Starting phenix.real_space_refine on Tue Feb 11 19:09:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrl_37779/02_2025/8wrl_37779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrl_37779/02_2025/8wrl_37779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrl_37779/02_2025/8wrl_37779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrl_37779/02_2025/8wrl_37779.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrl_37779/02_2025/8wrl_37779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrl_37779/02_2025/8wrl_37779.cif" } resolution = 3.36 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= 0.001 sd= 0.083 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 4143 2.51 5 N 1070 2.21 5 O 1222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6472 Number of models: 1 Model: "" Number of chains: 4 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: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 13, 'TRANS': 182} 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 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: 4.27, per 1000 atoms: 0.66 Number of scatterers: 6472 At special positions: 0 Unit cell: (74.336, 89.688, 117.968, 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 1222 8.00 N 1070 7.00 C 4143 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=2.03 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 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 53 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 896.3 milliseconds 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: 32 helices and 7 sheets defined 52.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.514A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.090A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 193 removed outlier: 4.289A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.564A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 218 through 252 Proline residue: A 235 - end of helix removed outlier: 4.002A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.961A 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 275 through 281 removed outlier: 3.718A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.765A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.529A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'A' and resid 376 through 385 removed outlier: 3.566A 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 398 through 413 removed outlier: 4.600A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.821A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.601A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.025A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.917A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.821A 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 364 through 371 removed outlier: 3.723A pdb=" N PHE B 371 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.594A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.042A 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 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.809A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.446A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) 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 474 301 hydrogen bonds defined for protein. 843 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: 1.92 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: 1177 1.33 - 1.45: 1839 1.45 - 1.57: 3582 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6656 Sorted by residual: bond pdb=" CG HIS A 378 " pdb=" CD2 HIS A 378 " ideal model delta sigma weight residual 1.354 1.318 0.036 1.10e-02 8.26e+03 1.05e+01 bond pdb=" N THR A 371 " pdb=" CA THR A 371 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 7.00e+00 bond pdb=" CA ALA A 372 " pdb=" CB ALA A 372 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.68e-02 3.54e+03 6.84e+00 bond pdb=" CG HIS A 373 " pdb=" CD2 HIS A 373 " ideal model delta sigma weight residual 1.354 1.326 0.028 1.10e-02 8.26e+03 6.49e+00 bond pdb=" N GLU A 375 " pdb=" CA GLU A 375 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.41e+00 ... (remaining 6651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 8925 2.58 - 5.15: 96 5.15 - 7.73: 21 7.73 - 10.31: 2 10.31 - 12.88: 2 Bond angle restraints: 9046 Sorted by residual: angle pdb=" N MET A 376 " pdb=" CA MET A 376 " pdb=" C MET A 376 " ideal model delta sigma weight residual 114.31 101.82 12.49 1.29e+00 6.01e-01 9.37e+01 angle pdb=" C HIS A 378 " pdb=" N ILE A 379 " pdb=" CA ILE A 379 " ideal model delta sigma weight residual 121.02 108.14 12.88 1.51e+00 4.39e-01 7.28e+01 angle pdb=" CA HIS A 373 " pdb=" CB HIS A 373 " pdb=" CG HIS A 373 " ideal model delta sigma weight residual 113.80 121.23 -7.43 1.00e+00 1.00e+00 5.52e+01 angle pdb=" N GLU A 375 " pdb=" CA GLU A 375 " pdb=" C GLU A 375 " ideal model delta sigma weight residual 112.88 104.91 7.97 1.29e+00 6.01e-01 3.82e+01 angle pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " pdb=" CG HIS A 378 " ideal model delta sigma weight residual 113.80 118.66 -4.86 1.00e+00 1.00e+00 2.36e+01 ... (remaining 9041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 3448 21.10 - 42.19: 432 42.19 - 63.29: 82 63.29 - 84.39: 17 84.39 - 105.49: 18 Dihedral angle restraints: 3997 sinusoidal: 1677 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 22.41 70.59 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -45.95 -40.05 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA TRP A 349 " pdb=" C TRP A 349 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 3994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 724 0.046 - 0.091: 171 0.091 - 0.137: 56 0.137 - 0.182: 6 0.182 - 0.227: 2 Chirality restraints: 959 Sorted by residual: chirality pdb=" CA GLU A 375 " pdb=" N GLU A 375 " pdb=" C GLU A 375 " pdb=" CB GLU A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB THR A 122 " pdb=" CA THR A 122 " pdb=" OG1 THR A 122 " pdb=" CG2 THR A 122 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA MET A 376 " pdb=" N MET A 376 " pdb=" C MET A 376 " pdb=" CB MET A 376 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.22e-01 ... (remaining 956 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 370 " -0.019 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C LEU A 370 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU A 370 " -0.022 2.00e-02 2.50e+03 pdb=" N THR A 371 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 478 " 0.052 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO B 479 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 378 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C HIS A 378 " -0.044 2.00e-02 2.50e+03 pdb=" O HIS A 378 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 379 " 0.015 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 22 2.40 - 3.02: 3617 3.02 - 3.65: 9842 3.65 - 4.27: 14297 4.27 - 4.90: 24817 Nonbonded interactions: 52595 Sorted by model distance: nonbonded pdb=" OH TYR A 279 " pdb=" O LYS A 441 " model vdw 1.771 3.040 nonbonded pdb=" CB PRO A 346 " pdb=" SD MET A 360 " model vdw 1.931 3.800 nonbonded pdb=" O ALA A 372 " pdb=" CG MET A 376 " model vdw 2.076 3.440 nonbonded pdb=" CD1 ILE A 358 " pdb=" SD MET A 376 " model vdw 2.152 3.820 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.229 3.040 ... (remaining 52590 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: 0.670 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.460 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 0.065 6656 Z= 0.275 Angle : 0.699 12.884 9046 Z= 0.410 Chirality : 0.045 0.227 959 Planarity : 0.005 0.076 1166 Dihedral : 19.509 105.486 2489 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.58 % Allowed : 23.34 % Favored : 76.08 % 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 (0.30), residues: 786 helix: 0.69 (0.27), residues: 365 sheet: -0.64 (0.76), residues: 35 loop : -0.96 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 594 HIS 0.013 0.001 HIS A 373 PHE 0.009 0.001 PHE A 32 TYR 0.030 0.002 TYR A 243 ARG 0.003 0.000 ARG B 454 *********************** 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 85 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.746 Fit side-chains REVERT: A 442 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7571 (mm-40) REVERT: A 483 GLU cc_start: 0.7827 (mp0) cc_final: 0.7485 (mp0) outliers start: 4 outliers final: 3 residues processed: 84 average time/residue: 0.1685 time to fit residues: 19.9657 Evaluate side-chains 77 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.196984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.149773 restraints weight = 6717.097| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.12 r_work: 0.3237 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6656 Z= 0.215 Angle : 0.539 8.028 9046 Z= 0.272 Chirality : 0.042 0.182 959 Planarity : 0.004 0.038 1166 Dihedral : 8.575 59.333 965 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.88 % Allowed : 21.76 % 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 (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: 0.03 (0.31), residues: 786 helix: 0.93 (0.28), residues: 377 sheet: -0.45 (0.79), residues: 35 loop : -0.86 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.005 0.001 HIS A 378 PHE 0.012 0.001 PHE A 32 TYR 0.015 0.001 TYR A 41 ARG 0.002 0.000 ARG A 393 *********************** 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 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.587 Fit side-chains REVERT: A 35 GLU cc_start: 0.8040 (tp30) cc_final: 0.7825 (tp30) REVERT: A 87 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 299 ASP cc_start: 0.6980 (m-30) cc_final: 0.6604 (m-30) REVERT: A 544 ILE cc_start: 0.5874 (OUTLIER) cc_final: 0.5519 (mt) outliers start: 20 outliers final: 10 residues processed: 96 average time/residue: 0.1739 time to fit residues: 22.8181 Evaluate side-chains 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE 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 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 62 optimal weight: 0.0010 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.199490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.151823 restraints weight = 6834.349| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.08 r_work: 0.3292 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6656 Z= 0.145 Angle : 0.494 6.200 9046 Z= 0.247 Chirality : 0.040 0.244 959 Planarity : 0.003 0.030 1166 Dihedral : 5.642 57.726 963 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.03 % Allowed : 21.61 % 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 (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: 0.15 (0.31), residues: 786 helix: 1.09 (0.28), residues: 385 sheet: -0.13 (0.79), residues: 35 loop : -0.94 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS A 493 PHE 0.007 0.001 PHE A 327 TYR 0.011 0.001 TYR A 41 ARG 0.002 0.000 ARG B 457 *********************** 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 113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.641 Fit side-chains REVERT: A 35 GLU cc_start: 0.8018 (tp30) cc_final: 0.7748 (tp30) REVERT: A 37 GLU cc_start: 0.8019 (tt0) cc_final: 0.7817 (mt-10) REVERT: A 87 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7145 (tm-30) REVERT: A 297 MET cc_start: 0.6941 (tpp) cc_final: 0.6721 (mmt) REVERT: A 299 ASP cc_start: 0.7062 (m-30) cc_final: 0.6734 (m-30) REVERT: A 398 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: A 544 ILE cc_start: 0.5844 (OUTLIER) cc_final: 0.5454 (mt) outliers start: 21 outliers final: 11 residues processed: 103 average time/residue: 0.1618 time to fit residues: 23.1531 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 : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 0.0070 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.197791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.150554 restraints weight = 6891.273| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.11 r_work: 0.3257 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6656 Z= 0.171 Angle : 0.492 5.427 9046 Z= 0.248 Chirality : 0.040 0.203 959 Planarity : 0.003 0.029 1166 Dihedral : 5.062 47.304 963 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.75 % Allowed : 20.75 % 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 (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: 0.37 (0.31), residues: 786 helix: 1.32 (0.28), residues: 377 sheet: -0.14 (0.80), residues: 35 loop : -0.82 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 566 HIS 0.003 0.001 HIS A 34 PHE 0.009 0.001 PHE A 523 TYR 0.012 0.001 TYR A 41 ARG 0.001 0.000 ARG B 457 *********************** 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 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.554 Fit side-chains REVERT: A 35 GLU cc_start: 0.8046 (tp30) cc_final: 0.7753 (tp30) REVERT: A 37 GLU cc_start: 0.8082 (tt0) cc_final: 0.7878 (mt-10) REVERT: A 87 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7144 (tm-30) REVERT: A 97 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7796 (mt) REVERT: A 299 ASP cc_start: 0.7088 (m-30) cc_final: 0.6802 (m-30) REVERT: A 398 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: A 544 ILE cc_start: 0.5945 (OUTLIER) cc_final: 0.5593 (mt) outliers start: 26 outliers final: 17 residues processed: 100 average time/residue: 0.1483 time to fit residues: 21.0478 Evaluate side-chains 100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE 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 64 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 45 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.198397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.151018 restraints weight = 6822.727| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.14 r_work: 0.3265 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6656 Z= 0.182 Angle : 0.491 5.889 9046 Z= 0.248 Chirality : 0.041 0.211 959 Planarity : 0.003 0.029 1166 Dihedral : 4.739 43.949 963 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.60 % Allowed : 21.18 % Favored : 75.22 % 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: 786 helix: 1.35 (0.28), residues: 377 sheet: -0.07 (0.82), residues: 35 loop : -0.78 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 566 HIS 0.003 0.001 HIS A 34 PHE 0.008 0.001 PHE A 523 TYR 0.012 0.001 TYR A 41 ARG 0.001 0.000 ARG B 454 *********************** 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 112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.680 Fit side-chains REVERT: A 35 GLU cc_start: 0.7995 (tp30) cc_final: 0.7698 (tp30) REVERT: A 37 GLU cc_start: 0.8044 (tt0) cc_final: 0.7769 (mt-10) REVERT: A 87 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7155 (tm-30) REVERT: A 97 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7644 (mt) REVERT: A 297 MET cc_start: 0.6848 (tpp) cc_final: 0.6618 (tpp) REVERT: A 299 ASP cc_start: 0.7108 (m-30) cc_final: 0.6905 (m-30) REVERT: A 398 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: A 483 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7742 (mp0) REVERT: A 544 ILE cc_start: 0.5887 (OUTLIER) cc_final: 0.5528 (mt) outliers start: 25 outliers final: 16 residues processed: 102 average time/residue: 0.1557 time to fit residues: 22.5313 Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.192775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.131121 restraints weight = 6821.243| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.35 r_work: 0.3287 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6656 Z= 0.321 Angle : 0.563 5.469 9046 Z= 0.292 Chirality : 0.044 0.238 959 Planarity : 0.004 0.033 1166 Dihedral : 5.052 45.346 963 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.32 % Allowed : 21.04 % Favored : 74.64 % 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: 0.19 (0.31), residues: 786 helix: 1.02 (0.27), residues: 383 sheet: -0.43 (0.79), residues: 35 loop : -0.73 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 271 HIS 0.005 0.001 HIS A 34 PHE 0.013 0.001 PHE A 32 TYR 0.016 0.002 TYR A 381 ARG 0.002 0.000 ARG B 454 *********************** 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 114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.645 Fit side-chains REVERT: A 35 GLU cc_start: 0.8145 (tp30) cc_final: 0.7888 (tp30) REVERT: A 37 GLU cc_start: 0.8274 (tt0) cc_final: 0.7919 (mt-10) REVERT: A 87 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 150 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6966 (pp20) REVERT: A 299 ASP cc_start: 0.7141 (m-30) cc_final: 0.6935 (m-30) REVERT: A 398 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: A 467 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6996 (mt-10) REVERT: A 483 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7921 (mm-30) REVERT: A 544 ILE cc_start: 0.6187 (OUTLIER) cc_final: 0.5833 (mt) REVERT: B 378 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7644 (mmtm) REVERT: B 472 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7700 (tt) outliers start: 30 outliers final: 21 residues processed: 106 average time/residue: 0.1391 time to fit residues: 21.4790 Evaluate side-chains 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 472 ILE 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 71 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 37 optimal weight: 0.0770 chunk 61 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.197545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.150225 restraints weight = 6719.772| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.17 r_work: 0.3281 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6656 Z= 0.164 Angle : 0.494 6.748 9046 Z= 0.253 Chirality : 0.040 0.222 959 Planarity : 0.003 0.029 1166 Dihedral : 4.636 43.412 963 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.60 % Allowed : 21.90 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.31), residues: 786 helix: 1.30 (0.28), residues: 379 sheet: -0.24 (0.79), residues: 35 loop : -0.75 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 271 HIS 0.003 0.001 HIS A 34 PHE 0.013 0.001 PHE B 374 TYR 0.038 0.001 TYR A 237 ARG 0.001 0.000 ARG A 204 *********************** 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 112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.696 Fit side-chains REVERT: A 35 GLU cc_start: 0.7975 (tp30) cc_final: 0.7727 (tp30) REVERT: A 37 GLU cc_start: 0.8025 (tt0) cc_final: 0.7782 (mt-10) REVERT: A 87 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 150 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: A 297 MET cc_start: 0.6952 (tpp) cc_final: 0.6625 (tpp) REVERT: A 398 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7741 (pm20) REVERT: A 483 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7690 (mp0) REVERT: A 544 ILE cc_start: 0.5891 (OUTLIER) cc_final: 0.5532 (mt) REVERT: B 378 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7444 (mmtm) outliers start: 25 outliers final: 15 residues processed: 106 average time/residue: 0.1466 time to fit residues: 22.5733 Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE 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 14 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 0.0060 chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 31 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.200408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.153029 restraints weight = 6771.816| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.18 r_work: 0.3308 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6656 Z= 0.145 Angle : 0.489 7.129 9046 Z= 0.249 Chirality : 0.040 0.216 959 Planarity : 0.003 0.029 1166 Dihedral : 4.438 40.386 963 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.88 % Allowed : 22.77 % 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 (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: 786 helix: 1.38 (0.28), residues: 379 sheet: -0.65 (0.79), residues: 40 loop : -0.64 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 271 HIS 0.003 0.001 HIS A 493 PHE 0.033 0.001 PHE B 374 TYR 0.015 0.001 TYR A 237 ARG 0.001 0.000 ARG A 177 *********************** 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 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.674 Fit side-chains REVERT: A 35 GLU cc_start: 0.7942 (tp30) cc_final: 0.7659 (tp30) REVERT: A 37 GLU cc_start: 0.7964 (tt0) cc_final: 0.7752 (mt-10) REVERT: A 87 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7154 (tm-30) REVERT: A 150 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: A 398 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: A 467 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: A 474 MET cc_start: 0.5545 (mmp) cc_final: 0.4296 (tpp) REVERT: A 483 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7782 (mp0) REVERT: A 544 ILE cc_start: 0.5902 (OUTLIER) cc_final: 0.5556 (mt) REVERT: B 378 LYS cc_start: 0.7670 (mmtt) cc_final: 0.7242 (mmtm) outliers start: 20 outliers final: 15 residues processed: 98 average time/residue: 0.1540 time to fit residues: 21.5853 Evaluate side-chains 99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.193756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.146715 restraints weight = 6915.329| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.05 r_work: 0.3200 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 6656 Z= 0.349 Angle : 0.580 6.765 9046 Z= 0.299 Chirality : 0.044 0.252 959 Planarity : 0.004 0.029 1166 Dihedral : 4.962 44.304 963 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.46 % Allowed : 22.05 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.31), residues: 786 helix: 1.05 (0.28), residues: 385 sheet: -1.17 (0.67), residues: 50 loop : -0.60 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 566 HIS 0.006 0.001 HIS A 34 PHE 0.036 0.002 PHE B 374 TYR 0.016 0.002 TYR B 453 ARG 0.003 0.000 ARG B 457 *********************** 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 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.661 Fit side-chains REVERT: A 35 GLU cc_start: 0.8114 (tp30) cc_final: 0.7803 (tp30) REVERT: A 37 GLU cc_start: 0.8192 (tt0) cc_final: 0.7903 (mt-10) REVERT: A 87 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7151 (tm-30) REVERT: A 150 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6984 (pp20) REVERT: A 398 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: A 455 MET cc_start: 0.7177 (ttp) cc_final: 0.6969 (ttp) REVERT: A 467 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6994 (mt-10) REVERT: A 483 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 544 ILE cc_start: 0.6115 (OUTLIER) cc_final: 0.5752 (mt) REVERT: B 378 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7635 (mmtm) outliers start: 24 outliers final: 18 residues processed: 104 average time/residue: 0.1469 time to fit residues: 21.8624 Evaluate side-chains 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.198804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.152285 restraints weight = 6815.165| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.14 r_work: 0.3263 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 0.065 6656 Z= 0.181 Angle : 0.514 7.157 9046 Z= 0.263 Chirality : 0.041 0.236 959 Planarity : 0.003 0.030 1166 Dihedral : 4.639 42.935 963 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.17 % Allowed : 22.48 % 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 (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: 0.34 (0.31), residues: 786 helix: 1.25 (0.28), residues: 379 sheet: -0.87 (0.76), residues: 40 loop : -0.70 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 271 HIS 0.003 0.001 HIS A 493 PHE 0.026 0.001 PHE B 374 TYR 0.026 0.001 TYR A 237 ARG 0.003 0.000 ARG B 457 ********************** 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 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.675 Fit side-chains REVERT: A 35 GLU cc_start: 0.7985 (tp30) cc_final: 0.7778 (tp30) REVERT: A 37 GLU cc_start: 0.8035 (tt0) cc_final: 0.7814 (mt-10) REVERT: A 87 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7170 (tm-30) REVERT: A 150 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: A 398 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: A 467 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6940 (mt-10) REVERT: A 483 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7778 (mp0) REVERT: A 544 ILE cc_start: 0.5953 (OUTLIER) cc_final: 0.5606 (mt) REVERT: B 378 LYS cc_start: 0.7770 (mmtt) cc_final: 0.7363 (mmtm) outliers start: 22 outliers final: 16 residues processed: 102 average time/residue: 0.1559 time to fit residues: 22.6155 Evaluate side-chains 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 45 optimal weight: 0.0050 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.197403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150245 restraints weight = 6935.292| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.13 r_work: 0.3273 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6656 Z= 0.180 Angle : 0.509 6.320 9046 Z= 0.260 Chirality : 0.041 0.233 959 Planarity : 0.003 0.030 1166 Dihedral : 4.512 41.429 963 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.60 % Allowed : 22.33 % Favored : 74.06 % 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: 0.40 (0.31), residues: 786 helix: 1.28 (0.28), residues: 379 sheet: -0.72 (0.77), residues: 40 loop : -0.67 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.003 0.001 HIS A 34 PHE 0.030 0.001 PHE B 374 TYR 0.015 0.001 TYR A 237 ARG 0.003 0.000 ARG B 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3185.12 seconds wall clock time: 57 minutes 25.08 seconds (3445.08 seconds total)