Starting phenix.real_space_refine on Sat Aug 23 02:34:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yv8_34120/08_2025/7yv8_34120.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yv8_34120/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yv8_34120/08_2025/7yv8_34120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yv8_34120/08_2025/7yv8_34120.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yv8_34120/08_2025/7yv8_34120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yv8_34120/08_2025/7yv8_34120.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 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: 1.37, per 1000 atoms: 0.21 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: 0.52 Conformation dependent library (CDL) restraints added in 330.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.22 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: 0.84 Time building geometry restraints manager: 0.71 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: 12.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.540 Find NCS groups from input model: 0.030 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- 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 : 0.006 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 : 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00505 ( 6692) covalent geometry : angle 0.65233 ( 9093) SS BOND : bond 0.00776 ( 7) SS BOND : angle 2.30373 ( 14) hydrogen bonds : bond 0.19979 ( 281) hydrogen bonds : angle 6.77916 ( 783) metal coordination : bond 0.19648 ( 2) link_NAG-ASN : bond 0.00252 ( 6) link_NAG-ASN : angle 2.36323 ( 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 : 0.223 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: 0.5057 time to fit residues: 79.8367 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 : 0.285 ------------------------------------------------------------------------------- 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... 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 = 0.3369 r_free = 0.3369 target = 0.104980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095145 restraints weight = 9531.826| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.81 r_work: 0.3109 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1144 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= 0.154 Angle : 0.615 14.156 9125 Z= 0.306 Chirality : 0.044 0.221 964 Planarity : 0.004 0.044 1174 Dihedral : 6.522 59.216 992 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.02 % Allowed : 8.13 % Favored : 90.86 % 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 aren not related in a simple way. whole: -0.27 (0.31), residues: 789 helix: 0.72 (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 385 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 covalent geometry : bond 0.00364 ( 6692) covalent geometry : angle 0.60485 ( 9093) SS BOND : bond 0.00730 ( 7) SS BOND : angle 2.06362 ( 14) hydrogen bonds : bond 0.05563 ( 281) hydrogen bonds : angle 4.57256 ( 783) metal coordination : bond 0.00496 ( 2) link_NAG-ASN : bond 0.00270 ( 6) link_NAG-ASN : angle 1.85957 ( 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 146 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.186 Fit side-chains REVERT: A 190 MET cc_start: 0.8221 (tmm) cc_final: 0.7981 (tmt) REVERT: A 375 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7816 (mm-30) REVERT: A 408 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7336 (mmm) REVERT: B 340 GLU cc_start: 0.7778 (mp0) cc_final: 0.7363 (mp0) REVERT: B 377 PHE cc_start: 0.8647 (t80) cc_final: 0.8436 (t80) outliers start: 7 outliers final: 3 residues processed: 141 average time/residue: 0.4891 time to fit residues: 72.3452 Evaluate side-chains 137 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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: 0.4980 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.102655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.093129 restraints weight = 9466.723| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.80 r_work: 0.3076 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 6707 Z= 0.244 Angle : 0.654 12.009 9125 Z= 0.328 Chirality : 0.047 0.241 964 Planarity : 0.005 0.045 1174 Dihedral : 5.741 56.614 992 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % 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 aren not related in a simple way. whole: -0.26 (0.31), residues: 789 helix: 0.82 (0.29), residues: 371 sheet: 1.28 (0.84), residues: 42 loop : -1.40 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 460 TYR 0.019 0.002 TYR A 385 PHE 0.015 0.002 PHE A 327 TRP 0.016 0.002 TRP A 163 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 6692) covalent geometry : angle 0.64130 ( 9093) SS BOND : bond 0.00687 ( 7) SS BOND : angle 2.29876 ( 14) hydrogen bonds : bond 0.06871 ( 281) hydrogen bonds : angle 4.51965 ( 783) metal coordination : bond 0.00303 ( 2) link_NAG-ASN : bond 0.00673 ( 6) link_NAG-ASN : angle 2.26946 ( 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 149 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 42 GLN cc_start: 0.8430 (mt0) cc_final: 0.8093 (mt0) REVERT: A 190 MET cc_start: 0.8149 (tmm) cc_final: 0.7937 (OUTLIER) REVERT: A 375 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 408 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7436 (mmm) REVERT: B 340 GLU cc_start: 0.7799 (mp0) cc_final: 0.7340 (mp0) REVERT: B 377 PHE cc_start: 0.8754 (t80) cc_final: 0.8538 (t80) REVERT: B 443 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8251 (p) outliers start: 14 outliers final: 7 residues processed: 141 average time/residue: 0.5295 time to fit residues: 77.9815 Evaluate side-chains 140 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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: 0.5980 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 11 optimal weight: 0.0470 chunk 20 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3345 r_free = 0.3345 target = 0.103658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.093960 restraints weight = 9602.009| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.83 r_work: 0.3084 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6707 Z= 0.197 Angle : 0.625 12.641 9125 Z= 0.311 Chirality : 0.045 0.249 964 Planarity : 0.004 0.046 1174 Dihedral : 5.504 54.546 992 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.03 % Allowed : 10.74 % Favored : 87.23 % 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 aren not related in a simple way. whole: -0.12 (0.31), residues: 789 helix: 0.98 (0.29), residues: 372 sheet: 1.31 (0.84), residues: 42 loop : -1.37 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 460 TYR 0.015 0.001 TYR A 385 PHE 0.012 0.002 PHE A 327 TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 6692) covalent geometry : angle 0.61112 ( 9093) SS BOND : bond 0.00704 ( 7) SS BOND : angle 2.33221 ( 14) hydrogen bonds : bond 0.06014 ( 281) hydrogen bonds : angle 4.40498 ( 783) metal coordination : bond 0.00252 ( 2) link_NAG-ASN : bond 0.00687 ( 6) link_NAG-ASN : angle 2.19402 ( 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 157 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 42 GLN cc_start: 0.8423 (mt0) cc_final: 0.8085 (mt0) REVERT: A 190 MET cc_start: 0.8130 (tmm) cc_final: 0.7910 (OUTLIER) REVERT: A 375 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7800 (mm-30) REVERT: A 408 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7365 (mmm) REVERT: B 340 GLU cc_start: 0.7842 (mp0) cc_final: 0.7334 (mp0) REVERT: B 377 PHE cc_start: 0.8665 (t80) cc_final: 0.8455 (t80) REVERT: B 443 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8246 (p) outliers start: 14 outliers final: 9 residues processed: 148 average time/residue: 0.5837 time to fit residues: 90.6094 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 : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 231 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.102917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.093214 restraints weight = 9606.026| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.84 r_work: 0.3073 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 6707 Z= 0.229 Angle : 0.653 14.084 9125 Z= 0.325 Chirality : 0.046 0.260 964 Planarity : 0.005 0.046 1174 Dihedral : 5.518 54.155 992 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.03 % Allowed : 12.48 % Favored : 85.49 % 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 aren not related in a simple way. whole: -0.15 (0.30), residues: 789 helix: 1.00 (0.29), residues: 371 sheet: 1.35 (0.84), residues: 42 loop : -1.45 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.020 0.002 TYR A 385 PHE 0.014 0.002 PHE A 327 TRP 0.018 0.002 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 6692) covalent geometry : angle 0.63976 ( 9093) SS BOND : bond 0.00757 ( 7) SS BOND : angle 2.44461 ( 14) hydrogen bonds : bond 0.06514 ( 281) hydrogen bonds : angle 4.45213 ( 783) metal coordination : bond 0.00294 ( 2) link_NAG-ASN : bond 0.00620 ( 6) link_NAG-ASN : angle 2.23636 ( 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 153 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 42 GLN cc_start: 0.8440 (mt0) cc_final: 0.8105 (mt0) REVERT: A 190 MET cc_start: 0.8141 (tmm) cc_final: 0.7915 (ttp) REVERT: A 408 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7427 (mmm) REVERT: B 340 GLU cc_start: 0.7856 (mp0) cc_final: 0.7322 (mp0) REVERT: B 443 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8254 (p) outliers start: 14 outliers final: 8 residues processed: 143 average time/residue: 0.6259 time to fit residues: 93.7768 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 : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 123 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.0470 chunk 56 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 22 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 overall best weight: 0.2256 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.105750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.095849 restraints weight = 9674.831| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.86 r_work: 0.3115 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6707 Z= 0.130 Angle : 0.580 12.363 9125 Z= 0.287 Chirality : 0.042 0.226 964 Planarity : 0.004 0.046 1174 Dihedral : 5.282 54.826 992 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.18 % Allowed : 13.21 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.31), residues: 789 helix: 1.24 (0.29), residues: 373 sheet: 2.14 (0.93), residues: 34 loop : -1.32 (0.30), residues: 382 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 0.007 0.001 PHE A 315 TRP 0.017 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6692) covalent geometry : angle 0.56873 ( 9093) SS BOND : bond 0.00646 ( 7) SS BOND : angle 2.06774 ( 14) hydrogen bonds : bond 0.04629 ( 281) hydrogen bonds : angle 4.23674 ( 783) metal coordination : bond 0.00132 ( 2) link_NAG-ASN : bond 0.00586 ( 6) link_NAG-ASN : angle 1.95863 ( 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 159 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.255 Fit side-chains REVERT: A 360 MET cc_start: 0.8590 (ttt) cc_final: 0.8354 (ttm) REVERT: A 375 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7848 (mm-30) REVERT: A 401 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.8051 (m-70) REVERT: B 340 GLU cc_start: 0.7883 (mp0) cc_final: 0.7325 (mp0) REVERT: B 377 PHE cc_start: 0.8508 (t80) cc_final: 0.8295 (t80) REVERT: B 420 ASP cc_start: 0.8203 (m-30) cc_final: 0.7749 (m-30) outliers start: 15 outliers final: 6 residues processed: 151 average time/residue: 0.5783 time to fit residues: 91.6153 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 : 0.297 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 76 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3336 r_free = 0.3336 target = 0.102973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.093362 restraints weight = 9460.356| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.81 r_work: 0.3077 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 6707 Z= 0.224 Angle : 0.654 14.351 9125 Z= 0.324 Chirality : 0.046 0.254 964 Planarity : 0.004 0.046 1174 Dihedral : 5.408 53.973 992 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.32 % Allowed : 14.08 % 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 aren not related in a simple way. whole: 0.01 (0.31), residues: 789 helix: 1.13 (0.29), residues: 371 sheet: 1.47 (0.86), residues: 42 loop : -1.37 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.017 0.002 TYR A 385 PHE 0.014 0.002 PHE A 327 TRP 0.016 0.002 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 6692) covalent geometry : angle 0.64126 ( 9093) SS BOND : bond 0.00852 ( 7) SS BOND : angle 2.41381 ( 14) hydrogen bonds : bond 0.06346 ( 281) hydrogen bonds : angle 4.41007 ( 783) metal coordination : bond 0.00268 ( 2) link_NAG-ASN : bond 0.00558 ( 6) link_NAG-ASN : angle 2.17859 ( 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 153 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.7855 (mp0) cc_final: 0.7294 (mp0) REVERT: B 443 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8235 (p) REVERT: B 452 LEU cc_start: 0.8743 (mp) cc_final: 0.8535 (mt) outliers start: 16 outliers final: 8 residues processed: 144 average time/residue: 0.6091 time to fit residues: 91.9110 Evaluate side-chains 141 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 123 MET 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 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: 0.0470 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.0470 chunk 54 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 chunk 65 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 23 optimal weight: 0.0770 chunk 47 optimal weight: 0.0980 chunk 67 optimal weight: 0.8980 overall best weight: 0.0692 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.108559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.098645 restraints weight = 9732.460| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.87 r_work: 0.3168 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 6707 Z= 0.108 Angle : 0.571 13.473 9125 Z= 0.279 Chirality : 0.041 0.210 964 Planarity : 0.004 0.045 1174 Dihedral : 5.088 55.041 992 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.87 % Allowed : 15.67 % Favored : 83.45 % 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 aren not related in a simple way. whole: 0.45 (0.31), residues: 789 helix: 1.58 (0.29), residues: 365 sheet: 1.64 (0.79), residues: 44 loop : -1.20 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 460 TYR 0.008 0.001 TYR B 351 PHE 0.009 0.001 PHE A 315 TRP 0.016 0.001 TRP A 163 HIS 0.002 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6692) covalent geometry : angle 0.56123 ( 9093) SS BOND : bond 0.00695 ( 7) SS BOND : angle 2.00405 ( 14) hydrogen bonds : bond 0.03439 ( 281) hydrogen bonds : angle 4.14438 ( 783) metal coordination : bond 0.00052 ( 2) link_NAG-ASN : bond 0.00571 ( 6) link_NAG-ASN : angle 1.79408 ( 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 151 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.241 Fit side-chains REVERT: A 50 TYR cc_start: 0.8577 (t80) cc_final: 0.8347 (t80) REVERT: A 375 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7910 (mm-30) REVERT: A 401 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.8022 (m-70) REVERT: B 340 GLU cc_start: 0.7894 (mp0) cc_final: 0.7314 (mp0) REVERT: B 362 VAL cc_start: 0.8434 (m) cc_final: 0.8104 (p) REVERT: B 377 PHE cc_start: 0.8357 (t80) cc_final: 0.8018 (t80) REVERT: B 420 ASP cc_start: 0.8213 (m-30) cc_final: 0.7741 (m-30) REVERT: B 438 SER cc_start: 0.7968 (p) cc_final: 0.7554 (p) outliers start: 6 outliers final: 3 residues processed: 147 average time/residue: 0.5626 time to fit residues: 86.9142 Evaluate side-chains 142 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 401 HIS Chi-restraints excluded: chain B residue 387 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 overall best weight: 0.2758 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.105221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.095132 restraints weight = 9642.544| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.89 r_work: 0.3109 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6707 Z= 0.147 Angle : 0.612 13.588 9125 Z= 0.301 Chirality : 0.043 0.219 964 Planarity : 0.004 0.046 1174 Dihedral : 5.102 53.511 992 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.87 % Allowed : 16.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.31), residues: 789 helix: 1.62 (0.29), residues: 363 sheet: 2.13 (0.95), residues: 34 loop : -1.26 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.014 0.001 TYR A 385 PHE 0.017 0.001 PHE B 374 TRP 0.014 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6692) covalent geometry : angle 0.60084 ( 9093) SS BOND : bond 0.00727 ( 7) SS BOND : angle 2.16700 ( 14) hydrogen bonds : bond 0.04834 ( 281) hydrogen bonds : angle 4.17854 ( 783) metal coordination : bond 0.00121 ( 2) link_NAG-ASN : bond 0.00493 ( 6) link_NAG-ASN : angle 1.90821 ( 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 152 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.271 Fit side-chains REVERT: A 198 ASP cc_start: 0.7266 (p0) cc_final: 0.7047 (p0) REVERT: A 259 THR cc_start: 0.8448 (p) cc_final: 0.8189 (m) REVERT: A 375 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 401 HIS cc_start: 0.8626 (OUTLIER) cc_final: 0.8074 (m-70) REVERT: B 340 GLU cc_start: 0.7894 (mp0) cc_final: 0.7312 (mp0) REVERT: B 377 PHE cc_start: 0.8570 (t80) cc_final: 0.8334 (t80) REVERT: B 438 SER cc_start: 0.8039 (p) cc_final: 0.7634 (p) outliers start: 6 outliers final: 3 residues processed: 147 average time/residue: 0.6073 time to fit residues: 93.6563 Evaluate side-chains 148 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 76 optimal weight: 0.0570 chunk 28 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.103752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.093978 restraints weight = 9483.372| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.83 r_work: 0.3102 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6707 Z= 0.182 Angle : 0.644 13.729 9125 Z= 0.320 Chirality : 0.044 0.230 964 Planarity : 0.004 0.045 1174 Dihedral : 5.249 54.117 992 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.02 % Allowed : 17.13 % Favored : 81.86 % 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 aren not related in a simple way. whole: 0.29 (0.31), residues: 789 helix: 1.48 (0.29), residues: 364 sheet: 2.12 (0.96), residues: 34 loop : -1.30 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.016 0.001 TYR A 385 PHE 0.019 0.001 PHE B 374 TRP 0.016 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 6692) covalent geometry : angle 0.63162 ( 9093) SS BOND : bond 0.00751 ( 7) SS BOND : angle 2.36042 ( 14) hydrogen bonds : bond 0.05614 ( 281) hydrogen bonds : angle 4.29519 ( 783) metal coordination : bond 0.00168 ( 2) link_NAG-ASN : bond 0.00481 ( 6) link_NAG-ASN : angle 2.04301 ( 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 153 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.7891 (mp0) cc_final: 0.7319 (mp0) outliers start: 7 outliers final: 6 residues processed: 148 average time/residue: 0.6038 time to fit residues: 93.5702 Evaluate side-chains 153 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU 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 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 0.0470 chunk 6 optimal weight: 0.0870 chunk 29 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 66 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 overall best weight: 0.2656 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.104995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095107 restraints weight = 9579.318| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.86 r_work: 0.3108 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6707 Z= 0.146 Angle : 0.635 13.561 9125 Z= 0.312 Chirality : 0.043 0.223 964 Planarity : 0.004 0.045 1174 Dihedral : 5.168 53.706 992 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.16 % Allowed : 17.56 % Favored : 81.28 % 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 aren not related in a simple way. whole: 0.34 (0.31), residues: 789 helix: 1.53 (0.29), residues: 365 sheet: 2.07 (0.95), residues: 34 loop : -1.28 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.013 0.001 TYR A 613 PHE 0.019 0.001 PHE B 374 TRP 0.016 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6692) covalent geometry : angle 0.62391 ( 9093) SS BOND : bond 0.00710 ( 7) SS BOND : angle 2.18162 ( 14) hydrogen bonds : bond 0.04827 ( 281) hydrogen bonds : angle 4.24694 ( 783) metal coordination : bond 0.00142 ( 2) link_NAG-ASN : bond 0.00464 ( 6) link_NAG-ASN : angle 1.93740 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2654.44 seconds wall clock time: 45 minutes 58.73 seconds (2758.73 seconds total)