Starting phenix.real_space_refine on Tue Sep 24 00:24:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbq_39907/09_2024/8zbq_39907_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbq_39907/09_2024/8zbq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbq_39907/09_2024/8zbq_39907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbq_39907/09_2024/8zbq_39907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbq_39907/09_2024/8zbq_39907_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zbq_39907/09_2024/8zbq_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-5461/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: 4.43, per 1000 atoms: 0.70 Number of scatterers: 6346 At special positions: 0 Unit cell: (75.9, 97.9, 105.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1186 8.00 N 1052 7.00 C 4072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.05 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.04 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 909.8 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: 0.66 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: 1.76 Time building geometry restraints manager: 1.82 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: 3.150 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.360 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.720 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 44 poor density : 139 time to evaluate : 0.654 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: 0.1956 time to fit residues: 41.6458 Evaluate side-chains 111 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 0.455 Fit side-chains REVERT: D 62 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7271 (ttt) REVERT: D 63 ASN cc_start: 0.7371 (m110) cc_final: 0.6808 (m110) REVERT: D 306 ARG cc_start: 0.7281 (ttt180) cc_final: 0.7074 (ttt180) REVERT: D 483 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7797 (pp20) REVERT: F 346 ARG cc_start: 0.5659 (OUTLIER) cc_final: 0.4993 (tmm160) outliers start: 24 outliers final: 12 residues processed: 121 average time/residue: 0.1405 time to fit residues: 22.2420 Evaluate side-chains 117 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 0.0070 chunk 62 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 ASN D 340 GLN D 345 HIS D 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6532 Z= 0.270 Angle : 0.606 5.892 8875 Z= 0.321 Chirality : 0.044 0.141 918 Planarity : 0.005 0.052 1150 Dihedral : 5.704 45.321 850 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.21 % Allowed : 14.43 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.30), residues: 775 helix: -0.35 (0.27), residues: 364 sheet: -1.52 (0.87), residues: 36 loop : -1.47 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.020 0.002 PHE D 523 TYR 0.022 0.002 TYR D 385 ARG 0.003 0.001 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 133 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7158 (ttt) REVERT: D 63 ASN cc_start: 0.7340 (m110) cc_final: 0.6861 (m110) REVERT: D 306 ARG cc_start: 0.7336 (ttt180) cc_final: 0.6991 (ttt180) REVERT: D 472 GLN cc_start: 0.8239 (mt0) cc_final: 0.8008 (mt0) REVERT: D 474 MET cc_start: 0.8702 (mmp) cc_final: 0.8435 (mmp) REVERT: D 483 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7811 (pp20) REVERT: F 439 ASN cc_start: 0.7618 (t0) cc_final: 0.7373 (t0) outliers start: 22 outliers final: 19 residues processed: 123 average time/residue: 0.1561 time to fit residues: 25.7937 Evaluate side-chains 124 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 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 62 MET 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 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 69 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6532 Z= 0.305 Angle : 0.618 6.234 8875 Z= 0.326 Chirality : 0.045 0.144 918 Planarity : 0.005 0.053 1150 Dihedral : 5.716 45.770 850 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.37 % Allowed : 15.60 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.30), residues: 775 helix: -0.33 (0.27), residues: 363 sheet: -1.53 (0.87), residues: 36 loop : -1.37 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 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 0.008 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 fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7411 (m110) cc_final: 0.6897 (m110) REVERT: D 472 GLN cc_start: 0.8337 (mt0) cc_final: 0.8074 (mt0) REVERT: D 474 MET cc_start: 0.8915 (mmp) cc_final: 0.8310 (mmp) REVERT: F 346 ARG cc_start: 0.5514 (OUTLIER) cc_final: 0.3549 (tmm160) REVERT: F 439 ASN cc_start: 0.7715 (t0) cc_final: 0.7437 (t0) outliers start: 30 outliers final: 23 residues processed: 127 average time/residue: 0.1733 time to fit residues: 29.8561 Evaluate side-chains 123 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 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 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 42 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 18 optimal weight: 0.0870 chunk 25 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6532 Z= 0.245 Angle : 0.579 6.275 8875 Z= 0.306 Chirality : 0.044 0.151 918 Planarity : 0.004 0.053 1150 Dihedral : 5.613 46.085 850 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.94 % Allowed : 17.06 % 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: -1.29 (0.30), residues: 775 helix: -0.07 (0.28), residues: 352 sheet: -1.51 (0.87), residues: 36 loop : -1.52 (0.32), residues: 387 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 0.019 0.001 TYR D 385 ARG 0.006 0.001 ARG F 454 *********************** 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 136 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7417 (m110) cc_final: 0.6898 (m110) REVERT: D 472 GLN cc_start: 0.8345 (mt0) cc_final: 0.8016 (mt0) REVERT: D 474 MET cc_start: 0.8892 (mmp) cc_final: 0.8277 (mmp) REVERT: D 483 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7718 (pp20) REVERT: F 346 ARG cc_start: 0.5605 (OUTLIER) cc_final: 0.3612 (tmm160) REVERT: F 439 ASN cc_start: 0.7690 (t0) cc_final: 0.7400 (t0) outliers start: 27 outliers final: 22 residues processed: 129 average time/residue: 0.1721 time to fit residues: 30.1736 Evaluate side-chains 127 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 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 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 67 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 18 optimal weight: 0.0070 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3147 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= 0.190 Angle : 0.545 6.977 8875 Z= 0.287 Chirality : 0.042 0.139 918 Planarity : 0.004 0.051 1150 Dihedral : 5.412 45.720 850 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % 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: -1.08 (0.30), residues: 775 helix: 0.18 (0.28), residues: 343 sheet: -1.89 (0.70), residues: 48 loop : -1.37 (0.32), residues: 384 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 0.020 0.001 PHE F 371 TYR 0.018 0.001 TYR D 385 ARG 0.004 0.001 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7392 (m110) cc_final: 0.6864 (m110) REVERT: D 150 GLU cc_start: 0.7401 (mp0) cc_final: 0.7111 (mp0) REVERT: D 472 GLN cc_start: 0.8357 (mt0) cc_final: 0.8117 (mt0) REVERT: D 474 MET cc_start: 0.8861 (mmp) cc_final: 0.8247 (mmp) REVERT: D 483 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7715 (pp20) REVERT: F 346 ARG cc_start: 0.5523 (OUTLIER) cc_final: 0.3795 (tmm160) REVERT: F 439 ASN cc_start: 0.7586 (t0) cc_final: 0.7329 (t0) outliers start: 27 outliers final: 21 residues processed: 135 average time/residue: 0.1695 time to fit residues: 30.9906 Evaluate side-chains 125 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE 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 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 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 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 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 74 optimal weight: 0.0670 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6532 Z= 0.204 Angle : 0.552 6.621 8875 Z= 0.290 Chirality : 0.042 0.135 918 Planarity : 0.004 0.052 1150 Dihedral : 5.388 46.648 850 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % 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: -1.10 (0.30), residues: 775 helix: 0.12 (0.28), residues: 351 sheet: -1.82 (0.70), residues: 48 loop : -1.37 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.019 0.001 PHE D 523 TYR 0.013 0.001 TYR D 385 ARG 0.005 0.001 ARG F 454 *********************** 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 134 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7394 (m110) cc_final: 0.6853 (m110) REVERT: D 150 GLU cc_start: 0.7340 (mp0) cc_final: 0.7033 (mp0) REVERT: D 472 GLN cc_start: 0.8296 (mt0) cc_final: 0.8050 (mt0) REVERT: D 474 MET cc_start: 0.8901 (mmp) cc_final: 0.8589 (mmp) REVERT: D 483 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7727 (pp20) REVERT: F 346 ARG cc_start: 0.5503 (OUTLIER) cc_final: 0.3720 (tmm160) outliers start: 30 outliers final: 23 residues processed: 125 average time/residue: 0.1678 time to fit residues: 28.3976 Evaluate side-chains 123 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 468 ILE Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 64 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3301 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= 0.219 Angle : 0.562 6.699 8875 Z= 0.295 Chirality : 0.043 0.179 918 Planarity : 0.004 0.052 1150 Dihedral : 5.412 47.364 850 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.23 % Allowed : 18.22 % 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: -1.11 (0.30), residues: 775 helix: 0.05 (0.28), residues: 356 sheet: -1.78 (0.70), residues: 46 loop : -1.33 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 302 HIS 0.007 0.001 HIS D 374 PHE 0.020 0.001 PHE D 523 TYR 0.017 0.001 TYR D 385 ARG 0.006 0.001 ARG F 454 *********************** 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 131 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7393 (m110) cc_final: 0.6857 (m110) REVERT: D 150 GLU cc_start: 0.7326 (mp0) cc_final: 0.7007 (mp0) REVERT: D 474 MET cc_start: 0.8891 (mmp) cc_final: 0.8399 (mmp) REVERT: D 483 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7718 (pp20) outliers start: 29 outliers final: 25 residues processed: 122 average time/residue: 0.1721 time to fit residues: 28.4649 Evaluate side-chains 123 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 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 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 71 optimal weight: 0.0370 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 21 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 73 optimal weight: 0.0470 chunk 44 optimal weight: 0.5980 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3418 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= 0.185 Angle : 0.546 6.355 8875 Z= 0.288 Chirality : 0.042 0.157 918 Planarity : 0.004 0.051 1150 Dihedral : 5.342 47.543 850 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.94 % Allowed : 18.95 % Favored : 77.11 % 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: 0.14 (0.28), residues: 357 sheet: -1.77 (0.70), residues: 46 loop : -1.27 (0.32), residues: 372 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 0.019 0.001 PHE D 523 TYR 0.021 0.001 TYR D 497 ARG 0.005 0.001 ARG D 582 *********************** 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 133 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7395 (m110) cc_final: 0.6860 (m110) REVERT: D 150 GLU cc_start: 0.7212 (mp0) cc_final: 0.6883 (mp0) REVERT: D 474 MET cc_start: 0.8902 (mmp) cc_final: 0.8399 (mmp) REVERT: D 483 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7623 (pp20) outliers start: 27 outliers final: 26 residues processed: 124 average time/residue: 0.1779 time to fit residues: 29.6192 Evaluate side-chains 125 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 579 MET Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain F residue 339 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 458 LYS Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 501 TYR Chi-restraints excluded: chain F residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.0050 chunk 37 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6532 Z= 0.230 Angle : 0.573 6.148 8875 Z= 0.302 Chirality : 0.043 0.148 918 Planarity : 0.004 0.052 1150 Dihedral : 5.391 47.997 850 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.08 % Allowed : 18.95 % Favored : 76.97 % 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: -0.99 (0.30), residues: 775 helix: 0.08 (0.28), residues: 355 sheet: -1.50 (0.74), residues: 46 loop : -1.22 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.020 0.001 PHE D 523 TYR 0.022 0.001 TYR D 497 ARG 0.007 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 129 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 ASN cc_start: 0.7384 (m110) cc_final: 0.6834 (m110) REVERT: D 150 GLU cc_start: 0.7224 (mp0) cc_final: 0.6930 (mp0) REVERT: D 462 MET cc_start: 0.8220 (ptm) cc_final: 0.8016 (ptp) REVERT: D 474 MET cc_start: 0.8946 (mmp) cc_final: 0.8465 (mmp) REVERT: D 483 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7727 (pp20) outliers start: 28 outliers final: 25 residues processed: 120 average time/residue: 0.1755 time to fit residues: 28.5001 Evaluate side-chains 126 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 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 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 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 56 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 0.0870 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 0.0010 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 overall best weight: 0.4164 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.159794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.129171 restraints weight = 7369.285| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.44 r_work: 0.3280 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6532 Z= 0.218 Angle : 0.569 6.773 8875 Z= 0.299 Chirality : 0.043 0.147 918 Planarity : 0.004 0.052 1150 Dihedral : 5.396 48.454 850 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.94 % Allowed : 18.95 % Favored : 77.11 % 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: -0.95 (0.30), residues: 775 helix: 0.10 (0.28), residues: 353 sheet: -1.45 (0.75), residues: 46 loop : -1.19 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 353 HIS 0.007 0.001 HIS D 374 PHE 0.019 0.001 PHE D 523 TYR 0.021 0.001 TYR D 497 ARG 0.006 0.001 ARG D 582 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1893.82 seconds wall clock time: 44 minutes 10.11 seconds (2650.11 seconds total)