Starting phenix.real_space_refine on Thu Jul 2 15:58:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yv8_34120/07_2026/7yv8_34120.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yv8_34120/07_2026/7yv8_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_34120/07_2026/7yv8_34120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yv8_34120/07_2026/7yv8_34120.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yv8_34120/07_2026/7yv8_34120.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yv8_34120/07_2026/7yv8_34120.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yv8_34120/07_2026/7yv8_34120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yv8_34120/07_2026/7yv8_34120.cif" } resolution = 2.94 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= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 chiralities: 1 Time building chain proxies: 1.26, per 1000 atoms: 0.19 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: 0.32 Conformation dependent library (CDL) restraints added in 251.8 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: 0.16 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: 0.79 Time building geometry restraints manager: 0.45 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 - 17.59: 3496 17.59 - 35.19: 340 35.19 - 52.78: 58 52.78 - 70.37: 11 70.37 - 87.97: 7 Dihedral angle restraints: 3912 sinusoidal: 1584 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 3909 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: 8.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.280 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:5.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.006 0.201 6707 Z= 0.245 Angle : 0.666 14.865 9125 Z= 0.344 Chirality : 0.045 0.210 964 Planarity : 0.005 0.041 1174 Dihedral : 13.906 84.592 2399 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 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: -0.89 (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 ARG 0.005 0.000 ARG A 460 TYR 0.024 0.002 TYR A 199 PHE 0.012 0.002 PHE B 377 TRP 0.015 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 ( 6692) covalent geometry : angle 0.65233 / 0.34 ( 9093) SS BOND : bond 0.00776 / 0.61 ( 7) SS BOND : angle 2.30373 / 1.45 ( 14) hydrogen bonds : bond 0.19979 / 12.81 ( 281) hydrogen bonds : angle 6.77916 / 4.74 ( 783) metal coordination : bond 0.19648 / 9.84 ( 2) link_NAG-ASN : bond 0.00252 / 0.14 ( 6) link_NAG-ASN : angle 2.36323 / 1.35 ( 18) *********************** 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 : 0.246 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: 0.6609 (mp0) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.4740 time to fit residues: 75.1561 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 : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095108 restraints weight = 9524.207| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.84 r_work: 0.3107 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6707 Z= 0.153 Angle : 0.604 14.148 9125 Z= 0.303 Chirality : 0.043 0.221 964 Planarity : 0.004 0.044 1174 Dihedral : 4.227 21.642 866 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.02 % Allowed : 7.98 % Favored : 91.00 % 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: -0.26 (0.31), residues: 789 helix: 0.73 (0.29), residues: 373 sheet: 2.16 (0.93), residues: 34 loop : -1.34 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.013 0.001 TYR A 199 PHE 0.009 0.001 PHE A 512 TRP 0.016 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 6692) covalent geometry : angle 0.59488 / 0.30 ( 9093) SS BOND : bond 0.00740 / 0.58 ( 7) SS BOND : angle 2.06676 / 1.36 ( 14) hydrogen bonds : bond 0.05496 / 3.57 ( 281) hydrogen bonds : angle 4.55601 / 3.17 ( 783) metal coordination : bond 0.00330 / 0.17 ( 2) link_NAG-ASN : bond 0.00240 / 0.12 ( 6) link_NAG-ASN : angle 1.71142 / 0.98 ( 18) *********************** 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 145 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.247 Fit side-chains REVERT: A 190 MET cc_start: 0.8216 (tmm) cc_final: 0.7983 (tmt) REVERT: A 375 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7816 (mm-30) REVERT: A 408 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7340 (mmm) REVERT: B 340 GLU cc_start: 0.7794 (mp0) cc_final: 0.7376 (mp0) REVERT: B 377 PHE cc_start: 0.8646 (t80) cc_final: 0.8439 (t80) outliers start: 7 outliers final: 3 residues processed: 140 average time/residue: 0.4350 time to fit residues: 64.2031 Evaluate side-chains 136 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 74 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.103371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.093785 restraints weight = 9468.825| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.82 r_work: 0.3083 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6707 Z= 0.216 Angle : 0.634 12.124 9125 Z= 0.318 Chirality : 0.046 0.234 964 Planarity : 0.005 0.045 1174 Dihedral : 4.314 21.657 866 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.03 % Allowed : 9.29 % Favored : 88.68 % 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: -0.20 (0.31), residues: 789 helix: 0.88 (0.29), residues: 371 sheet: 2.40 (0.92), residues: 32 loop : -1.42 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.018 0.002 TYR A 385 PHE 0.013 0.002 PHE A 327 TRP 0.016 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 ( 6692) covalent geometry : angle 0.62249 / 0.31 ( 9093) SS BOND : bond 0.00667 / 0.52 ( 7) SS BOND : angle 2.22677 / 1.51 ( 14) hydrogen bonds : bond 0.06447 / 4.20 ( 281) hydrogen bonds : angle 4.46568 / 3.13 ( 783) metal coordination : bond 0.00265 / 0.14 ( 2) link_NAG-ASN : bond 0.00702 / 0.36 ( 6) link_NAG-ASN : angle 2.06413 / 1.23 ( 18) *********************** 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 145 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8135 (tmm) cc_final: 0.7917 (OUTLIER) REVERT: A 375 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7813 (mm-30) REVERT: A 401 HIS cc_start: 0.8753 (OUTLIER) cc_final: 0.8106 (m-70) REVERT: A 408 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7423 (mmm) REVERT: B 340 GLU cc_start: 0.7811 (mp0) cc_final: 0.7363 (mp0) REVERT: B 377 PHE cc_start: 0.8730 (t80) cc_final: 0.8523 (t80) REVERT: B 443 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8235 (p) outliers start: 14 outliers final: 6 residues processed: 137 average time/residue: 0.4525 time to fit residues: 65.0398 Evaluate side-chains 139 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.3980 chunk 28 optimal weight: 0.0870 chunk 5 optimal weight: 0.3980 chunk 68 optimal weight: 0.1980 chunk 42 optimal weight: 0.0670 chunk 11 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 chunk 40 optimal weight: 0.0000 chunk 17 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 overall best weight: 0.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098188 restraints weight = 9721.024| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.86 r_work: 0.3155 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 6707 Z= 0.106 Angle : 0.549 12.824 9125 Z= 0.270 Chirality : 0.041 0.213 964 Planarity : 0.004 0.046 1174 Dihedral : 3.897 22.306 866 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.16 % Allowed : 11.03 % Favored : 87.81 % 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: 0.20 (0.31), residues: 789 helix: 1.28 (0.29), residues: 372 sheet: 2.19 (0.94), residues: 34 loop : -1.27 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.007 0.001 TYR B 351 PHE 0.006 0.001 PHE A 315 TRP 0.016 0.001 TRP A 163 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 6692) covalent geometry : angle 0.54021 / 0.27 ( 9093) SS BOND : bond 0.00635 / 0.50 ( 7) SS BOND : angle 1.86323 / 1.23 ( 14) hydrogen bonds : bond 0.03706 / 2.40 ( 281) hydrogen bonds : angle 4.16968 / 2.93 ( 783) metal coordination : bond 0.00068 / 0.04 ( 2) link_NAG-ASN : bond 0.00655 / 0.33 ( 6) link_NAG-ASN : angle 1.68410 / 1.04 ( 18) *********************** 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 149 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.249 Fit side-chains REVERT: A 75 GLU cc_start: 0.7981 (tp30) cc_final: 0.7777 (tp30) REVERT: A 190 MET cc_start: 0.8035 (tmm) cc_final: 0.7808 (tmt) REVERT: A 375 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 401 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.8060 (m-70) REVERT: B 340 GLU cc_start: 0.7888 (mp0) cc_final: 0.7393 (mp0) REVERT: B 420 ASP cc_start: 0.8176 (m-30) cc_final: 0.7701 (m-30) REVERT: B 438 SER cc_start: 0.8036 (p) cc_final: 0.7578 (p) outliers start: 8 outliers final: 2 residues processed: 145 average time/residue: 0.4730 time to fit residues: 72.1303 Evaluate side-chains 141 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 387 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN B 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.092985 restraints weight = 9616.156| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.82 r_work: 0.3067 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 6707 Z= 0.251 Angle : 0.650 10.637 9125 Z= 0.324 Chirality : 0.047 0.234 964 Planarity : 0.005 0.046 1174 Dihedral : 4.261 21.658 866 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.18 % Allowed : 12.48 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.00 (0.31), residues: 789 helix: 1.13 (0.29), residues: 371 sheet: 1.32 (0.86), residues: 42 loop : -1.35 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.019 0.002 TYR A 385 PHE 0.022 0.002 PHE B 374 TRP 0.015 0.002 TRP A 163 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.25 ( 6692) covalent geometry : angle 0.63713 / 0.32 ( 9093) SS BOND : bond 0.00682 / 0.53 ( 7) SS BOND : angle 2.38498 / 1.53 ( 14) hydrogen bonds : bond 0.06767 / 4.41 ( 281) hydrogen bonds : angle 4.40636 / 3.11 ( 783) metal coordination : bond 0.00290 / 0.15 ( 2) link_NAG-ASN : bond 0.00626 / 0.33 ( 6) link_NAG-ASN : angle 2.12828 / 1.30 ( 18) *********************** 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 154 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.299 Fit side-chains REVERT: A 42 GLN cc_start: 0.8451 (mt0) cc_final: 0.8120 (mt0) REVERT: A 77 SER cc_start: 0.8974 (t) cc_final: 0.8736 (m) REVERT: A 190 MET cc_start: 0.8149 (tmm) cc_final: 0.7921 (ttp) REVERT: B 340 GLU cc_start: 0.7870 (mp0) cc_final: 0.7359 (mp0) REVERT: B 443 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8259 (p) outliers start: 15 outliers final: 8 residues processed: 145 average time/residue: 0.6161 time to fit residues: 93.7685 Evaluate side-chains 147 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 449 THR Chi-restraints excluded: chain A residue 585 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.4980 chunk 56 optimal weight: 0.3980 chunk 47 optimal weight: 0.3980 chunk 50 optimal weight: 0.4980 chunk 5 optimal weight: 0.4980 chunk 45 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 20 optimal weight: 0.0670 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.104420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094542 restraints weight = 9639.512| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.86 r_work: 0.3092 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6707 Z= 0.166 Angle : 0.611 12.771 9125 Z= 0.300 Chirality : 0.044 0.240 964 Planarity : 0.004 0.046 1174 Dihedral : 4.136 22.031 866 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.03 % Allowed : 13.79 % 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 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: 0.14 (0.31), residues: 789 helix: 1.24 (0.29), residues: 372 sheet: 1.18 (0.85), residues: 44 loop : -1.27 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.013 0.001 TYR A 385 PHE 0.012 0.001 PHE B 374 TRP 0.018 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 6692) covalent geometry : angle 0.59899 / 0.30 ( 9093) SS BOND : bond 0.00763 / 0.60 ( 7) SS BOND : angle 2.24599 / 1.46 ( 14) hydrogen bonds : bond 0.05375 / 3.50 ( 281) hydrogen bonds : angle 4.30433 / 3.02 ( 783) metal coordination : bond 0.00195 / 0.10 ( 2) link_NAG-ASN : bond 0.00569 / 0.29 ( 6) link_NAG-ASN : angle 1.96048 / 1.22 ( 18) *********************** 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 157 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.266 Fit side-chains REVERT: A 75 GLU cc_start: 0.8054 (tp30) cc_final: 0.7773 (tp30) REVERT: A 190 MET cc_start: 0.8110 (tmm) cc_final: 0.7907 (OUTLIER) REVERT: A 375 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7822 (mm-30) REVERT: A 401 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.8049 (m-70) REVERT: B 340 GLU cc_start: 0.7886 (mp0) cc_final: 0.7356 (mp0) REVERT: B 443 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8234 (p) REVERT: B 452 LEU cc_start: 0.8749 (mp) cc_final: 0.8542 (mt) outliers start: 14 outliers final: 9 residues processed: 149 average time/residue: 0.5968 time to fit residues: 93.2888 Evaluate side-chains 146 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 585 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 66 optimal weight: 0.0670 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 76 optimal weight: 0.0770 chunk 13 optimal weight: 0.0980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN B 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094947 restraints weight = 9457.048| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.84 r_work: 0.3104 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: 0.8476 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6707 Z= 0.154 Angle : 0.609 13.990 9125 Z= 0.299 Chirality : 0.043 0.231 964 Planarity : 0.004 0.046 1174 Dihedral : 4.083 22.108 866 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.74 % Allowed : 14.66 % Favored : 83.60 % 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: 0.19 (0.31), residues: 789 helix: 1.29 (0.29), residues: 373 sheet: 2.14 (0.95), residues: 34 loop : -1.29 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.012 0.001 TYR A 385 PHE 0.020 0.001 PHE B 374 TRP 0.018 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 6692) covalent geometry : angle 0.59826 / 0.30 ( 9093) SS BOND : bond 0.00776 / 0.61 ( 7) SS BOND : angle 2.12271 / 1.37 ( 14) hydrogen bonds : bond 0.05134 / 3.34 ( 281) hydrogen bonds : angle 4.28978 / 3.01 ( 783) metal coordination : bond 0.00171 / 0.09 ( 2) link_NAG-ASN : bond 0.00529 / 0.27 ( 6) link_NAG-ASN : angle 1.92037 / 1.21 ( 18) *********************** 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 154 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.271 Fit side-chains REVERT: A 75 GLU cc_start: 0.8036 (tp30) cc_final: 0.7771 (tp30) REVERT: A 401 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.8051 (m-70) REVERT: B 340 GLU cc_start: 0.7874 (mp0) cc_final: 0.7318 (mp0) outliers start: 12 outliers final: 9 residues processed: 146 average time/residue: 0.5612 time to fit residues: 86.1432 Evaluate side-chains 147 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 190 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 585 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.0070 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 0.0470 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 65 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.105119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095128 restraints weight = 9555.896| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.87 r_work: 0.3104 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 6707 Z= 0.144 Angle : 0.605 13.784 9125 Z= 0.298 Chirality : 0.043 0.223 964 Planarity : 0.004 0.046 1174 Dihedral : 4.039 22.249 866 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.45 % Allowed : 15.53 % Favored : 83.02 % 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: 0.24 (0.31), residues: 789 helix: 1.34 (0.29), residues: 373 sheet: 2.09 (0.95), residues: 34 loop : -1.27 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.012 0.001 TYR A 385 PHE 0.018 0.001 PHE B 374 TRP 0.017 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 6692) covalent geometry : angle 0.59458 / 0.29 ( 9093) SS BOND : bond 0.00726 / 0.57 ( 7) SS BOND : angle 2.08195 / 1.36 ( 14) hydrogen bonds : bond 0.04880 / 3.18 ( 281) hydrogen bonds : angle 4.24752 / 2.98 ( 783) metal coordination : bond 0.00152 / 0.08 ( 2) link_NAG-ASN : bond 0.00512 / 0.26 ( 6) link_NAG-ASN : angle 1.88780 / 1.20 ( 18) *********************** 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 149 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.256 Fit side-chains REVERT: A 75 GLU cc_start: 0.8099 (tp30) cc_final: 0.7859 (tp30) REVERT: A 190 MET cc_start: 0.8119 (tmm) cc_final: 0.7910 (tmt) REVERT: A 401 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.8079 (m-70) REVERT: B 340 GLU cc_start: 0.7892 (mp0) cc_final: 0.7321 (mp0) outliers start: 10 outliers final: 7 residues processed: 144 average time/residue: 0.5372 time to fit residues: 81.3779 Evaluate side-chains 143 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 0.0980 chunk 20 optimal weight: 0.4980 chunk 72 optimal weight: 0.0010 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 0.0370 chunk 44 optimal weight: 0.5980 overall best weight: 0.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.105493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095491 restraints weight = 9618.695| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.87 r_work: 0.3110 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6707 Z= 0.138 Angle : 0.604 13.635 9125 Z= 0.298 Chirality : 0.043 0.219 964 Planarity : 0.004 0.046 1174 Dihedral : 3.984 22.464 866 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.18 % Allowed : 15.24 % Favored : 82.58 % 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: 0.31 (0.31), residues: 789 helix: 1.42 (0.29), residues: 372 sheet: 2.08 (0.95), residues: 34 loop : -1.26 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.010 0.001 TYR A 385 PHE 0.017 0.001 PHE B 374 TRP 0.018 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6692) covalent geometry : angle 0.59445 / 0.29 ( 9093) SS BOND : bond 0.00714 / 0.56 ( 7) SS BOND : angle 2.03398 / 1.34 ( 14) hydrogen bonds : bond 0.04672 / 3.05 ( 281) hydrogen bonds : angle 4.20313 / 2.95 ( 783) metal coordination : bond 0.00129 / 0.07 ( 2) link_NAG-ASN : bond 0.00497 / 0.25 ( 6) link_NAG-ASN : angle 1.85966 / 1.20 ( 18) *********************** 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 155 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.274 Fit side-chains REVERT: A 75 GLU cc_start: 0.8085 (tp30) cc_final: 0.7851 (tp30) REVERT: A 375 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 401 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8091 (m-70) REVERT: B 340 GLU cc_start: 0.7901 (mp0) cc_final: 0.7327 (mp0) REVERT: B 420 ASP cc_start: 0.8186 (m-30) cc_final: 0.7741 (m-30) outliers start: 15 outliers final: 9 residues processed: 148 average time/residue: 0.5336 time to fit residues: 83.0795 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 : 0.214 ------------------------------------------------------------------------------- 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 585 LEU 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 5 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 6 optimal weight: 0.0270 chunk 56 optimal weight: 0.0770 chunk 4 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.095696 restraints weight = 9484.071| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.85 r_work: 0.3119 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6707 Z= 0.136 Angle : 0.626 13.530 9125 Z= 0.304 Chirality : 0.043 0.216 964 Planarity : 0.004 0.046 1174 Dihedral : 3.952 22.504 866 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.60 % Allowed : 15.82 % Favored : 82.58 % 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: 0.44 (0.31), residues: 789 helix: 1.60 (0.29), residues: 364 sheet: 1.67 (0.80), residues: 44 loop : -1.24 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.010 0.001 TYR A 385 PHE 0.018 0.001 PHE B 374 TRP 0.017 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 6692) covalent geometry : angle 0.61548 / 0.30 ( 9093) SS BOND : bond 0.00716 / 0.56 ( 7) SS BOND : angle 2.17915 / 1.37 ( 14) hydrogen bonds : bond 0.04605 / 3.00 ( 281) hydrogen bonds : angle 4.18698 / 2.94 ( 783) metal coordination : bond 0.00128 / 0.07 ( 2) link_NAG-ASN : bond 0.00478 / 0.24 ( 6) link_NAG-ASN : angle 1.84703 / 1.20 ( 18) ********************** 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 152 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.258 Fit side-chains REVERT: A 75 GLU cc_start: 0.8086 (tp30) cc_final: 0.7859 (tp30) REVERT: A 259 THR cc_start: 0.8351 (p) cc_final: 0.8146 (m) REVERT: A 375 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7852 (mm-30) REVERT: A 401 HIS cc_start: 0.8585 (OUTLIER) cc_final: 0.8107 (m-70) REVERT: B 340 GLU cc_start: 0.7893 (mp0) cc_final: 0.7318 (mp0) REVERT: B 420 ASP cc_start: 0.8187 (m-30) cc_final: 0.7750 (m-30) outliers start: 11 outliers final: 7 residues processed: 145 average time/residue: 0.5586 time to fit residues: 85.1598 Evaluate side-chains 149 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 585 LEU 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 67 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094365 restraints weight = 9561.915| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.85 r_work: 0.3094 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6707 Z= 0.176 Angle : 0.650 13.627 9125 Z= 0.319 Chirality : 0.044 0.226 964 Planarity : 0.004 0.046 1174 Dihedral : 4.091 22.220 866 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.31 % Allowed : 16.69 % Favored : 82.00 % 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: 0.34 (0.31), residues: 789 helix: 1.50 (0.29), residues: 363 sheet: 1.68 (0.80), residues: 44 loop : -1.28 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.015 0.001 TYR A 385 PHE 0.022 0.002 PHE B 374 TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 6692) covalent geometry : angle 0.63818 / 0.32 ( 9093) SS BOND : bond 0.00738 / 0.58 ( 7) SS BOND : angle 2.36602 / 1.47 ( 14) hydrogen bonds : bond 0.05498 / 3.58 ( 281) hydrogen bonds : angle 4.26873 / 3.00 ( 783) metal coordination : bond 0.00191 / 0.10 ( 2) link_NAG-ASN : bond 0.00480 / 0.25 ( 6) link_NAG-ASN : angle 1.97042 / 1.25 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2635.73 seconds wall clock time: 45 minutes 35.43 seconds (2735.43 seconds total)