Starting phenix.real_space_refine on Thu Mar 13 19:59:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yv8_34120/03_2025/7yv8_34120.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yv8_34120/03_2025/7yv8_34120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yv8_34120/03_2025/7yv8_34120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yv8_34120/03_2025/7yv8_34120.map" model { file = "/net/cci-nas-00/data/ceres_data/7yv8_34120/03_2025/7yv8_34120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yv8_34120/03_2025/7yv8_34120.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3164 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4163 2.51 5 N 1077 2.21 5 O 1236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6513 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4854 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1574 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 12, 'TRANS': 184} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.29, per 1000 atoms: 0.97 Number of scatterers: 6513 At special positions: 0 Unit cell: (73.92, 102.08, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1236 8.00 N 1077 7.00 C 4163 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 Links applied NAG-ASN " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 53 " " NAG A 704 " - " ASN A 82 " " NAG A 705 " - " ASN A 432 " " NAG A 706 " - " ASN A 546 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 913.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 55.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.752A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.685A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.520A pdb=" N ALA A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.871A pdb=" N ASP A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.536A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.628A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.990A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.635A pdb=" N MET A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.719A pdb=" N TYR A 255 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.534A pdb=" N GLU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.829A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.738A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.737A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.954A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.546A pdb=" N ASN A 508 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 513 through 532 removed outlier: 4.119A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.657A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.808A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.714A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.550A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.872A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.812A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.964A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.255A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.635A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 281 hydrogen bonds defined for protein. 783 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: 1.70 Time building geometry restraints manager: 1.87 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: 2102 1.35 - 1.49: 1857 1.49 - 1.62: 2677 1.62 - 1.75: 0 1.75 - 1.88: 56 Bond restraints: 6692 Sorted by residual: bond pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 1.808 1.883 -0.075 3.30e-02 9.18e+02 5.10e+00 bond pdb=" N THR B 500 " pdb=" CA THR B 500 " ideal model delta sigma weight residual 1.456 1.477 -0.021 1.26e-02 6.30e+03 2.89e+00 bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.754 0.054 3.30e-02 9.18e+02 2.71e+00 bond pdb=" C1 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG A 705 " pdb=" O5 NAG A 705 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 6687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 9030 2.97 - 5.95: 59 5.95 - 8.92: 3 8.92 - 11.89: 0 11.89 - 14.86: 1 Bond angle restraints: 9093 Sorted by residual: angle pdb=" CA CYS B 379 " pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 114.40 129.26 -14.86 2.30e+00 1.89e-01 4.18e+01 angle pdb=" C LYS B 378 " pdb=" N CYS B 379 " pdb=" CA CYS B 379 " ideal model delta sigma weight residual 121.62 114.59 7.03 1.83e+00 2.99e-01 1.48e+01 angle pdb=" N CYS B 379 " pdb=" CA CYS B 379 " pdb=" C CYS B 379 " ideal model delta sigma weight residual 108.79 114.23 -5.44 1.53e+00 4.27e-01 1.27e+01 angle pdb=" N THR B 500 " pdb=" CA THR B 500 " pdb=" CB THR B 500 " ideal model delta sigma weight residual 110.56 106.86 3.70 1.46e+00 4.69e-01 6.42e+00 angle pdb=" N ASN B 388 " pdb=" CA ASN B 388 " pdb=" C ASN B 388 " ideal model delta sigma weight residual 110.80 105.51 5.29 2.13e+00 2.20e-01 6.16e+00 ... (remaining 9088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 3700 21.44 - 42.88: 284 42.88 - 64.32: 33 64.32 - 85.76: 12 85.76 - 107.20: 9 Dihedral angle restraints: 4038 sinusoidal: 1710 harmonic: 2328 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 -179.03 -87.97 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 168.61 -75.61 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 35.02 57.98 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 4035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 641 0.042 - 0.084: 249 0.084 - 0.126: 69 0.126 - 0.168: 4 0.168 - 0.210: 1 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA CYS B 379 " pdb=" N CYS B 379 " pdb=" C CYS B 379 " pdb=" CB CYS B 379 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" C PRO B 491 " pdb=" CB PRO B 491 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 961 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 388 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C ASN B 388 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN B 388 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 389 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 65 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ALA A 65 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA A 65 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 66 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 481 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ASN B 481 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN B 481 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY B 482 " 0.010 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 30 2.58 - 3.16: 5204 3.16 - 3.74: 9136 3.74 - 4.32: 12960 4.32 - 4.90: 22350 Nonbonded interactions: 49680 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.006 2.230 nonbonded pdb=" O ASN B 481 " pdb=" ND2 ASN B 481 " model vdw 2.234 3.120 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.239 3.040 nonbonded pdb=" OE2 GLU A 57 " pdb=" O6 NAG A 703 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR A 365 " pdb=" OD1 ASP A 367 " model vdw 2.298 3.040 ... (remaining 49675 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: 8.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.130 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:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.005 0.075 6692 Z= 0.326 Angle : 0.652 14.865 9093 Z= 0.340 Chirality : 0.045 0.210 964 Planarity : 0.005 0.041 1174 Dihedral : 15.362 107.195 2525 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.15 % Allowed : 0.29 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.30), residues: 789 helix: 0.07 (0.29), residues: 368 sheet: 2.02 (0.95), residues: 34 loop : -1.48 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.002 PHE B 377 TYR 0.024 0.002 TYR A 199 ARG 0.005 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.764 Fit side-chains REVERT: A 42 GLN cc_start: 0.7959 (mt0) cc_final: 0.7613 (mt0) REVERT: A 190 MET cc_start: 0.7969 (tmm) cc_final: 0.7633 (tmt) REVERT: A 375 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 340 GLU cc_start: 0.6942 (mp0) cc_final: 0.6610 (mp0) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 1.2918 time to fit residues: 204.1678 Evaluate side-chains 134 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094408 restraints weight = 9425.952| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.81 r_work: 0.3096 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6692 Z= 0.277 Angle : 0.621 14.266 9093 Z= 0.311 Chirality : 0.044 0.228 964 Planarity : 0.005 0.044 1174 Dihedral : 6.682 58.726 992 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.16 % Allowed : 8.13 % Favored : 90.71 % 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: -0.35 (0.31), residues: 789 helix: 0.67 (0.29), residues: 371 sheet: 2.14 (0.93), residues: 34 loop : -1.38 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 512 TYR 0.015 0.001 TYR A 385 ARG 0.003 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.713 Fit side-chains REVERT: A 190 MET cc_start: 0.8222 (tmm) cc_final: 0.7980 (tmt) REVERT: A 375 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 408 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7340 (mmm) REVERT: B 340 GLU cc_start: 0.7779 (mp0) cc_final: 0.7361 (mp0) REVERT: B 377 PHE cc_start: 0.8683 (t80) cc_final: 0.8468 (t80) outliers start: 8 outliers final: 4 residues processed: 141 average time/residue: 1.2434 time to fit residues: 183.7652 Evaluate side-chains 138 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 chunk 47 optimal weight: 0.0170 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 38 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.105866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095955 restraints weight = 9546.216| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.84 r_work: 0.3123 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6692 Z= 0.198 Angle : 0.565 12.117 9093 Z= 0.283 Chirality : 0.042 0.210 964 Planarity : 0.004 0.045 1174 Dihedral : 5.495 56.261 992 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.74 % Allowed : 9.29 % Favored : 88.97 % 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: -0.01 (0.31), residues: 789 helix: 1.03 (0.29), residues: 372 sheet: 2.16 (0.93), residues: 34 loop : -1.30 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.007 0.001 PHE A 327 TYR 0.010 0.001 TYR A 385 ARG 0.003 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.723 Fit side-chains REVERT: A 75 GLU cc_start: 0.8105 (tp30) cc_final: 0.7835 (tp30) REVERT: A 190 MET cc_start: 0.8118 (tmm) cc_final: 0.7914 (tmt) REVERT: A 360 MET cc_start: 0.8614 (ttt) cc_final: 0.8353 (ttm) REVERT: A 375 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7863 (mm-30) REVERT: A 401 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8140 (m-70) REVERT: B 340 GLU cc_start: 0.7847 (mp0) cc_final: 0.7382 (mp0) outliers start: 12 outliers final: 4 residues processed: 140 average time/residue: 1.3203 time to fit residues: 193.6937 Evaluate side-chains 132 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 72 optimal weight: 0.0470 chunk 4 optimal weight: 0.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094586 restraints weight = 9560.506| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.82 r_work: 0.3097 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6692 Z= 0.277 Angle : 0.589 13.512 9093 Z= 0.297 Chirality : 0.044 0.238 964 Planarity : 0.004 0.046 1174 Dihedral : 5.479 58.705 992 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.03 % Allowed : 10.60 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.31), residues: 789 helix: 1.10 (0.29), residues: 373 sheet: 2.10 (0.93), residues: 34 loop : -1.31 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.011 0.001 PHE A 327 TYR 0.015 0.001 TYR A 385 ARG 0.003 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.702 Fit side-chains REVERT: A 75 GLU cc_start: 0.8045 (tp30) cc_final: 0.7763 (tp30) REVERT: A 190 MET cc_start: 0.8116 (tmm) cc_final: 0.7903 (tmt) REVERT: A 375 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7839 (mm-30) REVERT: A 401 HIS cc_start: 0.8659 (OUTLIER) cc_final: 0.8130 (m-70) REVERT: B 340 GLU cc_start: 0.7852 (mp0) cc_final: 0.7362 (mp0) outliers start: 14 outliers final: 6 residues processed: 143 average time/residue: 1.2415 time to fit residues: 186.3952 Evaluate side-chains 147 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 chunk 40 optimal weight: 0.0470 chunk 13 optimal weight: 0.0980 chunk 69 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096668 restraints weight = 9600.896| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.85 r_work: 0.3131 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6692 Z= 0.180 Angle : 0.557 11.205 9093 Z= 0.276 Chirality : 0.042 0.206 964 Planarity : 0.004 0.046 1174 Dihedral : 5.281 55.459 992 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.74 % Allowed : 12.19 % Favored : 86.07 % 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: 0.25 (0.31), residues: 789 helix: 1.30 (0.29), residues: 373 sheet: 1.63 (0.80), residues: 44 loop : -1.24 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.007 0.001 PHE B 374 TYR 0.009 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8013 (tp30) cc_final: 0.7777 (tp30) REVERT: A 190 MET cc_start: 0.8083 (tmm) cc_final: 0.7878 (tmt) REVERT: A 360 MET cc_start: 0.8618 (ttt) cc_final: 0.8383 (ttm) REVERT: A 375 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 401 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8081 (m-70) REVERT: B 340 GLU cc_start: 0.7897 (mp0) cc_final: 0.7369 (mp0) REVERT: B 374 PHE cc_start: 0.8041 (m-10) cc_final: 0.7749 (m-80) REVERT: B 438 SER cc_start: 0.7998 (p) cc_final: 0.7574 (p) outliers start: 12 outliers final: 6 residues processed: 143 average time/residue: 1.2002 time to fit residues: 180.4519 Evaluate side-chains 146 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 0.0970 chunk 26 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 62 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 64 optimal weight: 0.9980 overall best weight: 0.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.096261 restraints weight = 9562.063| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.85 r_work: 0.3125 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 6692 Z= 0.199 Angle : 0.558 13.743 9093 Z= 0.278 Chirality : 0.042 0.222 964 Planarity : 0.004 0.047 1174 Dihedral : 5.173 55.322 992 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.60 % Allowed : 13.21 % Favored : 85.20 % 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: 0.39 (0.31), residues: 789 helix: 1.57 (0.29), residues: 364 sheet: 2.04 (0.94), residues: 34 loop : -1.23 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.008 0.001 PHE A 327 TYR 0.011 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.818 Fit side-chains REVERT: A 75 GLU cc_start: 0.8011 (tp30) cc_final: 0.7774 (tp30) REVERT: A 360 MET cc_start: 0.8650 (ttt) cc_final: 0.8405 (ttm) REVERT: A 375 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 401 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.8089 (m-70) REVERT: B 340 GLU cc_start: 0.7904 (mp0) cc_final: 0.7352 (mp0) REVERT: B 374 PHE cc_start: 0.8029 (m-10) cc_final: 0.7700 (m-80) REVERT: B 420 ASP cc_start: 0.8236 (m-30) cc_final: 0.7793 (m-30) REVERT: B 438 SER cc_start: 0.8013 (p) cc_final: 0.7578 (p) outliers start: 11 outliers final: 8 residues processed: 147 average time/residue: 1.3881 time to fit residues: 214.7099 Evaluate side-chains 146 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 16 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095261 restraints weight = 9509.622| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.82 r_work: 0.3109 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6692 Z= 0.245 Angle : 0.588 13.139 9093 Z= 0.292 Chirality : 0.043 0.227 964 Planarity : 0.004 0.047 1174 Dihedral : 5.215 54.351 992 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.89 % Allowed : 13.93 % Favored : 84.18 % 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: 0.35 (0.31), residues: 789 helix: 1.53 (0.29), residues: 364 sheet: 2.05 (0.94), residues: 34 loop : -1.25 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.010 0.001 PHE A 315 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.754 Fit side-chains REVERT: A 75 GLU cc_start: 0.8027 (tp30) cc_final: 0.7749 (tp30) REVERT: A 375 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7843 (mm-30) REVERT: A 401 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.8090 (m-70) REVERT: B 340 GLU cc_start: 0.7887 (mp0) cc_final: 0.7330 (mp0) REVERT: B 374 PHE cc_start: 0.8054 (m-10) cc_final: 0.7694 (m-80) outliers start: 13 outliers final: 7 residues processed: 146 average time/residue: 1.2013 time to fit residues: 184.3527 Evaluate side-chains 147 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 chunk 2 optimal weight: 0.0970 chunk 70 optimal weight: 0.0060 chunk 47 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 overall best weight: 0.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.096656 restraints weight = 9529.190| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.86 r_work: 0.3134 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6692 Z= 0.193 Angle : 0.579 12.761 9093 Z= 0.284 Chirality : 0.042 0.213 964 Planarity : 0.004 0.047 1174 Dihedral : 5.123 54.687 992 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.74 % Allowed : 14.95 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.31), residues: 789 helix: 1.66 (0.29), residues: 362 sheet: 2.04 (0.94), residues: 34 loop : -1.26 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.011 0.001 PHE A 315 TYR 0.010 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.750 Fit side-chains REVERT: A 75 GLU cc_start: 0.8003 (tp30) cc_final: 0.7775 (tp30) REVERT: A 360 MET cc_start: 0.8640 (ttt) cc_final: 0.8404 (ttm) REVERT: A 375 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7896 (mm-30) REVERT: A 401 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.8092 (m-70) REVERT: A 559 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7826 (ttp-110) REVERT: B 340 GLU cc_start: 0.7901 (mp0) cc_final: 0.7325 (mp0) REVERT: B 374 PHE cc_start: 0.8109 (m-10) cc_final: 0.7797 (m-80) REVERT: B 420 ASP cc_start: 0.8172 (m-30) cc_final: 0.7728 (m-30) REVERT: B 438 SER cc_start: 0.7984 (p) cc_final: 0.7550 (p) outliers start: 12 outliers final: 6 residues processed: 145 average time/residue: 1.2518 time to fit residues: 190.2906 Evaluate side-chains 146 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 21 optimal weight: 0.0370 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.095071 restraints weight = 9580.317| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.83 r_work: 0.3103 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6692 Z= 0.273 Angle : 0.613 14.049 9093 Z= 0.305 Chirality : 0.043 0.221 964 Planarity : 0.004 0.047 1174 Dihedral : 5.215 53.902 992 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.03 % Allowed : 15.09 % Favored : 82.87 % 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: 0.26 (0.31), residues: 789 helix: 1.37 (0.29), residues: 372 sheet: 2.45 (0.97), residues: 32 loop : -1.29 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 315 TYR 0.016 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8045 (tp30) cc_final: 0.7785 (tp30) REVERT: A 182 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: A 259 THR cc_start: 0.8448 (m) cc_final: 0.8218 (p) REVERT: A 375 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7833 (mm-30) REVERT: A 401 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.8074 (m-70) REVERT: A 559 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7771 (ttp-110) REVERT: B 340 GLU cc_start: 0.7888 (mp0) cc_final: 0.7328 (mp0) REVERT: B 374 PHE cc_start: 0.8070 (m-10) cc_final: 0.7723 (m-80) outliers start: 14 outliers final: 7 residues processed: 146 average time/residue: 1.4658 time to fit residues: 224.9888 Evaluate side-chains 150 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 22 optimal weight: 0.3980 chunk 76 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094888 restraints weight = 9565.911| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.87 r_work: 0.3103 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6692 Z= 0.251 Angle : 0.609 13.995 9093 Z= 0.305 Chirality : 0.043 0.218 964 Planarity : 0.004 0.046 1174 Dihedral : 5.202 53.988 992 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.89 % Allowed : 15.67 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.31), residues: 789 helix: 1.53 (0.29), residues: 364 sheet: 2.14 (0.95), residues: 34 loop : -1.26 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.011 0.001 PHE A 315 TYR 0.013 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8086 (tp30) cc_final: 0.7833 (tp30) REVERT: A 182 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: A 259 THR cc_start: 0.8492 (m) cc_final: 0.8241 (p) REVERT: A 375 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7839 (mm-30) REVERT: A 401 HIS cc_start: 0.8690 (OUTLIER) cc_final: 0.8062 (m-70) REVERT: A 559 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7793 (ttp-110) REVERT: B 340 GLU cc_start: 0.7917 (mp0) cc_final: 0.7357 (mp0) REVERT: B 374 PHE cc_start: 0.8120 (m-10) cc_final: 0.7771 (m-80) outliers start: 13 outliers final: 7 residues processed: 145 average time/residue: 1.5463 time to fit residues: 235.1221 Evaluate side-chains 149 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.1980 chunk 58 optimal weight: 0.0070 chunk 50 optimal weight: 0.6980 chunk 47 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095019 restraints weight = 9690.380| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.87 r_work: 0.3105 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6692 Z= 0.243 Angle : 0.621 13.942 9093 Z= 0.307 Chirality : 0.043 0.216 964 Planarity : 0.004 0.046 1174 Dihedral : 5.181 53.871 992 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.60 % Allowed : 16.26 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.31), residues: 789 helix: 1.53 (0.29), residues: 363 sheet: 2.13 (0.95), residues: 34 loop : -1.30 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.011 0.001 PHE A 315 TYR 0.013 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5621.39 seconds wall clock time: 98 minutes 46.48 seconds (5926.48 seconds total)