Starting phenix.real_space_refine on Sat May 10 13:22:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbq_39907/05_2025/8zbq_39907_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbq_39907/05_2025/8zbq_39907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zbq_39907/05_2025/8zbq_39907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbq_39907/05_2025/8zbq_39907.map" model { file = "/net/cci-nas-00/data/ceres_data/8zbq_39907/05_2025/8zbq_39907_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbq_39907/05_2025/8zbq_39907_neut.cif" } resolution = 3.03 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= 0.002 sd= 0.081 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 36 5.16 5 C 4072 2.51 5 N 1052 2.21 5 O 1186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6346 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1476 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 11, 'TRANS': 170} Time building chain proxies: 4.88, per 1000 atoms: 0.77 Number of scatterers: 6346 At special positions: 0 Unit cell: (75.9, 97.9, 105.6, 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 36 16.00 O 1186 8.00 N 1052 7.00 C 4072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.05 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.04 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.01 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 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 894.3 milliseconds 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1470 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 53.5% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 24 through 53 Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.514A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 165 through 171 Processing helix chain 'D' and resid 172 through 193 Proline residue: D 178 - end of helix removed outlier: 3.616A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 247 removed outlier: 3.748A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 292 through 296 removed outlier: 4.113A pdb=" N ASP D 295 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 318 removed outlier: 3.978A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 3.726A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 414 Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.072A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 421' Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.737A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.542A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.226A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 550 through 559 removed outlier: 3.706A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASN D 556 " --> pdb=" O GLN D 552 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 6.071A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'F' and resid 340 through 344 removed outlier: 3.604A pdb=" N ALA F 344 " --> pdb=" O VAL F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 371 Processing helix chain 'F' and resid 403 through 407 removed outlier: 3.509A pdb=" N VAL F 407 " --> pdb=" O GLY F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.805A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'F' and resid 354 through 358 removed outlier: 4.755A pdb=" N ILE F 434 " --> pdb=" O VAL F 511 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 452 through 454 280 hydrogen bonds defined for protein. 753 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: 1.97 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1060 1.31 - 1.44: 1921 1.44 - 1.58: 3494 1.58 - 1.72: 0 1.72 - 1.86: 57 Bond restraints: 6532 Sorted by residual: bond pdb=" CA ALA F 348 " pdb=" C ALA F 348 " ideal model delta sigma weight residual 1.527 1.419 0.108 1.35e-02 5.49e+03 6.35e+01 bond pdb=" CA LYS F 478 " pdb=" C LYS F 478 " ideal model delta sigma weight residual 1.523 1.424 0.099 1.31e-02 5.83e+03 5.67e+01 bond pdb=" C ASP F 442 " pdb=" O ASP F 442 " ideal model delta sigma weight residual 1.232 1.171 0.061 1.01e-02 9.80e+03 3.61e+01 bond pdb=" N GLU D 110 " pdb=" CA GLU D 110 " ideal model delta sigma weight residual 1.457 1.519 -0.062 1.17e-02 7.31e+03 2.77e+01 bond pdb=" C LYS F 478 " pdb=" O LYS F 478 " ideal model delta sigma weight residual 1.241 1.184 0.057 1.14e-02 7.69e+03 2.50e+01 ... (remaining 6527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 8587 2.25 - 4.51: 224 4.51 - 6.76: 46 6.76 - 9.02: 11 9.02 - 11.27: 7 Bond angle restraints: 8875 Sorted by residual: angle pdb=" C LYS F 478 " pdb=" CA LYS F 478 " pdb=" CB LYS F 478 " ideal model delta sigma weight residual 110.33 101.27 9.06 1.02e+00 9.61e-01 7.88e+01 angle pdb=" N ASN F 477 " pdb=" CA ASN F 477 " pdb=" C ASN F 477 " ideal model delta sigma weight residual 112.41 123.68 -11.27 1.30e+00 5.92e-01 7.52e+01 angle pdb=" N PRO F 499 " pdb=" CA PRO F 499 " pdb=" C PRO F 499 " ideal model delta sigma weight residual 113.98 103.70 10.28 1.29e+00 6.01e-01 6.35e+01 angle pdb=" N VAL D 298 " pdb=" CA VAL D 298 " pdb=" C VAL D 298 " ideal model delta sigma weight residual 113.71 106.57 7.14 9.50e-01 1.11e+00 5.66e+01 angle pdb=" N TYR D 158 " pdb=" CA TYR D 158 " pdb=" C TYR D 158 " ideal model delta sigma weight residual 114.04 105.17 8.87 1.24e+00 6.50e-01 5.12e+01 ... (remaining 8870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3367 17.97 - 35.95: 365 35.95 - 53.92: 79 53.92 - 71.90: 27 71.90 - 89.87: 11 Dihedral angle restraints: 3849 sinusoidal: 1559 harmonic: 2290 Sorted by residual: dihedral pdb=" CB CYS F 336 " pdb=" SG CYS F 336 " pdb=" SG CYS F 361 " pdb=" CB CYS F 361 " ideal model delta sinusoidal sigma weight residual 93.00 22.87 70.13 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 40.22 52.78 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" C LYS F 478 " pdb=" N LYS F 478 " pdb=" CA LYS F 478 " pdb=" CB LYS F 478 " ideal model delta harmonic sigma weight residual -122.60 -107.54 -15.06 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 3846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 743 0.055 - 0.109: 144 0.109 - 0.164: 23 0.164 - 0.218: 6 0.218 - 0.273: 2 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA GLU D 110 " pdb=" N GLU D 110 " pdb=" C GLU D 110 " pdb=" CB GLU D 110 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA LYS D 234 " pdb=" N LYS D 234 " pdb=" C LYS D 234 " pdb=" CB LYS D 234 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ASP D 111 " pdb=" N ASP D 111 " pdb=" C ASP D 111 " pdb=" CB ASP D 111 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 915 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 476 " -0.021 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C GLY F 476 " 0.075 2.00e-02 2.50e+03 pdb=" O GLY F 476 " -0.029 2.00e-02 2.50e+03 pdb=" N ASN F 477 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG F 498 " -0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO F 499 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO F 499 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 499 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 233 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C ILE D 233 " -0.056 2.00e-02 2.50e+03 pdb=" O ILE D 233 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS D 234 " 0.019 2.00e-02 2.50e+03 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1774 2.79 - 3.32: 6510 3.32 - 3.84: 11877 3.84 - 4.37: 14524 4.37 - 4.90: 23235 Nonbonded interactions: 57920 Sorted by model distance: nonbonded pdb=" O PHE D 327 " pdb=" OG SER D 331 " model vdw 2.261 3.040 nonbonded pdb=" OE2 GLU D 527 " pdb=" NE2 GLN D 531 " model vdw 2.273 3.120 nonbonded pdb=" O SER D 47 " pdb=" ND2 ASN D 51 " model vdw 2.292 3.120 nonbonded pdb=" NH2 ARG F 454 " pdb=" O ASP F 467 " model vdw 2.298 3.120 nonbonded pdb=" NH1 ARG D 482 " pdb=" O THR D 608 " model vdw 2.300 3.120 ... (remaining 57915 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: 2.920 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 6538 Z= 0.376 Angle : 0.923 11.273 8887 Z= 0.585 Chirality : 0.048 0.273 918 Planarity : 0.006 0.082 1150 Dihedral : 16.508 89.870 2361 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 6.41 % Allowed : 3.50 % Favored : 90.09 % Cbeta Deviations : 0.27 % 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: -2.05 (0.30), residues: 775 helix: -0.65 (0.28), residues: 351 sheet: -1.62 (0.82), residues: 39 loop : -2.01 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 353 HIS 0.008 0.002 HIS D 378 PHE 0.022 0.002 PHE F 375 TYR 0.021 0.001 TYR D 381 ARG 0.002 0.000 ARG D 482 Details of bonding type rmsd hydrogen bonds : bond 0.19583 ( 280) hydrogen bonds : angle 7.56001 ( 753) SS BOND : bond 0.01246 ( 6) SS BOND : angle 2.38743 ( 12) covalent geometry : bond 0.00560 ( 6532) covalent geometry : angle 0.91905 ( 8875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.690 Fit side-chains REVERT: D 63 ASN cc_start: 0.7280 (m110) cc_final: 0.6760 (m110) REVERT: D 111 ASP cc_start: 0.7840 (p0) cc_final: 0.7497 (p0) REVERT: D 189 GLU cc_start: 0.7186 (mp0) cc_final: 0.6461 (mp0) REVERT: F 500 THR cc_start: 0.6869 (OUTLIER) cc_final: 0.6573 (t) outliers start: 44 outliers final: 6 residues processed: 165 average time/residue: 0.1960 time to fit residues: 41.7340 Evaluate side-chains 111 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 ASN D 175 GLN D 378 HIS F 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.163230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132478 restraints weight = 7387.608| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.41 r_work: 0.3307 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6538 Z= 0.200 Angle : 0.648 6.248 8887 Z= 0.348 Chirality : 0.046 0.162 918 Planarity : 0.005 0.053 1150 Dihedral : 6.376 53.232 858 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 3.50 % Allowed : 11.37 % Favored : 85.13 % 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: -1.66 (0.30), residues: 775 helix: -0.56 (0.26), residues: 364 sheet: -1.48 (0.87), residues: 36 loop : -1.56 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 302 HIS 0.006 0.001 HIS D 374 PHE 0.020 0.002 PHE D 523 TYR 0.027 0.002 TYR D 385 ARG 0.007 0.001 ARG F 454 Details of bonding type rmsd hydrogen bonds : bond 0.05330 ( 280) hydrogen bonds : angle 5.39794 ( 753) SS BOND : bond 0.00573 ( 6) SS BOND : angle 1.07152 ( 12) covalent geometry : bond 0.00453 ( 6532) covalent geometry : angle 0.64752 ( 8875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.708 Fit side-chains REVERT: D 62 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7281 (ttt) REVERT: D 63 ASN cc_start: 0.7377 (m110) cc_final: 0.6758 (m110) REVERT: D 120 LEU cc_start: 0.8754 (mt) cc_final: 0.8550 (mt) REVERT: D 228 HIS cc_start: 0.8021 (m170) cc_final: 0.7758 (m-70) REVERT: D 306 ARG cc_start: 0.7470 (ttt180) cc_final: 0.7147 (ttt180) REVERT: D 307 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7936 (mt) REVERT: D 483 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8247 (pp20) REVERT: F 346 ARG cc_start: 0.5604 (OUTLIER) cc_final: 0.4884 (tmm160) outliers start: 24 outliers final: 12 residues processed: 121 average time/residue: 0.1991 time to fit residues: 31.6218 Evaluate side-chains 118 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 501 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 64 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 ASN D 345 HIS D 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.161250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.130226 restraints weight = 7520.623| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.45 r_work: 0.3288 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6538 Z= 0.154 Angle : 0.588 5.947 8887 Z= 0.311 Chirality : 0.043 0.143 918 Planarity : 0.005 0.052 1150 Dihedral : 5.634 45.104 850 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.50 % Allowed : 13.99 % Favored : 82.51 % 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: -1.35 (0.30), residues: 775 helix: -0.25 (0.27), residues: 357 sheet: -1.58 (0.86), residues: 36 loop : -1.42 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.018 0.001 PHE D 523 TYR 0.022 0.001 TYR D 385 ARG 0.004 0.000 ARG F 454 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 280) hydrogen bonds : angle 5.08679 ( 753) SS BOND : bond 0.00433 ( 6) SS BOND : angle 1.19063 ( 12) covalent geometry : bond 0.00347 ( 6532) covalent geometry : angle 0.58630 ( 8875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7541 (mm-30) REVERT: D 62 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7123 (ttt) REVERT: D 63 ASN cc_start: 0.7294 (m110) cc_final: 0.6742 (m110) REVERT: D 306 ARG cc_start: 0.7458 (ttt180) cc_final: 0.7051 (ttt180) REVERT: D 307 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7927 (mt) REVERT: D 323 MET cc_start: 0.8083 (mmm) cc_final: 0.7792 (mmt) REVERT: D 472 GLN cc_start: 0.8635 (mt0) cc_final: 0.8410 (mt0) REVERT: D 474 MET cc_start: 0.8884 (mmp) cc_final: 0.8643 (mmp) REVERT: D 483 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8252 (pp20) REVERT: D 518 ARG cc_start: 0.8311 (tmm160) cc_final: 0.8072 (tmm160) outliers start: 24 outliers final: 16 residues processed: 128 average time/residue: 0.1726 time to fit residues: 29.6232 Evaluate side-chains 122 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 501 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 340 GLN D 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.159356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127446 restraints weight = 7547.295| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.52 r_work: 0.3221 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6538 Z= 0.187 Angle : 0.607 6.002 8887 Z= 0.320 Chirality : 0.045 0.143 918 Planarity : 0.004 0.051 1150 Dihedral : 5.644 45.554 850 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 3.94 % Allowed : 15.89 % Favored : 80.17 % 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: -1.34 (0.30), residues: 775 helix: -0.28 (0.27), residues: 362 sheet: -1.44 (0.87), residues: 36 loop : -1.39 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.021 0.002 PHE D 523 TYR 0.022 0.002 TYR D 385 ARG 0.004 0.001 ARG F 454 Details of bonding type rmsd hydrogen bonds : bond 0.04895 ( 280) hydrogen bonds : angle 4.98217 ( 753) SS BOND : bond 0.00514 ( 6) SS BOND : angle 1.00742 ( 12) covalent geometry : bond 0.00431 ( 6532) covalent geometry : angle 0.60583 ( 8875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7376 (m110) cc_final: 0.6836 (m110) REVERT: D 81 GLN cc_start: 0.7686 (mm110) cc_final: 0.7465 (mm-40) REVERT: D 302 TRP cc_start: 0.8558 (m-10) cc_final: 0.8335 (m-10) REVERT: D 306 ARG cc_start: 0.7395 (ttt180) cc_final: 0.6948 (ttt180) REVERT: D 307 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7974 (mt) REVERT: D 472 GLN cc_start: 0.8746 (mt0) cc_final: 0.8518 (mt0) REVERT: D 474 MET cc_start: 0.9055 (mmp) cc_final: 0.8466 (mmp) REVERT: D 483 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8255 (pp20) REVERT: D 518 ARG cc_start: 0.8415 (tmm160) cc_final: 0.8160 (tmm160) REVERT: D 531 GLN cc_start: 0.8160 (mt0) cc_final: 0.7850 (mt0) REVERT: F 346 ARG cc_start: 0.5382 (OUTLIER) cc_final: 0.3426 (tmm160) REVERT: F 439 ASN cc_start: 0.8341 (t0) cc_final: 0.7947 (t0) outliers start: 27 outliers final: 19 residues processed: 127 average time/residue: 0.1775 time to fit residues: 29.9592 Evaluate side-chains 126 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 75 optimal weight: 0.0670 chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 54 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 overall best weight: 0.3096 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.161025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.130293 restraints weight = 7458.591| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.44 r_work: 0.3293 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6538 Z= 0.127 Angle : 0.548 6.909 8887 Z= 0.289 Chirality : 0.042 0.140 918 Planarity : 0.004 0.051 1150 Dihedral : 5.473 45.849 850 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.37 % Allowed : 15.60 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.30), residues: 775 helix: 0.00 (0.28), residues: 357 sheet: -1.37 (0.85), residues: 38 loop : -1.47 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 353 HIS 0.006 0.001 HIS D 374 PHE 0.018 0.001 PHE D 523 TYR 0.019 0.001 TYR D 385 ARG 0.003 0.000 ARG D 482 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 280) hydrogen bonds : angle 4.82047 ( 753) SS BOND : bond 0.00636 ( 6) SS BOND : angle 1.31227 ( 12) covalent geometry : bond 0.00282 ( 6532) covalent geometry : angle 0.54591 ( 8875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7546 (mm-30) REVERT: D 63 ASN cc_start: 0.7395 (m110) cc_final: 0.6809 (m110) REVERT: D 189 GLU cc_start: 0.7495 (mp0) cc_final: 0.6922 (mt-10) REVERT: D 302 TRP cc_start: 0.8446 (m-10) cc_final: 0.8226 (m-10) REVERT: D 306 ARG cc_start: 0.7453 (ttt180) cc_final: 0.6956 (ttt180) REVERT: D 307 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7958 (mt) REVERT: D 472 GLN cc_start: 0.8741 (mt0) cc_final: 0.8521 (mt0) REVERT: D 474 MET cc_start: 0.8982 (mmp) cc_final: 0.8382 (mmp) REVERT: D 483 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8196 (pp20) REVERT: D 531 GLN cc_start: 0.8057 (mt0) cc_final: 0.7817 (mt0) REVERT: D 578 ASN cc_start: 0.7200 (t0) cc_final: 0.6895 (p0) REVERT: F 346 ARG cc_start: 0.5410 (OUTLIER) cc_final: 0.3529 (tmm160) REVERT: F 439 ASN cc_start: 0.8221 (t0) cc_final: 0.7861 (t0) outliers start: 30 outliers final: 23 residues processed: 136 average time/residue: 0.1746 time to fit residues: 32.2592 Evaluate side-chains 130 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 527 GLU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.0170 chunk 57 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.0060 chunk 62 optimal weight: 10.0000 chunk 58 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 0.0270 chunk 56 optimal weight: 0.7980 overall best weight: 0.2292 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.163164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132706 restraints weight = 7400.117| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.44 r_work: 0.3322 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6538 Z= 0.117 Angle : 0.533 6.460 8887 Z= 0.280 Chirality : 0.041 0.134 918 Planarity : 0.004 0.052 1150 Dihedral : 5.298 46.069 850 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.79 % Allowed : 17.20 % Favored : 79.01 % 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: -0.96 (0.30), residues: 775 helix: 0.28 (0.28), residues: 344 sheet: -1.73 (0.71), residues: 48 loop : -1.33 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 353 HIS 0.006 0.001 HIS D 374 PHE 0.017 0.001 PHE D 523 TYR 0.011 0.001 TYR D 385 ARG 0.004 0.000 ARG D 582 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 280) hydrogen bonds : angle 4.64198 ( 753) SS BOND : bond 0.00520 ( 6) SS BOND : angle 1.02840 ( 12) covalent geometry : bond 0.00256 ( 6532) covalent geometry : angle 0.53160 ( 8875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7558 (mm-30) REVERT: D 63 ASN cc_start: 0.7292 (m110) cc_final: 0.6742 (m110) REVERT: D 150 GLU cc_start: 0.7586 (mp0) cc_final: 0.7124 (mp0) REVERT: D 189 GLU cc_start: 0.7533 (mp0) cc_final: 0.6992 (tt0) REVERT: D 306 ARG cc_start: 0.7468 (ttt180) cc_final: 0.6965 (ttt180) REVERT: D 307 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7993 (mt) REVERT: D 472 GLN cc_start: 0.8705 (mt0) cc_final: 0.8474 (mt0) REVERT: D 474 MET cc_start: 0.9018 (mmp) cc_final: 0.8385 (mmp) REVERT: D 483 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8108 (pp20) REVERT: D 578 ASN cc_start: 0.7071 (t0) cc_final: 0.6670 (p0) REVERT: F 346 ARG cc_start: 0.5429 (OUTLIER) cc_final: 0.3608 (tmm160) REVERT: F 439 ASN cc_start: 0.8243 (t0) cc_final: 0.7866 (t0) outliers start: 26 outliers final: 22 residues processed: 135 average time/residue: 0.1667 time to fit residues: 30.7509 Evaluate side-chains 130 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 527 GLU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.157307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.125831 restraints weight = 7498.762| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.47 r_work: 0.3247 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6538 Z= 0.173 Angle : 0.577 6.173 8887 Z= 0.304 Chirality : 0.043 0.138 918 Planarity : 0.004 0.053 1150 Dihedral : 5.462 47.473 850 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.81 % Allowed : 16.76 % Favored : 78.43 % 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: -1.10 (0.30), residues: 775 helix: 0.05 (0.28), residues: 351 sheet: -1.02 (0.85), residues: 38 loop : -1.42 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.019 0.002 PHE D 523 TYR 0.013 0.002 TYR D 497 ARG 0.003 0.000 ARG D 482 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 280) hydrogen bonds : angle 4.74788 ( 753) SS BOND : bond 0.00551 ( 6) SS BOND : angle 1.06473 ( 12) covalent geometry : bond 0.00397 ( 6532) covalent geometry : angle 0.57592 ( 8875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7548 (mm-30) REVERT: D 63 ASN cc_start: 0.7370 (m110) cc_final: 0.6766 (m110) REVERT: D 232 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: D 306 ARG cc_start: 0.7366 (ttt180) cc_final: 0.6970 (ttt180) REVERT: D 307 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7955 (mt) REVERT: D 472 GLN cc_start: 0.8735 (mt0) cc_final: 0.8532 (mt0) REVERT: D 474 MET cc_start: 0.9043 (mmp) cc_final: 0.8732 (mmp) REVERT: D 483 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8188 (pp20) REVERT: D 531 GLN cc_start: 0.8043 (mt0) cc_final: 0.7827 (mt0) REVERT: F 346 ARG cc_start: 0.5566 (OUTLIER) cc_final: 0.3815 (tmm160) REVERT: F 439 ASN cc_start: 0.8322 (t0) cc_final: 0.7935 (t0) outliers start: 33 outliers final: 28 residues processed: 135 average time/residue: 0.1605 time to fit residues: 29.4631 Evaluate side-chains 140 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 527 GLU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.159564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.129018 restraints weight = 7464.275| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.44 r_work: 0.3254 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6538 Z= 0.161 Angle : 0.569 6.408 8887 Z= 0.301 Chirality : 0.043 0.137 918 Planarity : 0.004 0.053 1150 Dihedral : 5.447 47.520 850 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.10 % Allowed : 16.76 % Favored : 78.13 % 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: -1.09 (0.30), residues: 775 helix: 0.01 (0.28), residues: 352 sheet: -1.45 (0.72), residues: 48 loop : -1.30 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 302 HIS 0.006 0.001 HIS D 374 PHE 0.023 0.002 PHE F 371 TYR 0.027 0.001 TYR D 497 ARG 0.005 0.001 ARG D 582 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 280) hydrogen bonds : angle 4.75006 ( 753) SS BOND : bond 0.00500 ( 6) SS BOND : angle 0.98004 ( 12) covalent geometry : bond 0.00367 ( 6532) covalent geometry : angle 0.56802 ( 8875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7436 (m110) cc_final: 0.6837 (m110) REVERT: D 150 GLU cc_start: 0.7820 (mp0) cc_final: 0.7405 (mp0) REVERT: D 189 GLU cc_start: 0.7384 (mp0) cc_final: 0.7004 (tt0) REVERT: D 270 MET cc_start: 0.8917 (tpp) cc_final: 0.8148 (tpp) REVERT: D 307 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7935 (mt) REVERT: D 472 GLN cc_start: 0.8782 (mt0) cc_final: 0.8562 (mt0) REVERT: D 474 MET cc_start: 0.9024 (mmp) cc_final: 0.8545 (mmp) REVERT: D 483 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: D 531 GLN cc_start: 0.8035 (mt0) cc_final: 0.7815 (mt0) REVERT: F 439 ASN cc_start: 0.8375 (t0) cc_final: 0.7977 (t0) outliers start: 35 outliers final: 29 residues processed: 127 average time/residue: 0.1572 time to fit residues: 27.3085 Evaluate side-chains 133 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 527 GLU Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 0.0060 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.155627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.124353 restraints weight = 7514.503| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.46 r_work: 0.3241 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6538 Z= 0.181 Angle : 0.595 6.581 8887 Z= 0.315 Chirality : 0.044 0.167 918 Planarity : 0.005 0.053 1150 Dihedral : 5.537 47.864 850 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.52 % Allowed : 17.35 % Favored : 78.13 % 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: -1.09 (0.30), residues: 775 helix: 0.00 (0.28), residues: 351 sheet: -1.25 (0.75), residues: 48 loop : -1.30 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.020 0.002 PHE D 523 TYR 0.024 0.002 TYR D 497 ARG 0.005 0.001 ARG D 192 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 280) hydrogen bonds : angle 4.79766 ( 753) SS BOND : bond 0.00729 ( 6) SS BOND : angle 1.53607 ( 12) covalent geometry : bond 0.00418 ( 6532) covalent geometry : angle 0.59306 ( 8875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8250 (tt) REVERT: D 35 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7597 (mm-30) REVERT: D 63 ASN cc_start: 0.7435 (m110) cc_final: 0.6841 (m110) REVERT: D 307 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7957 (mt) REVERT: D 472 GLN cc_start: 0.8784 (mt0) cc_final: 0.8483 (mt0) REVERT: D 474 MET cc_start: 0.9038 (mmp) cc_final: 0.8686 (mmp) REVERT: D 499 ASP cc_start: 0.8476 (m-30) cc_final: 0.8246 (m-30) REVERT: D 531 GLN cc_start: 0.8093 (mt0) cc_final: 0.7838 (mt0) REVERT: D 578 ASN cc_start: 0.7431 (t0) cc_final: 0.7040 (p0) REVERT: F 439 ASN cc_start: 0.8396 (t0) cc_final: 0.8006 (t0) outliers start: 31 outliers final: 29 residues processed: 125 average time/residue: 0.1602 time to fit residues: 27.4756 Evaluate side-chains 131 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 527 GLU Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.157100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.126202 restraints weight = 7505.148| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.46 r_work: 0.3247 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6538 Z= 0.173 Angle : 0.588 6.281 8887 Z= 0.311 Chirality : 0.044 0.164 918 Planarity : 0.005 0.053 1150 Dihedral : 5.538 48.095 850 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.10 % Allowed : 16.76 % Favored : 78.13 % 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: -1.01 (0.30), residues: 775 helix: 0.12 (0.28), residues: 344 sheet: -1.26 (0.76), residues: 48 loop : -1.30 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.020 0.002 PHE D 523 TYR 0.021 0.002 TYR D 497 ARG 0.005 0.001 ARG D 582 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 280) hydrogen bonds : angle 4.77727 ( 753) SS BOND : bond 0.00762 ( 6) SS BOND : angle 1.47390 ( 12) covalent geometry : bond 0.00398 ( 6532) covalent geometry : angle 0.58542 ( 8875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8230 (tt) REVERT: D 35 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7587 (mm-30) REVERT: D 63 ASN cc_start: 0.7433 (m110) cc_final: 0.6845 (m110) REVERT: D 171 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7730 (mm-30) REVERT: D 307 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7909 (mt) REVERT: D 472 GLN cc_start: 0.8853 (mt0) cc_final: 0.8580 (mt0) REVERT: D 474 MET cc_start: 0.9029 (mmp) cc_final: 0.8499 (mmp) REVERT: D 499 ASP cc_start: 0.8460 (m-30) cc_final: 0.8204 (m-30) REVERT: D 531 GLN cc_start: 0.8090 (mt0) cc_final: 0.7841 (mt0) REVERT: F 439 ASN cc_start: 0.8409 (t0) cc_final: 0.8014 (t0) outliers start: 35 outliers final: 31 residues processed: 130 average time/residue: 0.1625 time to fit residues: 28.9678 Evaluate side-chains 138 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 527 GLU Chi-restraints excluded: chain D residue 549 GLU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 0.0980 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.159299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127799 restraints weight = 7634.578| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.54 r_work: 0.3262 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6538 Z= 0.141 Angle : 0.562 6.227 8887 Z= 0.298 Chirality : 0.043 0.150 918 Planarity : 0.004 0.053 1150 Dihedral : 5.430 48.204 850 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.96 % Allowed : 17.06 % Favored : 77.99 % 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: -0.91 (0.30), residues: 775 helix: 0.25 (0.28), residues: 343 sheet: -1.27 (0.76), residues: 48 loop : -1.28 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.020 0.002 PHE D 523 TYR 0.019 0.001 TYR D 497 ARG 0.006 0.001 ARG D 582 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 280) hydrogen bonds : angle 4.68606 ( 753) SS BOND : bond 0.00679 ( 6) SS BOND : angle 1.30098 ( 12) covalent geometry : bond 0.00318 ( 6532) covalent geometry : angle 0.56001 ( 8875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3732.58 seconds wall clock time: 65 minutes 23.05 seconds (3923.05 seconds total)