Starting phenix.real_space_refine on Tue Jan 14 09:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbq_39907/01_2025/8zbq_39907_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbq_39907/01_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_39907/01_2025/8zbq_39907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbq_39907/01_2025/8zbq_39907.map" model { file = "/net/cci-nas-00/data/ceres_data/8zbq_39907/01_2025/8zbq_39907_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbq_39907/01_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-5571/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: 4.48, per 1000 atoms: 0.71 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: 1.78 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.85 Time building geometry restraints manager: 1.90 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.540 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.180 ------------------------------------------------------------------------------- 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 6532 Z= 0.370 Angle : 0.919 11.273 8875 Z= 0.584 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 *********************** 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 : 0.774 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: 0.2043 time to fit residues: 43.6117 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 : 0.732 ------------------------------------------------------------------------------- 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 6532 Z= 0.300 Angle : 0.648 6.248 8875 Z= 0.347 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 *********************** 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 : 0.700 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: 0.2078 time to fit residues: 32.9796 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 : 0.901 ------------------------------------------------------------------------------- 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 6532 Z= 0.233 Angle : 0.586 5.947 8875 Z= 0.310 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 *********************** 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 : 0.695 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: 0.1857 time to fit residues: 31.8102 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 : 0.775 ------------------------------------------------------------------------------- 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: 2.9990 chunk 57 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.160063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.128337 restraints weight = 7547.880| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.52 r_work: 0.3215 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6532 Z= 0.289 Angle : 0.608 6.080 8875 Z= 0.321 Chirality : 0.045 0.144 918 Planarity : 0.005 0.051 1150 Dihedral : 5.652 45.564 850 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 4.08 % Allowed : 15.60 % Favored : 80.32 % 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: -0.29 (0.27), residues: 362 sheet: -1.43 (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 0.005 0.001 ARG F 454 *********************** 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 137 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7378 (m110) cc_final: 0.6838 (m110) REVERT: D 81 GLN cc_start: 0.7640 (mm110) cc_final: 0.7415 (mm-40) REVERT: D 302 TRP cc_start: 0.8559 (m-10) cc_final: 0.8334 (m-10) REVERT: D 306 ARG cc_start: 0.7424 (ttt180) cc_final: 0.6985 (ttt180) REVERT: D 307 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7973 (mt) REVERT: D 472 GLN cc_start: 0.8748 (mt0) cc_final: 0.8520 (mt0) REVERT: D 474 MET cc_start: 0.9054 (mmp) cc_final: 0.8462 (mmp) REVERT: D 483 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8255 (pp20) REVERT: D 518 ARG cc_start: 0.8422 (tmm160) cc_final: 0.8160 (tmm160) REVERT: D 531 GLN cc_start: 0.8175 (mt0) cc_final: 0.7854 (mt0) REVERT: F 346 ARG cc_start: 0.5384 (OUTLIER) cc_final: 0.3452 (tmm160) REVERT: F 439 ASN cc_start: 0.8342 (t0) cc_final: 0.7940 (t0) outliers start: 28 outliers final: 19 residues processed: 127 average time/residue: 0.1906 time to fit residues: 32.6170 Evaluate side-chains 127 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 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: 0.6980 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.155028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.123440 restraints weight = 7534.887| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.46 r_work: 0.3252 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6532 Z= 0.271 Angle : 0.585 6.747 8875 Z= 0.309 Chirality : 0.044 0.145 918 Planarity : 0.004 0.051 1150 Dihedral : 5.628 46.201 850 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 4.52 % Allowed : 15.74 % Favored : 79.74 % 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: -0.20 (0.27), residues: 362 sheet: -1.40 (0.87), residues: 36 loop : -1.50 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 478 HIS 0.007 0.001 HIS D 374 PHE 0.019 0.002 PHE D 523 TYR 0.021 0.002 TYR D 385 ARG 0.003 0.000 ARG D 482 *********************** 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 139 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7429 (m110) cc_final: 0.6851 (m110) REVERT: D 189 GLU cc_start: 0.7586 (mp0) cc_final: 0.6991 (mt-10) REVERT: D 307 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7991 (mt) REVERT: D 472 GLN cc_start: 0.8721 (mt0) cc_final: 0.8483 (mt0) REVERT: D 474 MET cc_start: 0.9039 (mmp) cc_final: 0.8450 (mmp) REVERT: D 483 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8225 (pp20) REVERT: D 531 GLN cc_start: 0.8176 (mt0) cc_final: 0.7894 (mt0) REVERT: F 346 ARG cc_start: 0.5575 (OUTLIER) cc_final: 0.3532 (tmm160) REVERT: F 439 ASN cc_start: 0.8327 (t0) cc_final: 0.7918 (t0) outliers start: 31 outliers final: 25 residues processed: 131 average time/residue: 0.1773 time to fit residues: 31.2814 Evaluate side-chains 131 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.157731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126706 restraints weight = 7376.521| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.44 r_work: 0.3239 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6532 Z= 0.281 Angle : 0.590 6.880 8875 Z= 0.311 Chirality : 0.044 0.140 918 Planarity : 0.004 0.052 1150 Dihedral : 5.624 46.441 850 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.81 % Allowed : 15.60 % Favored : 79.59 % 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: -1.33 (0.30), residues: 775 helix: -0.23 (0.27), residues: 366 sheet: -1.20 (0.87), residues: 36 loop : -1.47 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.021 0.002 PHE D 523 TYR 0.020 0.002 TYR D 385 ARG 0.003 0.000 ARG D 482 *********************** 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 139 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7430 (m110) cc_final: 0.6846 (m110) REVERT: D 306 ARG cc_start: 0.7472 (ttt180) cc_final: 0.7012 (ttt180) REVERT: D 307 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8014 (mt) REVERT: D 472 GLN cc_start: 0.8738 (mt0) cc_final: 0.8495 (mt0) REVERT: D 474 MET cc_start: 0.9047 (mmp) cc_final: 0.8767 (mmp) REVERT: D 531 GLN cc_start: 0.8167 (mt0) cc_final: 0.7886 (mt0) REVERT: F 346 ARG cc_start: 0.5652 (OUTLIER) cc_final: 0.3824 (tmm160) REVERT: F 439 ASN cc_start: 0.8376 (t0) cc_final: 0.7987 (t0) outliers start: 33 outliers final: 27 residues processed: 131 average time/residue: 0.1814 time to fit residues: 32.0396 Evaluate side-chains 126 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.0000 overall best weight: 0.2722 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.160977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130508 restraints weight = 7501.394| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.46 r_work: 0.3287 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6532 Z= 0.187 Angle : 0.549 7.340 8875 Z= 0.289 Chirality : 0.042 0.138 918 Planarity : 0.004 0.052 1150 Dihedral : 5.424 46.263 850 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.52 % Allowed : 16.47 % 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: -1.07 (0.30), residues: 775 helix: 0.06 (0.28), residues: 357 sheet: -1.55 (0.73), residues: 48 loop : -1.33 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 302 HIS 0.007 0.001 HIS D 374 PHE 0.018 0.001 PHE D 523 TYR 0.017 0.001 TYR D 385 ARG 0.004 0.000 ARG D 582 *********************** 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 149 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7575 (mm-30) REVERT: D 63 ASN cc_start: 0.7400 (m110) cc_final: 0.6810 (m110) REVERT: D 189 GLU cc_start: 0.7317 (mp0) cc_final: 0.6888 (tt0) REVERT: D 306 ARG cc_start: 0.7380 (ttt180) cc_final: 0.7039 (ttt180) REVERT: D 307 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7958 (mt) REVERT: D 472 GLN cc_start: 0.8759 (mt0) cc_final: 0.8530 (mt0) REVERT: D 474 MET cc_start: 0.9005 (mmp) cc_final: 0.8429 (mmp) REVERT: D 483 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8212 (pp20) REVERT: D 531 GLN cc_start: 0.8078 (mt0) cc_final: 0.7852 (mt0) REVERT: D 578 ASN cc_start: 0.7199 (t0) cc_final: 0.6895 (p0) REVERT: F 439 ASN cc_start: 0.8287 (t0) cc_final: 0.7920 (t0) outliers start: 31 outliers final: 25 residues processed: 141 average time/residue: 0.1819 time to fit residues: 35.0115 Evaluate side-chains 131 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 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 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: 0.6980 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.156883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.124792 restraints weight = 7480.896| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.54 r_work: 0.3225 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6532 Z= 0.285 Angle : 0.597 7.463 8875 Z= 0.314 Chirality : 0.044 0.166 918 Planarity : 0.004 0.053 1150 Dihedral : 5.550 47.203 850 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.37 % Allowed : 16.18 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.30), residues: 775 helix: 0.03 (0.28), residues: 353 sheet: -1.49 (0.73), residues: 49 loop : -1.30 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 302 HIS 0.007 0.001 HIS D 374 PHE 0.022 0.002 PHE D 523 TYR 0.017 0.002 TYR D 497 ARG 0.005 0.001 ARG D 192 *********************** 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 134 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7589 (mm-30) REVERT: D 63 ASN cc_start: 0.7409 (m110) cc_final: 0.6812 (m110) REVERT: D 307 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7981 (mt) REVERT: D 472 GLN cc_start: 0.8793 (mt0) cc_final: 0.8557 (mt0) REVERT: D 474 MET cc_start: 0.9044 (mmp) cc_final: 0.8514 (mmp) REVERT: D 483 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8266 (pp20) REVERT: D 531 GLN cc_start: 0.8199 (mt0) cc_final: 0.7904 (mt0) REVERT: F 439 ASN cc_start: 0.8398 (t0) cc_final: 0.8069 (t0) outliers start: 30 outliers final: 28 residues processed: 126 average time/residue: 0.1673 time to fit residues: 28.7816 Evaluate side-chains 129 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.157362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.126405 restraints weight = 7462.322| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.43 r_work: 0.3239 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6532 Z= 0.282 Angle : 0.599 6.885 8875 Z= 0.317 Chirality : 0.044 0.173 918 Planarity : 0.004 0.052 1150 Dihedral : 5.606 47.815 850 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.66 % Allowed : 16.76 % Favored : 78.57 % 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: -0.07 (0.27), residues: 359 sheet: -1.38 (0.76), residues: 47 loop : -1.25 (0.33), residues: 369 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 0.021 0.002 PHE D 523 TYR 0.016 0.002 TYR D 385 ARG 0.005 0.001 ARG D 192 *********************** 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 136 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7561 (mm-30) REVERT: D 63 ASN cc_start: 0.7428 (m110) cc_final: 0.6844 (m110) REVERT: D 307 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8015 (mt) REVERT: D 472 GLN cc_start: 0.8735 (mt0) cc_final: 0.8528 (mt0) REVERT: D 474 MET cc_start: 0.9007 (mmp) cc_final: 0.8160 (mmp) REVERT: D 531 GLN cc_start: 0.8160 (mt0) cc_final: 0.7860 (mt0) REVERT: F 439 ASN cc_start: 0.8384 (t0) cc_final: 0.8073 (t0) outliers start: 32 outliers final: 30 residues processed: 126 average time/residue: 0.1675 time to fit residues: 28.8716 Evaluate side-chains 130 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 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: 0.0020 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.161098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130375 restraints weight = 7488.905| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.46 r_work: 0.3275 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6532 Z= 0.194 Angle : 0.554 6.679 8875 Z= 0.293 Chirality : 0.042 0.158 918 Planarity : 0.004 0.052 1150 Dihedral : 5.436 47.835 850 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.37 % Allowed : 17.49 % 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: -0.91 (0.30), residues: 775 helix: 0.22 (0.28), residues: 350 sheet: -1.31 (0.75), residues: 49 loop : -1.27 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.019 0.001 PHE D 523 TYR 0.015 0.001 TYR D 385 ARG 0.005 0.001 ARG D 582 ********************** 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 134 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7571 (mm-30) REVERT: D 63 ASN cc_start: 0.7413 (m110) cc_final: 0.6804 (m110) REVERT: D 150 GLU cc_start: 0.7671 (mp0) cc_final: 0.7215 (mp0) REVERT: D 307 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7948 (mt) REVERT: D 472 GLN cc_start: 0.8724 (mt0) cc_final: 0.8506 (mt0) REVERT: D 474 MET cc_start: 0.8997 (mmp) cc_final: 0.8454 (mmp) REVERT: D 483 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8225 (pp20) REVERT: D 578 ASN cc_start: 0.6943 (t0) cc_final: 0.6461 (p0) REVERT: F 439 ASN cc_start: 0.8338 (t0) cc_final: 0.8008 (t0) outliers start: 30 outliers final: 26 residues processed: 125 average time/residue: 0.1713 time to fit residues: 29.2509 Evaluate side-chains 130 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 325 GLN 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 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 5 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.0060 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.158803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127625 restraints weight = 7652.960| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.48 r_work: 0.3245 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6532 Z= 0.225 Angle : 0.569 6.596 8875 Z= 0.301 Chirality : 0.043 0.149 918 Planarity : 0.004 0.052 1150 Dihedral : 5.428 48.039 850 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.37 % Allowed : 17.06 % Favored : 78.57 % 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: -0.87 (0.30), residues: 775 helix: 0.20 (0.28), residues: 351 sheet: -1.19 (0.76), residues: 49 loop : -1.21 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.020 0.002 PHE D 523 TYR 0.017 0.001 TYR D 385 ARG 0.007 0.001 ARG D 582 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3713.90 seconds wall clock time: 66 minutes 43.23 seconds (4003.23 seconds total)