Starting phenix.real_space_refine on Wed Mar 4 08:05:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ram_24369/03_2026/7ram_24369.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ram_24369/03_2026/7ram_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ram_24369/03_2026/7ram_24369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ram_24369/03_2026/7ram_24369.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ram_24369/03_2026/7ram_24369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ram_24369/03_2026/7ram_24369.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.20, per 1000 atoms: 0.18 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 - 3.00 Amino acid : True - 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: 0.78 Conformation dependent library (CDL) restraints added in 523.2 milliseconds 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: 0.46 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: 2.03 Time building geometry restraints manager: 1.02 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: 0.00 - 1.55: 16336 1.55 - 3.10: 346 3.10 - 4.65: 40 4.65 - 6.19: 15 6.19 - 7.74: 8 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 3.040 nonbonded pdb=" O VAL C 146 " pdb=" ND2 ASN C 233 " model vdw 2.253 3.120 nonbonded pdb=" O VAL A 688 " pdb=" OH TYR A 695 " model vdw 2.256 3.040 nonbonded pdb=" OG SER A 653 " pdb=" O LEU A 698 " model vdw 2.257 3.040 nonbonded pdb=" O THR A 245 " pdb=" NE2 GLN A 286 " model vdw 2.259 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 3.250 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.650 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- 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 12307 Z= 0.116 Angle : 0.572 7.744 16773 Z= 0.311 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG D 48 TYR 0.009 0.001 TYR C 339 PHE 0.020 0.001 PHE C 172 TRP 0.023 0.001 TRP C 459 HIS 0.005 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00232 (12293) covalent geometry : angle 0.56875 (16745) SS BOND : bond 0.00207 ( 14) SS BOND : angle 1.58663 ( 28) hydrogen bonds : bond 0.26319 ( 409) hydrogen bonds : angle 8.47069 ( 1074) *********************** 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 to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.476 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: 0.0939 time to fit residues: 21.0116 Evaluate side-chains 104 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0170 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 84 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 236 HIS ** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.147264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108788 restraints weight = 17694.189| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.04 r_work: 0.3326 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12307 Z= 0.200 Angle : 0.645 9.651 16773 Z= 0.332 Chirality : 0.045 0.194 1921 Planarity : 0.005 0.056 2142 Dihedral : 4.738 28.388 1649 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.11 % Allowed : 7.76 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.22), residues: 1485 helix: 0.44 (0.27), residues: 382 sheet: -0.02 (0.33), residues: 282 loop : -0.80 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 48 TYR 0.016 0.001 TYR C 114 PHE 0.017 0.002 PHE A 235 TRP 0.030 0.002 TRP C 459 HIS 0.012 0.001 HIS C 446 Details of bonding type rmsd covalent geometry : bond 0.00475 (12293) covalent geometry : angle 0.64160 (16745) SS BOND : bond 0.00365 ( 14) SS BOND : angle 1.74463 ( 28) hydrogen bonds : bond 0.04358 ( 409) hydrogen bonds : angle 5.71026 ( 1074) *********************** 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 137 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.403 Fit side-chains REVERT: A 387 GLN cc_start: 0.7473 (tp40) cc_final: 0.6916 (tm-30) REVERT: A 402 ASP cc_start: 0.7724 (m-30) cc_final: 0.7338 (t0) REVERT: B 127 SER cc_start: 0.9210 (t) cc_final: 0.8895 (t) REVERT: C 445 GLU cc_start: 0.8007 (pp20) cc_final: 0.7595 (pp20) REVERT: D 40 GLN cc_start: 0.8644 (mm110) cc_final: 0.8402 (mm110) outliers start: 15 outliers final: 10 residues processed: 131 average time/residue: 0.0918 time to fit residues: 18.4000 Evaluate side-chains 112 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 531 HIS 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 244 THR Chi-restraints excluded: chain D residue 140 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 90 optimal weight: 0.0020 chunk 109 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 146 optimal weight: 0.0040 chunk 89 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 117 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.150149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.111965 restraints weight = 17544.218| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.05 r_work: 0.3363 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12307 Z= 0.118 Angle : 0.569 10.390 16773 Z= 0.291 Chirality : 0.042 0.189 1921 Planarity : 0.004 0.054 2142 Dihedral : 4.560 25.783 1649 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.03 % Allowed : 10.05 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.22), residues: 1485 helix: 0.80 (0.28), residues: 384 sheet: 0.07 (0.33), residues: 274 loop : -0.79 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 48 TYR 0.009 0.001 TYR D 273 PHE 0.015 0.001 PHE A 678 TRP 0.026 0.001 TRP C 459 HIS 0.008 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00274 (12293) covalent geometry : angle 0.56707 (16745) SS BOND : bond 0.00273 ( 14) SS BOND : angle 1.37205 ( 28) hydrogen bonds : bond 0.03764 ( 409) hydrogen bonds : angle 5.36235 ( 1074) *********************** 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 135 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.450 Fit side-chains REVERT: A 402 ASP cc_start: 0.7640 (m-30) cc_final: 0.7253 (t0) REVERT: D 40 GLN cc_start: 0.8591 (mm110) cc_final: 0.8348 (mm110) outliers start: 14 outliers final: 8 residues processed: 131 average time/residue: 0.0961 time to fit residues: 18.9165 Evaluate side-chains 114 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 61 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN C 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.145516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107223 restraints weight = 17833.866| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.25 r_work: 0.3273 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12307 Z= 0.219 Angle : 0.639 12.133 16773 Z= 0.323 Chirality : 0.045 0.183 1921 Planarity : 0.004 0.058 2142 Dihedral : 4.840 33.456 1649 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.55 % Allowed : 11.75 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1485 helix: 0.69 (0.28), residues: 387 sheet: -0.13 (0.32), residues: 285 loop : -0.87 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 48 TYR 0.016 0.001 TYR C 114 PHE 0.017 0.002 PHE A 235 TRP 0.033 0.002 TRP C 459 HIS 0.010 0.001 HIS C 446 Details of bonding type rmsd covalent geometry : bond 0.00535 (12293) covalent geometry : angle 0.63581 (16745) SS BOND : bond 0.00394 ( 14) SS BOND : angle 1.71938 ( 28) hydrogen bonds : bond 0.03865 ( 409) hydrogen bonds : angle 5.26691 ( 1074) *********************** 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 129 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.410 Fit side-chains REVERT: A 402 ASP cc_start: 0.7741 (m-30) cc_final: 0.7342 (t0) REVERT: D 40 GLN cc_start: 0.8644 (mm110) cc_final: 0.8375 (mm110) outliers start: 21 outliers final: 14 residues processed: 124 average time/residue: 0.0962 time to fit residues: 18.2522 Evaluate side-chains 115 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL 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 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 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 92 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.0470 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.147929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109021 restraints weight = 17659.375| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.14 r_work: 0.3313 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12307 Z= 0.136 Angle : 0.580 11.470 16773 Z= 0.294 Chirality : 0.043 0.183 1921 Planarity : 0.004 0.056 2142 Dihedral : 4.724 32.957 1649 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.40 % Allowed : 13.30 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1485 helix: 0.93 (0.28), residues: 383 sheet: -0.12 (0.31), residues: 285 loop : -0.77 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 48 TYR 0.019 0.001 TYR D 273 PHE 0.014 0.001 PHE A 235 TRP 0.022 0.001 TRP A 439 HIS 0.006 0.001 HIS C 446 Details of bonding type rmsd covalent geometry : bond 0.00327 (12293) covalent geometry : angle 0.57760 (16745) SS BOND : bond 0.00279 ( 14) SS BOND : angle 1.52843 ( 28) hydrogen bonds : bond 0.03360 ( 409) hydrogen bonds : angle 5.08458 ( 1074) *********************** 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 132 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.425 Fit side-chains REVERT: A 378 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: A 402 ASP cc_start: 0.7665 (m-30) cc_final: 0.7263 (t0) REVERT: A 559 MET cc_start: 0.7565 (mmt) cc_final: 0.7257 (mmp) REVERT: D 40 GLN cc_start: 0.8604 (mm110) cc_final: 0.8336 (mm110) outliers start: 19 outliers final: 11 residues processed: 129 average time/residue: 0.0946 time to fit residues: 18.5976 Evaluate side-chains 116 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 GLN 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 A residue 588 VAL 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 D residue 140 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 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 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.148068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.109660 restraints weight = 17684.718| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.06 r_work: 0.3324 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12307 Z= 0.134 Angle : 0.581 14.510 16773 Z= 0.292 Chirality : 0.042 0.189 1921 Planarity : 0.004 0.057 2142 Dihedral : 4.667 32.666 1649 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.92 % Allowed : 13.82 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.22), residues: 1485 helix: 0.99 (0.28), residues: 383 sheet: -0.12 (0.31), residues: 285 loop : -0.75 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 48 TYR 0.015 0.001 TYR D 273 PHE 0.019 0.001 PHE D 178 TRP 0.024 0.001 TRP A 439 HIS 0.006 0.001 HIS C 446 Details of bonding type rmsd covalent geometry : bond 0.00324 (12293) covalent geometry : angle 0.57838 (16745) SS BOND : bond 0.00368 ( 14) SS BOND : angle 1.55281 ( 28) hydrogen bonds : bond 0.03227 ( 409) hydrogen bonds : angle 4.97651 ( 1074) *********************** 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 136 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.440 Fit side-chains REVERT: C 88 MET cc_start: 0.8081 (mtp) cc_final: 0.7782 (mtp) REVERT: D 40 GLN cc_start: 0.8624 (mm110) cc_final: 0.8346 (mm110) REVERT: D 116 HIS cc_start: 0.7980 (p90) cc_final: 0.7744 (p90) outliers start: 26 outliers final: 16 residues processed: 131 average time/residue: 0.0988 time to fit residues: 19.5367 Evaluate side-chains 123 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU 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 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 209 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 321 ILE 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 67 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 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 152 GLN A 378 GLN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.147411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108726 restraints weight = 17473.778| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.11 r_work: 0.3301 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12307 Z= 0.150 Angle : 0.601 15.481 16773 Z= 0.300 Chirality : 0.043 0.185 1921 Planarity : 0.004 0.057 2142 Dihedral : 4.679 31.285 1649 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.77 % Allowed : 14.56 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.22), residues: 1485 helix: 0.98 (0.28), residues: 383 sheet: -0.15 (0.31), residues: 291 loop : -0.78 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 48 TYR 0.015 0.001 TYR D 273 PHE 0.014 0.001 PHE A 235 TRP 0.020 0.001 TRP A 439 HIS 0.007 0.001 HIS C 446 Details of bonding type rmsd covalent geometry : bond 0.00366 (12293) covalent geometry : angle 0.59629 (16745) SS BOND : bond 0.00261 ( 14) SS BOND : angle 1.84708 ( 28) hydrogen bonds : bond 0.03266 ( 409) hydrogen bonds : angle 4.97045 ( 1074) *********************** 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 136 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.480 Fit side-chains REVERT: A 402 ASP cc_start: 0.7728 (m-30) cc_final: 0.7301 (t0) REVERT: A 478 MET cc_start: 0.5985 (tpt) cc_final: 0.5349 (tpt) REVERT: A 575 LEU cc_start: 0.8227 (mm) cc_final: 0.7997 (mm) REVERT: C 88 MET cc_start: 0.8030 (mtp) cc_final: 0.7693 (mtp) REVERT: C 115 SER cc_start: 0.7403 (OUTLIER) cc_final: 0.7188 (p) REVERT: D 40 GLN cc_start: 0.8607 (mm110) cc_final: 0.8312 (mm110) REVERT: D 116 HIS cc_start: 0.7951 (p90) cc_final: 0.7624 (p90) outliers start: 24 outliers final: 17 residues processed: 131 average time/residue: 0.0918 time to fit residues: 18.5244 Evaluate side-chains 124 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU 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 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 115 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 428 ILE 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 137 optimal weight: 0.0060 chunk 108 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 135 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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** A 587 HIS C 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.149400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.110909 restraints weight = 17422.429| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.12 r_work: 0.3350 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12307 Z= 0.115 Angle : 0.578 15.163 16773 Z= 0.290 Chirality : 0.042 0.197 1921 Planarity : 0.004 0.057 2142 Dihedral : 4.563 31.199 1649 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.48 % Allowed : 15.59 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.23), residues: 1485 helix: 1.11 (0.28), residues: 383 sheet: -0.10 (0.32), residues: 290 loop : -0.70 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 48 TYR 0.014 0.001 TYR D 273 PHE 0.012 0.001 PHE A 235 TRP 0.025 0.001 TRP A 439 HIS 0.005 0.001 HIS C 446 Details of bonding type rmsd covalent geometry : bond 0.00274 (12293) covalent geometry : angle 0.57472 (16745) SS BOND : bond 0.00240 ( 14) SS BOND : angle 1.71296 ( 28) hydrogen bonds : bond 0.03029 ( 409) hydrogen bonds : angle 4.85765 ( 1074) *********************** 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 135 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.469 Fit side-chains REVERT: A 402 ASP cc_start: 0.7628 (m-30) cc_final: 0.7228 (t0) REVERT: A 478 MET cc_start: 0.5863 (tpt) cc_final: 0.5308 (tpt) REVERT: A 559 MET cc_start: 0.7583 (mmt) cc_final: 0.7292 (mmm) REVERT: A 670 MET cc_start: 0.6082 (mtm) cc_final: 0.5833 (mtm) REVERT: B 208 LEU cc_start: 0.8470 (mt) cc_final: 0.8213 (mt) REVERT: C 88 MET cc_start: 0.8041 (mtp) cc_final: 0.7732 (mtp) REVERT: C 115 SER cc_start: 0.7350 (OUTLIER) cc_final: 0.7139 (p) REVERT: D 40 GLN cc_start: 0.8552 (mm110) cc_final: 0.8259 (mm110) REVERT: D 116 HIS cc_start: 0.7864 (p90) cc_final: 0.7471 (p90) outliers start: 20 outliers final: 16 residues processed: 130 average time/residue: 0.0917 time to fit residues: 18.3626 Evaluate side-chains 123 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU 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 A residue 587 HIS 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 143 GLU 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 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 64 optimal weight: 0.0050 chunk 88 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 31 optimal weight: 0.0050 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 9 optimal weight: 0.0980 chunk 132 optimal weight: 0.7980 overall best weight: 0.0726 ------------------------------------------------------------------------------- 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** A 652 GLN C 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.151968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.113758 restraints weight = 17207.636| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.11 r_work: 0.3396 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12307 Z= 0.100 Angle : 0.570 13.989 16773 Z= 0.285 Chirality : 0.042 0.211 1921 Planarity : 0.004 0.056 2142 Dihedral : 4.419 30.318 1649 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.11 % Allowed : 16.26 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.23), residues: 1485 helix: 1.25 (0.28), residues: 382 sheet: -0.01 (0.32), residues: 289 loop : -0.66 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 48 TYR 0.013 0.001 TYR D 273 PHE 0.020 0.001 PHE A 678 TRP 0.023 0.001 TRP A 439 HIS 0.009 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00224 (12293) covalent geometry : angle 0.56633 (16745) SS BOND : bond 0.00236 ( 14) SS BOND : angle 1.62579 ( 28) hydrogen bonds : bond 0.02843 ( 409) hydrogen bonds : angle 4.80719 ( 1074) *********************** 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 126 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.410 Fit side-chains REVERT: A 402 ASP cc_start: 0.7610 (m-30) cc_final: 0.7198 (t0) REVERT: A 478 MET cc_start: 0.5763 (tpt) cc_final: 0.5301 (tpt) REVERT: A 559 MET cc_start: 0.7612 (mmt) cc_final: 0.7318 (mmm) REVERT: A 670 MET cc_start: 0.6048 (mtm) cc_final: 0.5829 (mtm) REVERT: B 208 LEU cc_start: 0.8428 (mt) cc_final: 0.8151 (mt) REVERT: D 40 GLN cc_start: 0.8537 (mm110) cc_final: 0.8286 (mm110) REVERT: D 116 HIS cc_start: 0.7699 (p90) cc_final: 0.7258 (p90) outliers start: 15 outliers final: 13 residues processed: 122 average time/residue: 0.0926 time to fit residues: 17.1028 Evaluate side-chains 121 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 588 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain B residue 143 GLU 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 378 ASP 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: 2.9990 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.146124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.108661 restraints weight = 18123.617| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.96 r_work: 0.3353 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12307 Z= 0.151 Angle : 0.597 13.330 16773 Z= 0.296 Chirality : 0.043 0.186 1921 Planarity : 0.004 0.057 2142 Dihedral : 4.526 31.646 1649 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.18 % Allowed : 16.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.22), residues: 1485 helix: 1.13 (0.28), residues: 381 sheet: -0.10 (0.31), residues: 295 loop : -0.73 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 48 TYR 0.014 0.001 TYR D 273 PHE 0.019 0.001 PHE A 678 TRP 0.021 0.001 TRP A 439 HIS 0.008 0.001 HIS C 446 Details of bonding type rmsd covalent geometry : bond 0.00368 (12293) covalent geometry : angle 0.59332 (16745) SS BOND : bond 0.00262 ( 14) SS BOND : angle 1.67426 ( 28) hydrogen bonds : bond 0.03101 ( 409) hydrogen bonds : angle 4.83874 ( 1074) ********************** 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 to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.371 Fit side-chains REVERT: A 559 MET cc_start: 0.7783 (mmt) cc_final: 0.7501 (mmm) REVERT: C 88 MET cc_start: 0.8182 (mtp) cc_final: 0.7852 (mtp) REVERT: D 40 GLN cc_start: 0.8646 (mm110) cc_final: 0.8355 (mm110) REVERT: D 116 HIS cc_start: 0.7740 (p90) cc_final: 0.7305 (p90) outliers start: 16 outliers final: 13 residues processed: 124 average time/residue: 0.0923 time to fit residues: 17.6053 Evaluate side-chains 122 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 588 VAL 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 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 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 122 optimal weight: 0.0040 chunk 123 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 132 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 C 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.150262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112524 restraints weight = 17240.342| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.99 r_work: 0.3374 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12307 Z= 0.118 Angle : 0.582 13.129 16773 Z= 0.290 Chirality : 0.043 0.268 1921 Planarity : 0.004 0.056 2142 Dihedral : 4.484 31.153 1649 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.18 % Allowed : 16.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.22), residues: 1485 helix: 1.19 (0.28), residues: 382 sheet: -0.01 (0.32), residues: 289 loop : -0.70 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 48 TYR 0.012 0.001 TYR D 273 PHE 0.012 0.001 PHE A 235 TRP 0.021 0.001 TRP A 439 HIS 0.005 0.001 HIS C 446 Details of bonding type rmsd covalent geometry : bond 0.00284 (12293) covalent geometry : angle 0.57861 (16745) SS BOND : bond 0.00241 ( 14) SS BOND : angle 1.60883 ( 28) hydrogen bonds : bond 0.02936 ( 409) hydrogen bonds : angle 4.82805 ( 1074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2596.29 seconds wall clock time: 45 minutes 20.73 seconds (2720.73 seconds total)