: 382 sheet: -0.20 (0.32), residues: 281 loop : -0.94 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 459 HIS 0.011 0.001 HIS C 446 PHE 0.022 0.002 PHE D 178 TYR 0.016 0.002 TYR C 114 ARG 0.009 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: C 88 MET cc_start: 0.8261 (mtp) cc_final: 0.8007 (mtp) REVERT: C 112 ASP cc_start: 0.7991 (t0) cc_final: 0.7285 (t0) REVERT: C 115 SER cc_start: 0.7326 (OUTLIER) cc_final: 0.6743 (p) outliers start: 26 outliers final: 21 residues processed: 128 average time/residue: 0.2225 time to fit residues: 43.2604 Evaluate side-chains 126 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 140 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12293 Z= 0.190 Angle : 0.575 15.511 16745 Z= 0.286 Chirality : 0.042 0.199 1921 Planarity : 0.004 0.055 2142 Dihedral : 4.697 32.067 1649 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.85 % Allowed : 15.15 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.41 (0.23), residues: 1485 helix: 0.94 (0.28), residues: 380 sheet: -0.21 (0.31), residues: 299 loop : -0.87 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 439 HIS 0.006 0.001 HIS C 446 PHE 0.012 0.001 PHE A 235 TYR 0.008 0.001 TYR C 383 ARG 0.008 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.332 Fit side-chains REVERT: A 559 MET cc_start: 0.7589 (mmt) cc_final: 0.7312 (mmm) REVERT: A 575 LEU cc_start: 0.8271 (mm) cc_final: 0.8039 (mm) REVERT: C 88 MET cc_start: 0.8189 (mtp) cc_final: 0.7911 (mtp) outliers start: 25 outliers final: 18 residues processed: 132 average time/residue: 0.2191 time to fit residues: 44.5647 Evaluate side-chains 126 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain D residue 140 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 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 378 GLN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12293 Z= 0.230 Angle : 0.587 15.676 16745 Z= 0.291 Chirality : 0.043 0.192 1921 Planarity : 0.004 0.058 2142 Dihedral : 4.687 32.575 1649 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.70 % Allowed : 16.11 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.44 (0.22), residues: 1485 helix: 0.92 (0.28), residues: 383 sheet: -0.26 (0.31), residues: 295 loop : -0.89 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 439 HIS 0.008 0.001 HIS C 446 PHE 0.013 0.001 PHE A 235 TYR 0.010 0.001 TYR C 114 ARG 0.008 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.445 Fit side-chains REVERT: A 559 MET cc_start: 0.7729 (mmt) cc_final: 0.7450 (mmm) REVERT: C 88 MET cc_start: 0.8216 (mtp) cc_final: 0.7933 (mtp) outliers start: 23 outliers final: 21 residues processed: 126 average time/residue: 0.2173 time to fit residues: 41.7840 Evaluate side-chains 128 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.4980 chunk 132 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 0.0770 chunk 124 optimal weight: 0.0670 chunk 131 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12293 Z= 0.177 Angle : 0.568 15.713 16745 Z= 0.281 Chirality : 0.042 0.200 1921 Planarity : 0.004 0.056 2142 Dihedral : 4.552 31.639 1649 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.70 % Allowed : 15.96 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.31 (0.23), residues: 1485 helix: 1.05 (0.28), residues: 383 sheet: -0.14 (0.31), residues: 301 loop : -0.84 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 439 HIS 0.005 0.001 HIS C 446 PHE 0.011 0.001 PHE A 235 TYR 0.008 0.001 TYR A 658 ARG 0.008 0.000 ARG D 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.329 Fit side-chains REVERT: A 559 MET cc_start: 0.7719 (mmt) cc_final: 0.7441 (mmm) REVERT: A 697 MET cc_start: 0.6648 (tpt) cc_final: 0.6230 (tpt) REVERT: C 88 MET cc_start: 0.8188 (mtp) cc_final: 0.7901 (mtp) outliers start: 23 outliers final: 20 residues processed: 131 average time/residue: 0.2183 time to fit residues: 43.8261 Evaluate side-chains 128 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12293 Z= 0.333 Angle : 0.644 14.083 16745 Z= 0.317 Chirality : 0.045 0.193 1921 Planarity : 0.004 0.057 2142 Dihedral : 4.831 33.540 1649 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.63 % Allowed : 16.41 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.53 (0.22), residues: 1485 helix: 0.75 (0.28), residues: 383 sheet: -0.24 (0.32), residues: 290 loop : -0.91 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 439 HIS 0.010 0.001 HIS C 446 PHE 0.017 0.002 PHE A 235 TYR 0.018 0.001 TYR C 114 ARG 0.009 0.000 ARG D 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 478 MET cc_start: 0.6121 (tpt) cc_final: 0.5312 (tpt) REVERT: A 559 MET cc_start: 0.7807 (mmt) cc_final: 0.7545 (mmm) REVERT: C 88 MET cc_start: 0.8245 (mtp) cc_final: 0.7935 (mtp) REVERT: C 112 ASP cc_start: 0.7852 (t0) cc_final: 0.7527 (t0) outliers start: 22 outliers final: 20 residues processed: 124 average time/residue: 0.2252 time to fit residues: 42.9862 Evaluate side-chains 124 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 107 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 119 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 102 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.148402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.111108 restraints weight = 17354.278| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.89 r_work: 0.3342 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12293 Z= 0.185 Angle : 0.583 14.856 16745 Z= 0.286 Chirality : 0.042 0.200 1921 Planarity : 0.004 0.055 2142 Dihedral : 4.630 31.530 1649 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.63 % Allowed : 16.26 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.37 (0.23), residues: 1485 helix: 0.97 (0.28), residues: 383 sheet: -0.15 (0.31), residues: 303 loop : -0.86 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 439 HIS 0.006 0.001 HIS D 116 PHE 0.017 0.001 PHE A 678 TYR 0.009 0.001 TYR C 114 ARG 0.008 0.000 ARG D 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2490.73 seconds wall clock time: 46 minutes 32.66 seconds (2792.66 seconds total)