Starting phenix.real_space_refine on Sun Jul 27 08:22:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yv8_34120/07_2025/7yv8_34120.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yv8_34120/07_2025/7yv8_34120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yv8_34120/07_2025/7yv8_34120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yv8_34120/07_2025/7yv8_34120.map" model { file = "/net/cci-nas-00/data/ceres_data/7yv8_34120/07_2025/7yv8_34120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yv8_34120/07_2025/7yv8_34120.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3164 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4163 2.51 5 N 1077 2.21 5 O 1236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6513 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4854 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1574 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 12, 'TRANS': 184} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.26, per 1000 atoms: 0.96 Number of scatterers: 6513 At special positions: 0 Unit cell: (73.92, 102.08, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1236 8.00 N 1077 7.00 C 4163 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 53 " " NAG A 704 " - " ASN A 82 " " NAG A 705 " - " ASN A 432 " " NAG A 706 " - " ASN A 546 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 969.0 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: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.752A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.685A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.520A pdb=" N ALA A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.871A pdb=" N ASP A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.536A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.628A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.990A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.635A pdb=" N MET A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.719A pdb=" N TYR A 255 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.534A pdb=" N GLU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.829A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.738A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.737A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.954A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.546A pdb=" N ASN A 508 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 513 through 532 removed outlier: 4.119A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.657A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.808A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.714A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.550A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.872A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.812A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.964A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.255A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.635A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 281 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 2.05 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: 9.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.640 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.760 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.30), residues: 789 helix: 0.07 (0.29), residues: 368 sheet: 2.02 (0.95), residues: 34 loop : -1.48 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.002 PHE B 377 TYR 0.024 0.002 TYR A 199 ARG 0.005 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 6) link_NAG-ASN : angle 2.36323 ( 18) hydrogen bonds : bond 0.19979 ( 281) hydrogen bonds : angle 6.77916 ( 783) metal coordination : bond 0.19648 ( 2) SS BOND : bond 0.00776 ( 7) SS BOND : angle 2.30373 ( 14) covalent geometry : bond 0.00505 ( 6692) covalent geometry : angle 0.65233 ( 9093) *********************** 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 : 0.705 Fit side-chains REVERT: A 42 GLN cc_start: 0.7959 (mt0) cc_final: 0.7613 (mt0) REVERT: A 190 MET cc_start: 0.7969 (tmm) cc_final: 0.7633 (tmt) REVERT: A 375 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 340 GLU cc_start: 0.6942 (mp0) cc_final: 0.6610 (mp0) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 1.2525 time to fit residues: 198.0988 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 : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094408 restraints weight = 9425.952| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.81 r_work: 0.3096 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6707 Z= 0.178 Angle : 0.631 14.266 9125 Z= 0.315 Chirality : 0.044 0.228 964 Planarity : 0.005 0.044 1174 Dihedral : 6.682 58.726 992 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.16 % Allowed : 8.13 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.31), residues: 789 helix: 0.67 (0.29), residues: 371 sheet: 2.14 (0.93), residues: 34 loop : -1.38 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 512 TYR 0.015 0.001 TYR A 385 ARG 0.003 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 6) link_NAG-ASN : angle 1.92478 ( 18) hydrogen bonds : bond 0.06080 ( 281) hydrogen bonds : angle 4.62563 ( 783) metal coordination : bond 0.00716 ( 2) SS BOND : bond 0.00742 ( 7) SS BOND : angle 2.15083 ( 14) covalent geometry : bond 0.00427 ( 6692) covalent geometry : angle 0.62086 ( 9093) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.759 Fit side-chains REVERT: A 190 MET cc_start: 0.8222 (tmm) cc_final: 0.7980 (tmt) REVERT: A 375 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 408 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7340 (mmm) REVERT: B 340 GLU cc_start: 0.7779 (mp0) cc_final: 0.7361 (mp0) REVERT: B 377 PHE cc_start: 0.8683 (t80) cc_final: 0.8468 (t80) outliers start: 8 outliers final: 4 residues processed: 141 average time/residue: 1.1839 time to fit residues: 175.3903 Evaluate side-chains 138 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 chunk 47 optimal weight: 0.0170 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 38 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.105866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095955 restraints weight = 9546.216| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.84 r_work: 0.3123 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6707 Z= 0.130 Angle : 0.576 12.117 9125 Z= 0.286 Chirality : 0.042 0.210 964 Planarity : 0.004 0.045 1174 Dihedral : 5.495 56.261 992 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.74 % Allowed : 9.29 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.31), residues: 789 helix: 1.03 (0.29), residues: 372 sheet: 2.16 (0.93), residues: 34 loop : -1.30 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.007 0.001 PHE A 327 TYR 0.010 0.001 TYR A 385 ARG 0.003 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 6) link_NAG-ASN : angle 1.90387 ( 18) hydrogen bonds : bond 0.04740 ( 281) hydrogen bonds : angle 4.31355 ( 783) metal coordination : bond 0.00149 ( 2) SS BOND : bond 0.00614 ( 7) SS BOND : angle 1.95415 ( 14) covalent geometry : bond 0.00303 ( 6692) covalent geometry : angle 0.56528 ( 9093) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.718 Fit side-chains REVERT: A 75 GLU cc_start: 0.8105 (tp30) cc_final: 0.7835 (tp30) REVERT: A 190 MET cc_start: 0.8118 (tmm) cc_final: 0.7914 (tmt) REVERT: A 360 MET cc_start: 0.8614 (ttt) cc_final: 0.8353 (ttm) REVERT: A 375 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7863 (mm-30) REVERT: A 401 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8140 (m-70) REVERT: B 340 GLU cc_start: 0.7847 (mp0) cc_final: 0.7382 (mp0) outliers start: 12 outliers final: 4 residues processed: 140 average time/residue: 1.2636 time to fit residues: 185.6166 Evaluate side-chains 132 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 72 optimal weight: 0.0470 chunk 4 optimal weight: 0.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094586 restraints weight = 9560.506| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.82 r_work: 0.3097 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6707 Z= 0.177 Angle : 0.602 13.512 9125 Z= 0.301 Chirality : 0.044 0.238 964 Planarity : 0.004 0.046 1174 Dihedral : 5.479 58.705 992 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.03 % Allowed : 10.60 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.31), residues: 789 helix: 1.10 (0.29), residues: 373 sheet: 2.10 (0.93), residues: 34 loop : -1.31 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.011 0.001 PHE A 327 TYR 0.015 0.001 TYR A 385 ARG 0.003 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 6) link_NAG-ASN : angle 2.00671 ( 18) hydrogen bonds : bond 0.05665 ( 281) hydrogen bonds : angle 4.32771 ( 783) metal coordination : bond 0.00204 ( 2) SS BOND : bond 0.00693 ( 7) SS BOND : angle 2.37252 ( 14) covalent geometry : bond 0.00427 ( 6692) covalent geometry : angle 0.58869 ( 9093) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.639 Fit side-chains REVERT: A 75 GLU cc_start: 0.8045 (tp30) cc_final: 0.7763 (tp30) REVERT: A 190 MET cc_start: 0.8116 (tmm) cc_final: 0.7903 (tmt) REVERT: A 375 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7839 (mm-30) REVERT: A 401 HIS cc_start: 0.8659 (OUTLIER) cc_final: 0.8130 (m-70) REVERT: B 340 GLU cc_start: 0.7852 (mp0) cc_final: 0.7362 (mp0) outliers start: 14 outliers final: 6 residues processed: 143 average time/residue: 1.1893 time to fit residues: 178.6423 Evaluate side-chains 147 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.0470 chunk 13 optimal weight: 0.0980 chunk 69 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 overall best weight: 0.1394 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.107067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097098 restraints weight = 9601.184| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.86 r_work: 0.3143 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6707 Z= 0.110 Angle : 0.561 11.272 9125 Z= 0.275 Chirality : 0.041 0.204 964 Planarity : 0.004 0.046 1174 Dihedral : 5.279 57.425 992 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.74 % Allowed : 12.05 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.31), residues: 789 helix: 1.37 (0.29), residues: 371 sheet: 1.63 (0.80), residues: 44 loop : -1.28 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 540 PHE 0.007 0.001 PHE B 374 TYR 0.008 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 6) link_NAG-ASN : angle 1.82255 ( 18) hydrogen bonds : bond 0.04035 ( 281) hydrogen bonds : angle 4.16041 ( 783) metal coordination : bond 0.00058 ( 2) SS BOND : bond 0.00592 ( 7) SS BOND : angle 1.97475 ( 14) covalent geometry : bond 0.00250 ( 6692) covalent geometry : angle 0.55058 ( 9093) *********************** 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: 12 poor density : 141 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8002 (tp30) cc_final: 0.7775 (tp30) REVERT: A 190 MET cc_start: 0.8052 (tmm) cc_final: 0.7843 (tmt) REVERT: A 360 MET cc_start: 0.8618 (ttt) cc_final: 0.8388 (ttm) REVERT: A 375 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7870 (mm-30) REVERT: A 401 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.8084 (m-70) REVERT: B 340 GLU cc_start: 0.7898 (mp0) cc_final: 0.7371 (mp0) REVERT: B 374 PHE cc_start: 0.8035 (m-10) cc_final: 0.7743 (m-80) REVERT: B 377 PHE cc_start: 0.8459 (t80) cc_final: 0.8091 (t80) REVERT: B 438 SER cc_start: 0.7989 (p) cc_final: 0.7563 (p) outliers start: 12 outliers final: 5 residues processed: 146 average time/residue: 1.1633 time to fit residues: 178.6598 Evaluate side-chains 146 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 387 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 0.0060 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 62 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 71 optimal weight: 0.0970 chunk 64 optimal weight: 0.6980 overall best weight: 0.1932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.096521 restraints weight = 9556.124| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.86 r_work: 0.3131 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1745 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= 0.122 Angle : 0.568 13.547 9125 Z= 0.279 Chirality : 0.041 0.218 964 Planarity : 0.004 0.047 1174 Dihedral : 5.140 55.188 992 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.31 % Allowed : 13.50 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.31), residues: 789 helix: 1.61 (0.29), residues: 364 sheet: 1.62 (0.79), residues: 44 loop : -1.19 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.008 0.001 PHE A 327 TYR 0.010 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 6) link_NAG-ASN : angle 1.82324 ( 18) hydrogen bonds : bond 0.04302 ( 281) hydrogen bonds : angle 4.15502 ( 783) metal coordination : bond 0.00112 ( 2) SS BOND : bond 0.00694 ( 7) SS BOND : angle 1.98705 ( 14) covalent geometry : bond 0.00286 ( 6692) covalent geometry : angle 0.55747 ( 9093) *********************** 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 152 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.736 Fit side-chains REVERT: A 75 GLU cc_start: 0.8012 (tp30) cc_final: 0.7782 (tp30) REVERT: A 360 MET cc_start: 0.8612 (ttt) cc_final: 0.8393 (ttm) REVERT: A 375 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7870 (mm-30) REVERT: A 401 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.8091 (m-70) REVERT: B 340 GLU cc_start: 0.7900 (mp0) cc_final: 0.7347 (mp0) REVERT: B 374 PHE cc_start: 0.8024 (m-10) cc_final: 0.7691 (m-80) REVERT: B 420 ASP cc_start: 0.8194 (m-30) cc_final: 0.7755 (m-30) REVERT: B 438 SER cc_start: 0.8006 (p) cc_final: 0.7562 (p) outliers start: 9 outliers final: 6 residues processed: 147 average time/residue: 1.1727 time to fit residues: 181.6732 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 : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 chunk 66 optimal weight: 0.0040 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.2792 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.105408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.095525 restraints weight = 9524.876| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.86 r_work: 0.3111 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6707 Z= 0.144 Angle : 0.590 13.040 9125 Z= 0.291 Chirality : 0.042 0.221 964 Planarity : 0.004 0.047 1174 Dihedral : 5.170 54.440 992 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.89 % Allowed : 14.08 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.31), residues: 789 helix: 1.59 (0.29), residues: 364 sheet: 2.06 (0.95), residues: 34 loop : -1.21 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.010 0.001 PHE A 327 TYR 0.012 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 6) link_NAG-ASN : angle 1.90458 ( 18) hydrogen bonds : bond 0.04872 ( 281) hydrogen bonds : angle 4.19262 ( 783) metal coordination : bond 0.00151 ( 2) SS BOND : bond 0.00680 ( 7) SS BOND : angle 2.14364 ( 14) covalent geometry : bond 0.00344 ( 6692) covalent geometry : angle 0.57875 ( 9093) *********************** 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 157 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.634 Fit side-chains REVERT: A 75 GLU cc_start: 0.8040 (tp30) cc_final: 0.7795 (tp30) REVERT: A 182 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: A 360 MET cc_start: 0.8641 (ttt) cc_final: 0.8383 (ttm) REVERT: A 375 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 401 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.8096 (m-70) REVERT: B 340 GLU cc_start: 0.7915 (mp0) cc_final: 0.7348 (mp0) REVERT: B 374 PHE cc_start: 0.8045 (m-10) cc_final: 0.7704 (m-80) REVERT: B 420 ASP cc_start: 0.8171 (m-30) cc_final: 0.7739 (m-30) outliers start: 13 outliers final: 6 residues processed: 149 average time/residue: 1.4840 time to fit residues: 233.5818 Evaluate side-chains 148 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 2 optimal weight: 0.0670 chunk 70 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 63 optimal weight: 0.0770 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095138 restraints weight = 9521.843| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.84 r_work: 0.3107 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1679 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= 0.159 Angle : 0.605 12.801 9125 Z= 0.299 Chirality : 0.043 0.227 964 Planarity : 0.004 0.047 1174 Dihedral : 5.206 54.195 992 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.74 % Allowed : 14.37 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.31), residues: 789 helix: 1.60 (0.29), residues: 363 sheet: 2.03 (0.95), residues: 34 loop : -1.26 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.011 0.001 PHE A 315 TYR 0.015 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 6) link_NAG-ASN : angle 1.96173 ( 18) hydrogen bonds : bond 0.05170 ( 281) hydrogen bonds : angle 4.22112 ( 783) metal coordination : bond 0.00174 ( 2) SS BOND : bond 0.00680 ( 7) SS BOND : angle 2.20955 ( 14) covalent geometry : bond 0.00384 ( 6692) covalent geometry : angle 0.59308 ( 9093) *********************** 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: 12 poor density : 139 time to evaluate : 0.668 Fit side-chains REVERT: A 75 GLU cc_start: 0.8041 (tp30) cc_final: 0.7783 (tp30) REVERT: A 182 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7491 (pm20) REVERT: A 259 THR cc_start: 0.8432 (p) cc_final: 0.8189 (m) REVERT: A 360 MET cc_start: 0.8619 (ttt) cc_final: 0.8360 (ttm) REVERT: A 375 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7859 (mm-30) REVERT: A 401 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.8062 (m-70) REVERT: B 340 GLU cc_start: 0.7898 (mp0) cc_final: 0.7335 (mp0) REVERT: B 374 PHE cc_start: 0.8046 (m-10) cc_final: 0.7714 (m-80) outliers start: 12 outliers final: 5 residues processed: 143 average time/residue: 1.1967 time to fit residues: 179.5731 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 : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 0.0000 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 75 optimal weight: 0.0970 chunk 21 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 39 optimal weight: 0.0030 chunk 24 optimal weight: 0.0970 overall best weight: 0.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.108498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.098549 restraints weight = 9667.279| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.87 r_work: 0.3166 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 6707 Z= 0.107 Angle : 0.572 13.617 9125 Z= 0.278 Chirality : 0.041 0.203 964 Planarity : 0.004 0.047 1174 Dihedral : 5.009 54.852 992 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.02 % Allowed : 15.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.31), residues: 789 helix: 1.82 (0.29), residues: 364 sheet: 1.56 (0.78), residues: 44 loop : -1.19 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.002 0.001 HIS A 401 PHE 0.011 0.001 PHE A 315 TYR 0.007 0.001 TYR B 351 ARG 0.001 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 6) link_NAG-ASN : angle 1.74494 ( 18) hydrogen bonds : bond 0.03475 ( 281) hydrogen bonds : angle 4.09842 ( 783) metal coordination : bond 0.00049 ( 2) SS BOND : bond 0.00683 ( 7) SS BOND : angle 1.85244 ( 14) covalent geometry : bond 0.00244 ( 6692) covalent geometry : angle 0.56290 ( 9093) *********************** 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: 7 poor density : 148 time to evaluate : 0.710 Fit side-chains REVERT: A 259 THR cc_start: 0.8379 (p) cc_final: 0.8152 (m) REVERT: A 401 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.8049 (m-70) REVERT: B 340 GLU cc_start: 0.7922 (mp0) cc_final: 0.7391 (mp0) REVERT: B 362 VAL cc_start: 0.8344 (m) cc_final: 0.8018 (p) REVERT: B 374 PHE cc_start: 0.8065 (m-10) cc_final: 0.7830 (m-80) REVERT: B 420 ASP cc_start: 0.8177 (m-30) cc_final: 0.7732 (m-30) REVERT: B 438 SER cc_start: 0.7940 (p) cc_final: 0.7503 (p) outliers start: 7 outliers final: 3 residues processed: 153 average time/residue: 1.1859 time to fit residues: 190.9497 Evaluate side-chains 149 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 145 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 3 optimal weight: 0.4980 chunk 63 optimal weight: 0.0070 chunk 36 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 chunk 76 optimal weight: 0.0980 chunk 74 optimal weight: 0.5980 overall best weight: 0.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.097421 restraints weight = 9692.279| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.87 r_work: 0.3148 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2067 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= 0.117 Angle : 0.585 13.454 9125 Z= 0.287 Chirality : 0.041 0.198 964 Planarity : 0.004 0.047 1174 Dihedral : 4.977 54.070 992 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.02 % Allowed : 16.84 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.31), residues: 789 helix: 1.80 (0.29), residues: 365 sheet: 1.64 (0.79), residues: 44 loop : -1.13 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.003 0.001 HIS A 540 PHE 0.009 0.001 PHE A 315 TYR 0.009 0.001 TYR A 385 ARG 0.001 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 6) link_NAG-ASN : angle 1.79708 ( 18) hydrogen bonds : bond 0.03919 ( 281) hydrogen bonds : angle 4.08596 ( 783) metal coordination : bond 0.00101 ( 2) SS BOND : bond 0.00712 ( 7) SS BOND : angle 1.91069 ( 14) covalent geometry : bond 0.00277 ( 6692) covalent geometry : angle 0.57593 ( 9093) ********************** 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 156 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.867 Fit side-chains REVERT: A 85 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8352 (mt) REVERT: A 129 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7673 (p) REVERT: A 182 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7459 (pm20) REVERT: A 401 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.8082 (m-70) REVERT: A 416 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7720 (mt-10) REVERT: B 340 GLU cc_start: 0.7908 (mp0) cc_final: 0.7378 (mp0) REVERT: B 374 PHE cc_start: 0.8115 (m-10) cc_final: 0.7858 (m-80) REVERT: B 420 ASP cc_start: 0.8198 (m-30) cc_final: 0.7758 (m-30) REVERT: B 438 SER cc_start: 0.7952 (p) cc_final: 0.7519 (p) outliers start: 7 outliers final: 3 residues processed: 152 average time/residue: 1.1823 time to fit residues: 189.3473 Evaluate side-chains 156 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 129 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 47 optimal weight: 0.0270 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 63 optimal weight: 0.0870 chunk 71 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.104862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.094846 restraints weight = 9761.421| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.89 r_work: 0.3104 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1830 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= 0.161 Angle : 0.627 13.781 9125 Z= 0.310 Chirality : 0.043 0.211 964 Planarity : 0.004 0.047 1174 Dihedral : 5.126 53.946 992 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.31), residues: 789 helix: 1.70 (0.29), residues: 362 sheet: 2.14 (0.97), residues: 34 loop : -1.22 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.011 0.001 PHE A 315 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 6) link_NAG-ASN : angle 1.99303 ( 18) hydrogen bonds : bond 0.05110 ( 281) hydrogen bonds : angle 4.21986 ( 783) metal coordination : bond 0.00146 ( 2) SS BOND : bond 0.00756 ( 7) SS BOND : angle 2.15224 ( 14) covalent geometry : bond 0.00389 ( 6692) covalent geometry : angle 0.61634 ( 9093) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6848.31 seconds wall clock time: 120 minutes 40.78 seconds (7240.78 seconds total)