Starting phenix.real_space_refine on Fri Aug 22 17:39:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrh_37776/08_2025/8wrh_37776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrh_37776/08_2025/8wrh_37776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrh_37776/08_2025/8wrh_37776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrh_37776/08_2025/8wrh_37776.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrh_37776/08_2025/8wrh_37776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrh_37776/08_2025/8wrh_37776.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4137 2.51 5 N 1069 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s 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: 6459 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Chain: "B" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1558 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 14, 'TRANS': 181} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.47, per 1000 atoms: 0.23 Number of scatterers: 6459 At special positions: 0 Unit cell: (71.912, 89.688, 117.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1216 8.00 N 1069 7.00 C 4137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 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 901 " - " ASN A 546 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 322 " " NAG A 904 " - " ASN A 53 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 315.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 54.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.620A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.568A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.517A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.871A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 Proline residue: A 235 - end of helix removed outlier: 3.794A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) 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 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.837A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.504A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.672A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.547A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.141A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.570A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.774A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.723A 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 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.655A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.554A pdb=" N PHE B 371 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.669A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.537A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.571A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.527A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.757A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.406A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 448 through 454 removed outlier: 8.338A pdb=" N ASN B 450 " --> pdb=" O SER B 494 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N SER B 494 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU B 452 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LEU B 492 " --> pdb=" O LEU B 452 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 858 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: 0.87 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1257 1.33 - 1.45: 1774 1.45 - 1.57: 3555 1.57 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6644 Sorted by residual: bond pdb=" N TYR B 489 " pdb=" CA TYR B 489 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" CA ALA A 80 " pdb=" CB ALA A 80 " ideal model delta sigma weight residual 1.534 1.483 0.050 1.58e-02 4.01e+03 1.02e+01 bond pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.19e-02 7.06e+03 8.06e+00 bond pdb=" CA TYR B 489 " pdb=" C TYR B 489 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.34e-02 5.57e+03 7.11e+00 bond pdb=" N PRO B 486 " pdb=" CA PRO B 486 " ideal model delta sigma weight residual 1.473 1.440 0.033 1.32e-02 5.74e+03 6.22e+00 ... (remaining 6639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 8929 2.62 - 5.24: 87 5.24 - 7.86: 13 7.86 - 10.48: 1 10.48 - 13.10: 1 Bond angle restraints: 9031 Sorted by residual: angle pdb=" N TYR B 489 " pdb=" CA TYR B 489 " pdb=" CB TYR B 489 " ideal model delta sigma weight residual 110.49 123.59 -13.10 1.69e+00 3.50e-01 6.01e+01 angle pdb=" CA PHE B 455 " pdb=" CB PHE B 455 " pdb=" CG PHE B 455 " ideal model delta sigma weight residual 113.80 121.46 -7.66 1.00e+00 1.00e+00 5.87e+01 angle pdb=" N ALA A 80 " pdb=" CA ALA A 80 " pdb=" C ALA A 80 " ideal model delta sigma weight residual 113.50 105.68 7.82 1.23e+00 6.61e-01 4.04e+01 angle pdb=" N LEU A 79 " pdb=" CA LEU A 79 " pdb=" C LEU A 79 " ideal model delta sigma weight residual 113.30 106.59 6.71 1.34e+00 5.57e-01 2.50e+01 angle pdb=" N VAL B 483 " pdb=" CA VAL B 483 " pdb=" C VAL B 483 " ideal model delta sigma weight residual 109.34 119.45 -10.11 2.08e+00 2.31e-01 2.36e+01 ... (remaining 9026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.80: 3457 20.80 - 41.59: 394 41.59 - 62.39: 103 62.39 - 83.18: 13 83.18 - 103.98: 11 Dihedral angle restraints: 3978 sinusoidal: 1658 harmonic: 2320 Sorted by residual: 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 93.00 141.28 -48.28 1 1.00e+01 1.00e-02 3.21e+01 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 44.98 48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 153.39 26.61 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 3975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 749 0.050 - 0.099: 164 0.099 - 0.149: 36 0.149 - 0.198: 2 0.198 - 0.248: 3 Chirality restraints: 954 Sorted by residual: chirality pdb=" CA CYS B 488 " pdb=" N CYS B 488 " pdb=" C CYS B 488 " pdb=" CB CYS B 488 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA TYR B 489 " pdb=" N TYR B 489 " pdb=" C TYR B 489 " pdb=" CB TYR B 489 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA LEU A 79 " pdb=" N LEU A 79 " pdb=" C LEU A 79 " pdb=" CB LEU A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 951 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 482 " 0.023 2.00e-02 2.50e+03 4.54e-02 2.07e+01 pdb=" C GLY B 482 " -0.079 2.00e-02 2.50e+03 pdb=" O GLY B 482 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL B 483 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 483 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C VAL B 483 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL B 483 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 484 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 455 " 0.019 2.00e-02 2.50e+03 1.73e-02 5.25e+00 pdb=" CG PHE B 455 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 455 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 455 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 455 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 455 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 455 " 0.004 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 172 2.70 - 3.25: 6326 3.25 - 3.80: 10667 3.80 - 4.35: 13447 4.35 - 4.90: 22970 Nonbonded interactions: 53582 Sorted by model distance: nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.151 3.040 nonbonded pdb=" O ASP A 499 " pdb=" OG SER A 502 " model vdw 2.172 3.040 nonbonded pdb=" OE1 GLN A 102 " pdb=" OH TYR A 202 " model vdw 2.193 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.210 3.120 nonbonded pdb=" OG SER B 438 " pdb=" OD2 ASP B 442 " model vdw 2.216 3.040 ... (remaining 53577 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.770 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.004 0.050 6654 Z= 0.209 Angle : 0.678 13.100 9055 Z= 0.375 Chirality : 0.045 0.248 954 Planarity : 0.004 0.045 1166 Dihedral : 18.702 103.977 2470 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.83 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 24.64 % Favored : 75.36 % Cbeta Deviations : 0.13 % 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: 0.28 (0.30), residues: 786 helix: 1.21 (0.26), residues: 396 sheet: 0.89 (0.81), residues: 44 loop : -1.13 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.021 0.002 TYR A 279 PHE 0.040 0.002 PHE B 455 TRP 0.012 0.001 TRP A 168 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 6644) covalent geometry : angle 0.67571 ( 9031) SS BOND : bond 0.00437 ( 6) SS BOND : angle 0.91632 ( 12) hydrogen bonds : bond 0.12653 ( 302) hydrogen bonds : angle 5.87823 ( 858) link_NAG-ASN : bond 0.00112 ( 4) link_NAG-ASN : angle 1.43160 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8023 (mtp) cc_final: 0.7782 (mtp) REVERT: A 478 TRP cc_start: 0.6722 (m100) cc_final: 0.6478 (m100) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0518 time to fit residues: 6.3334 Evaluate side-chains 83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.187144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146359 restraints weight = 7376.645| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.19 r_work: 0.3459 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6654 Z= 0.132 Angle : 0.551 7.261 9055 Z= 0.274 Chirality : 0.043 0.192 954 Planarity : 0.004 0.043 1166 Dihedral : 7.306 59.922 940 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 1.59 % Allowed : 23.05 % Favored : 75.36 % 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: 0.40 (0.30), residues: 786 helix: 1.42 (0.26), residues: 396 sheet: 0.94 (0.78), residues: 44 loop : -1.23 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.012 0.001 TYR A 385 PHE 0.015 0.001 PHE B 455 TRP 0.010 0.001 TRP A 477 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6644) covalent geometry : angle 0.54706 ( 9031) SS BOND : bond 0.00389 ( 6) SS BOND : angle 1.10312 ( 12) hydrogen bonds : bond 0.04125 ( 302) hydrogen bonds : angle 4.70586 ( 858) link_NAG-ASN : bond 0.00144 ( 4) link_NAG-ASN : angle 1.67704 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.7476 (m-80) cc_final: 0.7129 (m-80) REVERT: A 347 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8624 (p) REVERT: A 360 MET cc_start: 0.6915 (ptm) cc_final: 0.6612 (ptm) REVERT: A 364 VAL cc_start: 0.7790 (t) cc_final: 0.7481 (t) REVERT: A 435 GLU cc_start: 0.6829 (pt0) cc_final: 0.6617 (pt0) REVERT: A 544 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.7067 (mt) REVERT: B 500 THR cc_start: 0.8610 (p) cc_final: 0.8363 (p) outliers start: 11 outliers final: 6 residues processed: 95 average time/residue: 0.0680 time to fit residues: 8.9188 Evaluate side-chains 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 338 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 31 optimal weight: 0.0370 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.186421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145292 restraints weight = 7332.735| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.22 r_work: 0.3457 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6654 Z= 0.122 Angle : 0.532 7.076 9055 Z= 0.263 Chirality : 0.041 0.150 954 Planarity : 0.004 0.042 1166 Dihedral : 5.054 32.184 940 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.87 % Allowed : 22.62 % Favored : 75.50 % 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: 0.47 (0.30), residues: 786 helix: 1.50 (0.26), residues: 396 sheet: 0.88 (0.77), residues: 44 loop : -1.21 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 306 TYR 0.018 0.001 TYR A 279 PHE 0.013 0.001 PHE B 455 TRP 0.008 0.001 TRP A 477 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6644) covalent geometry : angle 0.52515 ( 9031) SS BOND : bond 0.00312 ( 6) SS BOND : angle 1.04456 ( 12) hydrogen bonds : bond 0.03989 ( 302) hydrogen bonds : angle 4.51493 ( 858) link_NAG-ASN : bond 0.00094 ( 4) link_NAG-ASN : angle 2.17103 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8598 (p) REVERT: A 360 MET cc_start: 0.6942 (ptm) cc_final: 0.6649 (ptm) REVERT: A 364 VAL cc_start: 0.7842 (t) cc_final: 0.7521 (t) REVERT: A 544 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.7133 (mt) REVERT: B 493 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: B 500 THR cc_start: 0.8587 (p) cc_final: 0.8307 (p) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 0.0514 time to fit residues: 7.0067 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 493 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 0.0060 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.185750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146158 restraints weight = 7405.006| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.06 r_work: 0.3500 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6654 Z= 0.110 Angle : 0.506 7.193 9055 Z= 0.251 Chirality : 0.041 0.143 954 Planarity : 0.004 0.043 1166 Dihedral : 4.482 26.808 940 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.87 % Allowed : 22.62 % Favored : 75.50 % 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: 0.57 (0.30), residues: 786 helix: 1.68 (0.26), residues: 391 sheet: 0.84 (0.77), residues: 44 loop : -1.23 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.010 0.001 TYR A 385 PHE 0.011 0.001 PHE B 455 TRP 0.008 0.001 TRP A 477 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6644) covalent geometry : angle 0.49978 ( 9031) SS BOND : bond 0.00321 ( 6) SS BOND : angle 0.83396 ( 12) hydrogen bonds : bond 0.03776 ( 302) hydrogen bonds : angle 4.41280 ( 858) link_NAG-ASN : bond 0.00174 ( 4) link_NAG-ASN : angle 2.07428 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8039 (mtp) cc_final: 0.7699 (mtp) REVERT: A 225 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.6540 (m-30) REVERT: A 347 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8702 (p) REVERT: A 360 MET cc_start: 0.6950 (ptm) cc_final: 0.6676 (ptm) REVERT: A 364 VAL cc_start: 0.7927 (t) cc_final: 0.7569 (t) REVERT: A 467 GLU cc_start: 0.4351 (OUTLIER) cc_final: 0.3894 (pm20) REVERT: A 544 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7235 (mt) REVERT: B 338 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7813 (t80) REVERT: B 500 THR cc_start: 0.8613 (p) cc_final: 0.8328 (p) outliers start: 13 outliers final: 6 residues processed: 98 average time/residue: 0.0552 time to fit residues: 7.9458 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 338 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 0.1980 chunk 19 optimal weight: 0.0060 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.0370 chunk 59 optimal weight: 0.0970 chunk 72 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 overall best weight: 0.1472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.194784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154133 restraints weight = 7395.398| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.17 r_work: 0.3611 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6654 Z= 0.095 Angle : 0.481 6.961 9055 Z= 0.239 Chirality : 0.039 0.142 954 Planarity : 0.003 0.042 1166 Dihedral : 3.897 21.588 940 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.30 % Allowed : 23.92 % Favored : 74.78 % 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: 0.83 (0.30), residues: 786 helix: 2.04 (0.27), residues: 379 sheet: 0.62 (0.76), residues: 46 loop : -1.14 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.021 0.001 TYR A 279 PHE 0.008 0.001 PHE A 327 TRP 0.010 0.001 TRP A 478 HIS 0.002 0.000 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 6644) covalent geometry : angle 0.47583 ( 9031) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.68991 ( 12) hydrogen bonds : bond 0.03420 ( 302) hydrogen bonds : angle 4.21437 ( 858) link_NAG-ASN : bond 0.00152 ( 4) link_NAG-ASN : angle 1.89457 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 347 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8611 (p) REVERT: A 360 MET cc_start: 0.6698 (ptm) cc_final: 0.6430 (ptm) REVERT: A 364 VAL cc_start: 0.7890 (t) cc_final: 0.7491 (t) REVERT: B 338 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7973 (t80) REVERT: B 493 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8042 (tt0) outliers start: 9 outliers final: 4 residues processed: 104 average time/residue: 0.0567 time to fit residues: 8.4115 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 493 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.0070 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 0.0070 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.192412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152946 restraints weight = 7347.367| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.16 r_work: 0.3586 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6654 Z= 0.110 Angle : 0.488 7.016 9055 Z= 0.245 Chirality : 0.040 0.136 954 Planarity : 0.003 0.042 1166 Dihedral : 3.872 20.359 940 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.16 % Allowed : 22.91 % Favored : 74.93 % 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: 0.92 (0.30), residues: 786 helix: 2.06 (0.27), residues: 383 sheet: 0.77 (0.77), residues: 44 loop : -1.07 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.011 0.001 TYR A 385 PHE 0.008 0.001 PHE A 230 TRP 0.009 0.001 TRP A 477 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6644) covalent geometry : angle 0.48418 ( 9031) SS BOND : bond 0.00256 ( 6) SS BOND : angle 0.78294 ( 12) hydrogen bonds : bond 0.03643 ( 302) hydrogen bonds : angle 4.25893 ( 858) link_NAG-ASN : bond 0.00126 ( 4) link_NAG-ASN : angle 1.68970 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 347 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8717 (p) REVERT: A 360 MET cc_start: 0.6904 (ptm) cc_final: 0.6633 (ptm) REVERT: A 364 VAL cc_start: 0.8007 (t) cc_final: 0.7631 (t) REVERT: B 338 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7953 (t80) outliers start: 15 outliers final: 5 residues processed: 99 average time/residue: 0.0605 time to fit residues: 8.5591 Evaluate side-chains 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 0.0170 chunk 19 optimal weight: 0.4980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.190508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151456 restraints weight = 7304.350| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.09 r_work: 0.3561 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6654 Z= 0.112 Angle : 0.495 7.085 9055 Z= 0.247 Chirality : 0.041 0.135 954 Planarity : 0.003 0.041 1166 Dihedral : 3.875 20.366 940 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.87 % Allowed : 22.33 % Favored : 75.79 % 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: 0.91 (0.30), residues: 786 helix: 2.02 (0.27), residues: 382 sheet: 0.78 (0.78), residues: 44 loop : -1.03 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.021 0.001 TYR A 279 PHE 0.008 0.001 PHE B 429 TRP 0.010 0.001 TRP A 566 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6644) covalent geometry : angle 0.49139 ( 9031) SS BOND : bond 0.00266 ( 6) SS BOND : angle 0.80718 ( 12) hydrogen bonds : bond 0.03675 ( 302) hydrogen bonds : angle 4.32156 ( 858) link_NAG-ASN : bond 0.00155 ( 4) link_NAG-ASN : angle 1.63142 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7984 (mtp) cc_final: 0.7641 (mtp) REVERT: A 347 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8634 (p) REVERT: A 360 MET cc_start: 0.6978 (ptm) cc_final: 0.6684 (ptm) REVERT: A 364 VAL cc_start: 0.7947 (t) cc_final: 0.7569 (t) REVERT: A 467 GLU cc_start: 0.4039 (OUTLIER) cc_final: 0.2869 (pt0) REVERT: A 510 TYR cc_start: 0.8342 (m-80) cc_final: 0.8071 (m-80) REVERT: B 338 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7904 (t80) REVERT: B 503 VAL cc_start: 0.8790 (t) cc_final: 0.8581 (t) outliers start: 13 outliers final: 8 residues processed: 95 average time/residue: 0.0685 time to fit residues: 9.2810 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.0170 chunk 58 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.189712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149454 restraints weight = 7298.618| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.22 r_work: 0.3548 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6654 Z= 0.127 Angle : 0.518 7.198 9055 Z= 0.259 Chirality : 0.041 0.161 954 Planarity : 0.003 0.042 1166 Dihedral : 3.965 21.262 940 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.73 % Allowed : 22.48 % Favored : 75.79 % 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: 786 helix: 1.98 (0.27), residues: 382 sheet: 0.75 (0.77), residues: 44 loop : -1.01 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.013 0.001 TYR A 385 PHE 0.009 0.001 PHE A 32 TRP 0.010 0.001 TRP A 566 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6644) covalent geometry : angle 0.51409 ( 9031) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.89485 ( 12) hydrogen bonds : bond 0.03865 ( 302) hydrogen bonds : angle 4.37512 ( 858) link_NAG-ASN : bond 0.00084 ( 4) link_NAG-ASN : angle 1.59475 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8712 (p) REVERT: A 467 GLU cc_start: 0.4379 (OUTLIER) cc_final: 0.3209 (pt0) REVERT: B 338 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7773 (t80) REVERT: B 466 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.4741 (ttm170) REVERT: B 503 VAL cc_start: 0.8844 (t) cc_final: 0.8634 (t) outliers start: 12 outliers final: 8 residues processed: 96 average time/residue: 0.0579 time to fit residues: 7.8827 Evaluate side-chains 100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 466 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.180773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139546 restraints weight = 7515.811| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.29 r_work: 0.3394 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 6654 Z= 0.190 Angle : 0.586 7.653 9055 Z= 0.295 Chirality : 0.044 0.168 954 Planarity : 0.004 0.042 1166 Dihedral : 4.459 24.391 940 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.87 % Allowed : 23.20 % Favored : 74.93 % 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: 0.60 (0.30), residues: 786 helix: 1.61 (0.27), residues: 388 sheet: 0.67 (0.75), residues: 42 loop : -1.03 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 192 TYR 0.022 0.002 TYR A 279 PHE 0.013 0.002 PHE A 230 TRP 0.012 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 6644) covalent geometry : angle 0.58185 ( 9031) SS BOND : bond 0.00437 ( 6) SS BOND : angle 1.26550 ( 12) hydrogen bonds : bond 0.04549 ( 302) hydrogen bonds : angle 4.62025 ( 858) link_NAG-ASN : bond 0.00147 ( 4) link_NAG-ASN : angle 1.77130 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7988 (mtp) cc_final: 0.7679 (mtp) REVERT: A 347 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8542 (p) REVERT: A 360 MET cc_start: 0.7116 (ptm) cc_final: 0.6843 (ptm) REVERT: A 467 GLU cc_start: 0.4377 (OUTLIER) cc_final: 0.3385 (pt0) REVERT: B 466 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.4633 (ttm170) outliers start: 13 outliers final: 7 residues processed: 97 average time/residue: 0.0641 time to fit residues: 8.5540 Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 466 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 55 optimal weight: 0.0770 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 0.0870 chunk 46 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.183919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143883 restraints weight = 7353.122| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.15 r_work: 0.3451 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6654 Z= 0.118 Angle : 0.547 9.229 9055 Z= 0.269 Chirality : 0.042 0.158 954 Planarity : 0.004 0.042 1166 Dihedral : 4.125 22.685 940 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.44 % Allowed : 24.21 % Favored : 74.35 % 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: 0.72 (0.30), residues: 786 helix: 1.86 (0.27), residues: 382 sheet: 0.59 (0.76), residues: 44 loop : -1.10 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.020 0.001 TYR A 279 PHE 0.009 0.001 PHE B 429 TRP 0.015 0.001 TRP A 168 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6644) covalent geometry : angle 0.54269 ( 9031) SS BOND : bond 0.00315 ( 6) SS BOND : angle 1.03551 ( 12) hydrogen bonds : bond 0.03872 ( 302) hydrogen bonds : angle 4.46068 ( 858) link_NAG-ASN : bond 0.00106 ( 4) link_NAG-ASN : angle 1.64651 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7970 (mtp) cc_final: 0.7633 (mtp) REVERT: A 166 GLU cc_start: 0.7642 (tp30) cc_final: 0.6804 (tp30) REVERT: A 279 TYR cc_start: 0.7066 (t80) cc_final: 0.6847 (t80) REVERT: A 347 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8620 (p) REVERT: A 360 MET cc_start: 0.7079 (ptm) cc_final: 0.6786 (ptm) REVERT: A 467 GLU cc_start: 0.4430 (OUTLIER) cc_final: 0.3565 (pt0) REVERT: B 508 TYR cc_start: 0.8835 (m-80) cc_final: 0.8417 (m-80) outliers start: 10 outliers final: 6 residues processed: 96 average time/residue: 0.0600 time to fit residues: 8.2561 Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 19 optimal weight: 0.0670 chunk 32 optimal weight: 0.0020 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.0270 chunk 23 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.3184 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.185806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145752 restraints weight = 7347.168| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.16 r_work: 0.3477 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6654 Z= 0.106 Angle : 0.527 8.695 9055 Z= 0.258 Chirality : 0.041 0.142 954 Planarity : 0.004 0.043 1166 Dihedral : 3.902 21.087 940 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.01 % Allowed : 23.92 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.82 (0.30), residues: 786 helix: 1.93 (0.27), residues: 382 sheet: 0.61 (0.75), residues: 44 loop : -1.04 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.020 0.001 TYR A 279 PHE 0.008 0.001 PHE A 327 TRP 0.014 0.001 TRP A 168 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6644) covalent geometry : angle 0.52303 ( 9031) SS BOND : bond 0.00281 ( 6) SS BOND : angle 0.94403 ( 12) hydrogen bonds : bond 0.03681 ( 302) hydrogen bonds : angle 4.34553 ( 858) link_NAG-ASN : bond 0.00095 ( 4) link_NAG-ASN : angle 1.61732 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1693.72 seconds wall clock time: 29 minutes 39.63 seconds (1779.63 seconds total)