Starting phenix.real_space_refine on Sun Apr 27 18:02:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbq_39907/04_2025/8zbq_39907_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbq_39907/04_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_39907/04_2025/8zbq_39907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbq_39907/04_2025/8zbq_39907.map" model { file = "/net/cci-nas-00/data/ceres_data/8zbq_39907/04_2025/8zbq_39907_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbq_39907/04_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-5669/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: 4.83, per 1000 atoms: 0.76 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: 1.60 Conformation dependent library (CDL) restraints added in 910.8 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: 0.62 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: 2.05 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: 1.17 - 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: 2.960 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.110 Process input model: 19.790 Find NCS groups from input model: 0.060 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.110 ------------------------------------------------------------------------------- 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 : 0.778 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: 0.2333 time to fit residues: 49.6675 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 : 0.758 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.162284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.131207 restraints weight = 7410.078| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.45 r_work: 0.3295 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 6.247 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 1.07151 ( 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 : 1.190 Fit side-chains REVERT: D 62 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7242 (ttt) REVERT: D 63 ASN cc_start: 0.7337 (m110) cc_final: 0.6707 (m110) REVERT: D 120 LEU cc_start: 0.8727 (mt) cc_final: 0.8519 (mt) REVERT: D 228 HIS cc_start: 0.8026 (m170) cc_final: 0.7747 (m-70) REVERT: D 306 ARG cc_start: 0.7441 (ttt180) cc_final: 0.7099 (ttt180) REVERT: D 307 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7932 (mt) REVERT: D 483 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8243 (pp20) REVERT: F 346 ARG cc_start: 0.5576 (OUTLIER) cc_final: 0.4854 (tmm160) outliers start: 24 outliers final: 12 residues processed: 121 average time/residue: 0.3142 time to fit residues: 50.2962 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 : 0.741 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 64 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.161455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130416 restraints weight = 7458.440| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.45 r_work: 0.3257 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6538 Z= 0.185 Angle : 0.613 5.940 8887 Z= 0.325 Chirality : 0.045 0.141 918 Planarity : 0.005 0.052 1150 Dihedral : 5.733 45.540 850 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.21 % Allowed : 14.87 % Favored : 81.92 % 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: -1.41 (0.30), residues: 775 helix: -0.31 (0.27), residues: 356 sheet: -1.54 (0.87), residues: 36 loop : -1.45 (0.33), residues: 383 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 0.020 0.002 PHE D 523 TYR 0.023 0.002 TYR D 385 ARG 0.004 0.001 ARG F 454 Details of bonding type rmsd hydrogen bonds : bond 0.04950 ( 280) hydrogen bonds : angle 5.14973 ( 753) SS BOND : bond 0.00642 ( 6) SS BOND : angle 1.29963 ( 12) covalent geometry : bond 0.00425 ( 6532) covalent geometry : angle 0.61177 ( 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 136 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7318 (ttt) REVERT: D 63 ASN cc_start: 0.7336 (m110) cc_final: 0.6789 (m110) REVERT: D 306 ARG cc_start: 0.7500 (ttt180) cc_final: 0.7104 (ttt180) REVERT: D 307 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7969 (mt) REVERT: D 323 MET cc_start: 0.8150 (mmm) cc_final: 0.7830 (mmt) REVERT: D 472 GLN cc_start: 0.8651 (mt0) cc_final: 0.8431 (mt0) REVERT: D 474 MET cc_start: 0.8890 (mmp) cc_final: 0.8633 (mmp) REVERT: D 483 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8281 (pp20) REVERT: D 518 ARG cc_start: 0.8336 (tmm160) cc_final: 0.8102 (tmm160) REVERT: F 439 ASN cc_start: 0.8219 (t0) cc_final: 0.7858 (t0) outliers start: 22 outliers final: 17 residues processed: 126 average time/residue: 0.1935 time to fit residues: 32.3006 Evaluate side-chains 123 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 142 LEU 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: 0.6980 chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.156478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125035 restraints weight = 7662.163| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.47 r_work: 0.3245 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6538 Z= 0.169 Angle : 0.593 6.245 8887 Z= 0.312 Chirality : 0.044 0.141 918 Planarity : 0.004 0.053 1150 Dihedral : 5.628 45.607 850 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 4.23 % Allowed : 15.89 % Favored : 79.88 % 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: -1.27 (0.30), residues: 775 helix: -0.10 (0.28), residues: 351 sheet: -1.50 (0.86), residues: 38 loop : -1.46 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.019 0.001 PHE D 523 TYR 0.021 0.002 TYR D 385 ARG 0.003 0.000 ARG D 482 Details of bonding type rmsd hydrogen bonds : bond 0.04724 ( 280) hydrogen bonds : angle 4.96448 ( 753) SS BOND : bond 0.00468 ( 6) SS BOND : angle 0.96723 ( 12) covalent geometry : bond 0.00383 ( 6532) covalent geometry : angle 0.59204 ( 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 140 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 1.837 Fit side-chains revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7402 (m110) cc_final: 0.6823 (m110) REVERT: D 81 GLN cc_start: 0.7628 (mm110) cc_final: 0.7427 (mm-40) REVERT: D 306 ARG cc_start: 0.7364 (ttt180) cc_final: 0.6952 (ttt180) REVERT: D 307 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7941 (mt) REVERT: D 472 GLN cc_start: 0.8685 (mt0) cc_final: 0.8451 (mt0) REVERT: D 474 MET cc_start: 0.9032 (mmp) cc_final: 0.8417 (mmp) REVERT: D 483 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8230 (pp20) REVERT: D 518 ARG cc_start: 0.8420 (tmm160) cc_final: 0.8162 (tmm160) REVERT: F 346 ARG cc_start: 0.5422 (OUTLIER) cc_final: 0.3364 (tmm160) REVERT: F 439 ASN cc_start: 0.8319 (t0) cc_final: 0.7936 (t0) outliers start: 29 outliers final: 21 residues processed: 129 average time/residue: 0.3288 time to fit residues: 58.4557 Evaluate side-chains 129 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 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 463 VAL 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: 0.2980 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.155941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124381 restraints weight = 7542.598| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.47 r_work: 0.3254 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2990 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= 0.158 Angle : 0.575 6.342 8887 Z= 0.303 Chirality : 0.043 0.145 918 Planarity : 0.004 0.054 1150 Dihedral : 5.573 46.062 850 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.52 % Allowed : 16.18 % Favored : 79.30 % 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: -1.24 (0.30), residues: 775 helix: -0.01 (0.28), residues: 355 sheet: -1.51 (0.85), residues: 38 loop : -1.51 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 302 HIS 0.007 0.001 HIS D 374 PHE 0.021 0.001 PHE D 523 TYR 0.020 0.001 TYR D 385 ARG 0.003 0.000 ARG D 482 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 280) hydrogen bonds : angle 4.87580 ( 753) SS BOND : bond 0.00734 ( 6) SS BOND : angle 1.42923 ( 12) covalent geometry : bond 0.00359 ( 6532) covalent geometry : angle 0.57324 ( 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 137 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7385 (m110) cc_final: 0.6801 (m110) REVERT: D 306 ARG cc_start: 0.7391 (ttt180) cc_final: 0.6881 (ttt180) REVERT: D 307 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7945 (mt) REVERT: D 472 GLN cc_start: 0.8764 (mt0) cc_final: 0.8538 (mt0) REVERT: D 474 MET cc_start: 0.9029 (mmp) cc_final: 0.8426 (mmp) REVERT: D 483 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8204 (pp20) REVERT: F 346 ARG cc_start: 0.5570 (OUTLIER) cc_final: 0.3775 (tmm160) REVERT: F 439 ASN cc_start: 0.8351 (t0) cc_final: 0.7938 (t0) outliers start: 31 outliers final: 24 residues processed: 129 average time/residue: 0.1809 time to fit residues: 32.1757 Evaluate side-chains 129 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 56 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.158988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128165 restraints weight = 7416.186| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.46 r_work: 0.3259 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6538 Z= 0.151 Angle : 0.567 7.059 8887 Z= 0.298 Chirality : 0.043 0.138 918 Planarity : 0.004 0.054 1150 Dihedral : 5.498 46.108 850 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.37 % Allowed : 17.35 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.30), residues: 775 helix: 0.05 (0.28), residues: 351 sheet: -1.88 (0.70), residues: 48 loop : -1.44 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 353 HIS 0.006 0.001 HIS D 374 PHE 0.021 0.002 PHE F 371 TYR 0.019 0.001 TYR D 385 ARG 0.003 0.000 ARG D 582 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 280) hydrogen bonds : angle 4.78339 ( 753) SS BOND : bond 0.00564 ( 6) SS BOND : angle 1.11805 ( 12) covalent geometry : bond 0.00343 ( 6532) covalent geometry : angle 0.56563 ( 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 137 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7404 (m110) cc_final: 0.6812 (m110) REVERT: D 306 ARG cc_start: 0.7411 (ttt180) cc_final: 0.7055 (ttt180) REVERT: D 307 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7941 (mt) REVERT: D 472 GLN cc_start: 0.8708 (mt0) cc_final: 0.8471 (mt0) REVERT: D 474 MET cc_start: 0.9045 (mmp) cc_final: 0.8769 (mmp) REVERT: D 483 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8203 (pp20) REVERT: D 578 ASN cc_start: 0.7381 (t0) cc_final: 0.7074 (p0) REVERT: F 346 ARG cc_start: 0.5549 (OUTLIER) cc_final: 0.3828 (tmm160) REVERT: F 439 ASN cc_start: 0.8315 (t0) cc_final: 0.7945 (t0) outliers start: 30 outliers final: 25 residues processed: 128 average time/residue: 0.1866 time to fit residues: 31.9864 Evaluate side-chains 129 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 299 ASP Chi-restraints excluded: chain D residue 307 ILE 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 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: 0.6980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 43 optimal weight: 0.0870 chunk 59 optimal weight: 0.0020 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 69 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 overall best weight: 0.2966 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.159114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.128237 restraints weight = 7543.409| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.48 r_work: 0.3292 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6538 Z= 0.123 Angle : 0.541 6.632 8887 Z= 0.284 Chirality : 0.041 0.135 918 Planarity : 0.004 0.051 1150 Dihedral : 5.392 46.684 850 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.94 % Allowed : 17.78 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.30), residues: 775 helix: 0.18 (0.28), residues: 351 sheet: -1.86 (0.69), residues: 48 loop : -1.38 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 302 HIS 0.007 0.001 HIS D 374 PHE 0.019 0.001 PHE D 523 TYR 0.018 0.001 TYR D 385 ARG 0.003 0.000 ARG D 582 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 280) hydrogen bonds : angle 4.70792 ( 753) SS BOND : bond 0.00476 ( 6) SS BOND : angle 0.87485 ( 12) covalent geometry : bond 0.00270 ( 6532) covalent geometry : angle 0.54086 ( 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 141 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7543 (mm-30) REVERT: D 63 ASN cc_start: 0.7385 (m110) cc_final: 0.6796 (m110) REVERT: D 150 GLU cc_start: 0.7691 (mp0) cc_final: 0.7208 (mp0) REVERT: D 306 ARG cc_start: 0.7331 (ttt180) cc_final: 0.7071 (ttt180) REVERT: D 307 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7961 (mt) REVERT: D 472 GLN cc_start: 0.8754 (mt0) cc_final: 0.8523 (mt0) REVERT: D 474 MET cc_start: 0.9015 (mmp) cc_final: 0.8406 (mmp) REVERT: D 483 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8216 (pp20) REVERT: D 578 ASN cc_start: 0.7193 (t0) cc_final: 0.6803 (p0) REVERT: F 346 ARG cc_start: 0.5477 (OUTLIER) cc_final: 0.3581 (tmm160) REVERT: F 439 ASN cc_start: 0.8290 (t0) cc_final: 0.7912 (t0) outliers start: 27 outliers final: 22 residues processed: 132 average time/residue: 0.1704 time to fit residues: 30.5526 Evaluate side-chains 133 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 332 MET 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 485 VAL Chi-restraints excluded: chain D residue 549 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 59 optimal weight: 0.0770 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.159749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.128925 restraints weight = 7477.234| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.47 r_work: 0.3267 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6538 Z= 0.143 Angle : 0.562 6.758 8887 Z= 0.294 Chirality : 0.043 0.179 918 Planarity : 0.004 0.051 1150 Dihedral : 5.405 47.287 850 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.52 % Allowed : 17.20 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.30), residues: 775 helix: 0.17 (0.28), residues: 351 sheet: -1.83 (0.68), residues: 48 loop : -1.32 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 302 HIS 0.007 0.001 HIS D 374 PHE 0.019 0.002 PHE D 523 TYR 0.014 0.001 TYR D 385 ARG 0.005 0.000 ARG D 582 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 280) hydrogen bonds : angle 4.67517 ( 753) SS BOND : bond 0.00788 ( 6) SS BOND : angle 1.41037 ( 12) covalent geometry : bond 0.00326 ( 6532) covalent geometry : angle 0.55972 ( 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 139 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7568 (mm-30) REVERT: D 63 ASN cc_start: 0.7398 (m110) cc_final: 0.6803 (m110) REVERT: D 150 GLU cc_start: 0.7711 (mp0) cc_final: 0.7221 (mp0) REVERT: D 189 GLU cc_start: 0.7327 (mp0) cc_final: 0.7007 (tt0) REVERT: D 306 ARG cc_start: 0.7433 (ttt180) cc_final: 0.6951 (ttt180) REVERT: D 307 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.7913 (mt) REVERT: D 472 GLN cc_start: 0.8710 (mt0) cc_final: 0.8480 (mt0) REVERT: D 474 MET cc_start: 0.9041 (mmp) cc_final: 0.8756 (mmp) REVERT: D 483 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8222 (pp20) REVERT: F 346 ARG cc_start: 0.5466 (OUTLIER) cc_final: 0.3793 (tmm160) REVERT: F 439 ASN cc_start: 0.8284 (t0) cc_final: 0.7910 (t0) outliers start: 31 outliers final: 25 residues processed: 129 average time/residue: 0.1747 time to fit residues: 30.2737 Evaluate side-chains 135 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 491 VAL Chi-restraints excluded: chain D residue 549 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 458 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 0.0270 chunk 61 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.159737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.128821 restraints weight = 7503.444| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.45 r_work: 0.3288 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3351 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= 0.140 Angle : 0.569 7.256 8887 Z= 0.299 Chirality : 0.043 0.168 918 Planarity : 0.004 0.051 1150 Dihedral : 5.412 47.673 850 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.08 % Allowed : 18.22 % Favored : 77.70 % 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: -1.00 (0.30), residues: 775 helix: 0.19 (0.28), residues: 350 sheet: -1.68 (0.71), residues: 48 loop : -1.33 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 353 HIS 0.006 0.001 HIS D 374 PHE 0.019 0.001 PHE D 523 TYR 0.017 0.001 TYR D 385 ARG 0.005 0.000 ARG D 582 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 280) hydrogen bonds : angle 4.63805 ( 753) SS BOND : bond 0.00644 ( 6) SS BOND : angle 1.30949 ( 12) covalent geometry : bond 0.00314 ( 6532) covalent geometry : angle 0.56696 ( 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 135 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7562 (mm-30) REVERT: D 63 ASN cc_start: 0.7391 (m110) cc_final: 0.6799 (m110) REVERT: D 150 GLU cc_start: 0.7666 (mp0) cc_final: 0.7163 (mp0) REVERT: D 189 GLU cc_start: 0.7291 (mp0) cc_final: 0.6979 (tt0) REVERT: D 306 ARG cc_start: 0.7437 (ttt180) cc_final: 0.7039 (ttt180) REVERT: D 307 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7947 (mt) REVERT: D 474 MET cc_start: 0.9005 (mmp) cc_final: 0.8546 (mmp) REVERT: D 483 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8214 (pp20) REVERT: D 578 ASN cc_start: 0.6991 (t0) cc_final: 0.6437 (p0) REVERT: F 439 ASN cc_start: 0.8317 (t0) cc_final: 0.7990 (t0) outliers start: 28 outliers final: 26 residues processed: 126 average time/residue: 0.1897 time to fit residues: 32.1800 Evaluate side-chains 134 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 491 VAL Chi-restraints excluded: chain D residue 549 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 458 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 12 optimal weight: 0.0050 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 = 0.161057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.130355 restraints weight = 7495.062| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.47 r_work: 0.3278 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3416 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= 0.139 Angle : 0.569 7.949 8887 Z= 0.300 Chirality : 0.043 0.156 918 Planarity : 0.004 0.051 1150 Dihedral : 5.394 47.990 850 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.37 % Allowed : 18.08 % Favored : 77.55 % 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: -0.97 (0.30), residues: 775 helix: 0.22 (0.28), residues: 349 sheet: -1.51 (0.73), residues: 48 loop : -1.32 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.019 0.001 PHE D 523 TYR 0.026 0.001 TYR D 497 ARG 0.004 0.000 ARG D 582 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 280) hydrogen bonds : angle 4.62773 ( 753) SS BOND : bond 0.00635 ( 6) SS BOND : angle 1.24757 ( 12) covalent geometry : bond 0.00313 ( 6532) covalent geometry : angle 0.56783 ( 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 138 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7554 (mm-30) REVERT: D 63 ASN cc_start: 0.7395 (m110) cc_final: 0.6786 (m110) REVERT: D 150 GLU cc_start: 0.7635 (mp0) cc_final: 0.7142 (mp0) REVERT: D 189 GLU cc_start: 0.7276 (mp0) cc_final: 0.6967 (tt0) REVERT: D 306 ARG cc_start: 0.7452 (ttt180) cc_final: 0.7049 (ttt180) REVERT: D 307 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7953 (mt) REVERT: D 474 MET cc_start: 0.9015 (mmp) cc_final: 0.8508 (mmp) REVERT: D 483 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8210 (pp20) REVERT: D 578 ASN cc_start: 0.6985 (t0) cc_final: 0.6416 (p0) REVERT: F 439 ASN cc_start: 0.8339 (t0) cc_final: 0.7995 (t0) outliers start: 30 outliers final: 26 residues processed: 128 average time/residue: 0.1682 time to fit residues: 29.1405 Evaluate side-chains 134 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 363 LYS Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 447 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.0370 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 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: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.160902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129938 restraints weight = 7616.753| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.49 r_work: 0.3258 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6538 Z= 0.151 Angle : 0.576 8.359 8887 Z= 0.303 Chirality : 0.043 0.151 918 Planarity : 0.005 0.052 1150 Dihedral : 5.428 48.057 850 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.08 % Allowed : 18.22 % Favored : 77.70 % 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: -0.98 (0.30), residues: 775 helix: 0.17 (0.28), residues: 351 sheet: -1.41 (0.73), residues: 48 loop : -1.32 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.019 0.001 PHE D 523 TYR 0.025 0.001 TYR D 497 ARG 0.004 0.000 ARG D 192 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 280) hydrogen bonds : angle 4.64783 ( 753) SS BOND : bond 0.00642 ( 6) SS BOND : angle 1.25337 ( 12) covalent geometry : bond 0.00344 ( 6532) covalent geometry : angle 0.57487 ( 8875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4395.54 seconds wall clock time: 77 minutes 58.39 seconds (4678.39 seconds total)