Starting phenix.real_space_refine on Tue Feb 11 17:51:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yzd_39690/02_2025/8yzd_39690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yzd_39690/02_2025/8yzd_39690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yzd_39690/02_2025/8yzd_39690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yzd_39690/02_2025/8yzd_39690.map" model { file = "/net/cci-nas-00/data/ceres_data/8yzd_39690/02_2025/8yzd_39690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yzd_39690/02_2025/8yzd_39690.cif" } resolution = 3.07 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= -0.008 sd= 0.325 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4128 2.51 5 N 1069 2.21 5 O 1202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6436 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "B" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Time building chain proxies: 4.52, per 1000 atoms: 0.70 Number of scatterers: 6436 At special positions: 0 Unit cell: (84.49, 101.15, 116.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1202 8.00 N 1069 7.00 C 4128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 876.3 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 54.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.946A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'B' and resid 20 through 53 removed outlier: 3.971A pdb=" N GLN B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 77 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.853A pdb=" N MET B 82 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.520A pdb=" N GLU B 87 " --> pdb=" O PRO B 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 88 " --> pdb=" O LEU B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 88' Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.997A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 108' Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.571A pdb=" N ILE B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 172 removed outlier: 3.605A pdb=" N TRP B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 194 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 220 through 252 removed outlier: 3.877A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.712A pdb=" N LYS B 247 " --> pdb=" O TYR B 243 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.518A pdb=" N LEU B 278 " --> pdb=" O TRP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 303 through 318 removed outlier: 3.843A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 3.547A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.713A pdb=" N PHE B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 400 through 413 removed outlier: 3.505A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 431 through 447 removed outlier: 3.634A pdb=" N GLU B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 512 through 533 removed outlier: 4.166A pdb=" N TYR B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.854A pdb=" N GLY B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 575 removed outlier: 3.626A pdb=" N VAL B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 600 Proline residue: B 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.021A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.849A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263 removed outlier: 5.718A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 350 294 hydrogen bonds defined for protein. 846 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: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2060 1.34 - 1.46: 1621 1.46 - 1.58: 2886 1.58 - 1.70: 0 1.70 - 1.81: 58 Bond restraints: 6625 Sorted by residual: bond pdb=" C GLU B 145 " pdb=" N PRO B 146 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.06e+00 bond pdb=" CA LYS A 378 " pdb=" C LYS A 378 " ideal model delta sigma weight residual 1.530 1.512 0.018 1.08e-02 8.57e+03 2.91e+00 bond pdb=" CA PHE A 371 " pdb=" C PHE A 371 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.26e-02 6.30e+03 1.67e+00 bond pdb=" C ALA A 372 " pdb=" O ALA A 372 " ideal model delta sigma weight residual 1.238 1.225 0.013 1.28e-02 6.10e+03 1.07e+00 bond pdb=" CA ASN A 370 " pdb=" C ASN A 370 " ideal model delta sigma weight residual 1.519 1.509 0.010 1.32e-02 5.74e+03 5.63e-01 ... (remaining 6620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 8920 1.66 - 3.33: 70 3.33 - 4.99: 10 4.99 - 6.65: 3 6.65 - 8.31: 1 Bond angle restraints: 9004 Sorted by residual: angle pdb=" N PHE A 371 " pdb=" CA PHE A 371 " pdb=" C PHE A 371 " ideal model delta sigma weight residual 111.14 102.83 8.31 1.08e+00 8.57e-01 5.93e+01 angle pdb=" N ASN A 370 " pdb=" CA ASN A 370 " pdb=" C ASN A 370 " ideal model delta sigma weight residual 113.88 107.25 6.63 1.23e+00 6.61e-01 2.91e+01 angle pdb=" N CYS A 379 " pdb=" CA CYS A 379 " pdb=" C CYS A 379 " ideal model delta sigma weight residual 109.46 115.41 -5.95 1.66e+00 3.63e-01 1.28e+01 angle pdb=" C ASN A 370 " pdb=" CA ASN A 370 " pdb=" CB ASN A 370 " ideal model delta sigma weight residual 109.03 113.66 -4.63 1.62e+00 3.81e-01 8.16e+00 angle pdb=" C LYS A 378 " pdb=" CA LYS A 378 " pdb=" CB LYS A 378 " ideal model delta sigma weight residual 111.70 108.19 3.51 1.31e+00 5.83e-01 7.19e+00 ... (remaining 8999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 3790 17.45 - 34.90: 102 34.90 - 52.36: 11 52.36 - 69.81: 1 69.81 - 87.26: 2 Dihedral angle restraints: 3906 sinusoidal: 1579 harmonic: 2327 Sorted by residual: dihedral pdb=" CB GLU B 495 " pdb=" CG GLU B 495 " pdb=" CD GLU B 495 " pdb=" OE1 GLU B 495 " ideal model delta sinusoidal sigma weight residual 0.00 87.26 -87.26 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" N ASN A 370 " pdb=" CA ASN A 370 " pdb=" CB ASN A 370 " pdb=" CG ASN A 370 " ideal model delta sinusoidal sigma weight residual 60.00 114.24 -54.24 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" N GLN B 60 " pdb=" CA GLN B 60 " pdb=" CB GLN B 60 " pdb=" CG GLN B 60 " ideal model delta sinusoidal sigma weight residual -60.00 -112.24 52.24 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 3903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 828 0.056 - 0.112: 98 0.112 - 0.168: 7 0.168 - 0.225: 0 0.225 - 0.281: 1 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA CYS A 379 " pdb=" N CYS A 379 " pdb=" C CYS A 379 " pdb=" CB CYS A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA PHE A 371 " pdb=" N PHE A 371 " pdb=" C PHE A 371 " pdb=" CB PHE A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA PHE A 377 " pdb=" N PHE A 377 " pdb=" C PHE A 377 " pdb=" CB PHE A 377 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 931 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 369 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C TYR A 369 " -0.027 2.00e-02 2.50e+03 pdb=" O TYR A 369 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN A 370 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 582 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO B 583 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 499 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO B 500 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 500 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 500 " -0.016 5.00e-02 4.00e+02 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1894 2.82 - 3.34: 5529 3.34 - 3.86: 9786 3.86 - 4.38: 11195 4.38 - 4.90: 20139 Nonbonded interactions: 48543 Sorted by model distance: nonbonded pdb=" OG1 THR B 20 " pdb=" OE1 GLU B 23 " model vdw 2.299 3.040 nonbonded pdb=" O ASN B 117 " pdb=" ND2 ASN B 121 " model vdw 2.360 3.120 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR B 41 " model vdw 2.362 3.040 nonbonded pdb=" O SER B 47 " pdb=" ND2 ASN B 51 " model vdw 2.365 3.120 nonbonded pdb=" O VAL B 59 " pdb=" ND2 ASN B 63 " model vdw 2.391 3.120 ... (remaining 48538 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: 1.510 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.160 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.002 0.041 6625 Z= 0.093 Angle : 0.416 8.314 9004 Z= 0.245 Chirality : 0.038 0.281 934 Planarity : 0.003 0.036 1167 Dihedral : 7.782 87.258 2394 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.29 % Allowed : 3.02 % Favored : 95.69 % 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: -1.69 (0.27), residues: 788 helix: -0.02 (0.26), residues: 397 sheet: 1.26 (0.68), residues: 45 loop : -2.88 (0.25), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 165 HIS 0.001 0.000 HIS B 374 PHE 0.008 0.001 PHE A 375 TYR 0.007 0.001 TYR B 516 ARG 0.002 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8202 (m-30) cc_final: 0.7990 (m-30) REVERT: B 323 MET cc_start: 0.8501 (mmt) cc_final: 0.7735 (mmt) outliers start: 9 outliers final: 3 residues processed: 151 average time/residue: 0.2533 time to fit residues: 47.3086 Evaluate side-chains 87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 199 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 493 GLN A 506 GLN B 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.051263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.044521 restraints weight = 19785.361| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 1.82 r_work: 0.2482 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2395 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6625 Z= 0.218 Angle : 0.547 6.604 9004 Z= 0.288 Chirality : 0.042 0.138 934 Planarity : 0.004 0.033 1167 Dihedral : 4.450 43.466 867 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.30 % Allowed : 6.47 % Favored : 91.24 % 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: -0.48 (0.29), residues: 788 helix: 1.12 (0.27), residues: 391 sheet: 1.76 (0.75), residues: 40 loop : -2.34 (0.26), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.004 0.001 HIS B 34 PHE 0.016 0.002 PHE B 438 TYR 0.022 0.002 TYR B 385 ARG 0.005 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: B 190 MET cc_start: 0.9202 (ttp) cc_final: 0.8949 (tmm) REVERT: B 323 MET cc_start: 0.8897 (mmt) cc_final: 0.8292 (mmt) REVERT: B 512 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8634 (m-80) outliers start: 16 outliers final: 10 residues processed: 92 average time/residue: 0.1754 time to fit residues: 22.1928 Evaluate side-chains 83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.048491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.041734 restraints weight = 20127.251| |-----------------------------------------------------------------------------| r_work (start): 0.2482 rms_B_bonded: 1.85 r_work: 0.2401 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2314 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6625 Z= 0.237 Angle : 0.558 6.397 9004 Z= 0.294 Chirality : 0.042 0.127 934 Planarity : 0.004 0.032 1167 Dihedral : 4.809 42.521 867 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.44 % Allowed : 7.47 % Favored : 90.09 % 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: -0.06 (0.29), residues: 788 helix: 1.45 (0.27), residues: 384 sheet: 1.85 (0.81), residues: 40 loop : -2.03 (0.27), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.004 0.001 HIS B 493 PHE 0.015 0.002 PHE B 438 TYR 0.021 0.002 TYR B 385 ARG 0.006 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.804 Fit side-chains REVERT: A 364 ASP cc_start: 0.8759 (t0) cc_final: 0.8436 (p0) REVERT: B 131 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8407 (ttpp) REVERT: B 190 MET cc_start: 0.9230 (ttp) cc_final: 0.8964 (tmm) REVERT: B 199 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8562 (t80) REVERT: B 323 MET cc_start: 0.8922 (mmt) cc_final: 0.8314 (mmt) outliers start: 17 outliers final: 8 residues processed: 84 average time/residue: 0.2008 time to fit residues: 22.5543 Evaluate side-chains 81 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.047996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.041278 restraints weight = 20180.695| |-----------------------------------------------------------------------------| r_work (start): 0.2468 rms_B_bonded: 1.83 r_work: 0.2386 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2299 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 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 0.045 6625 Z= 0.227 Angle : 0.539 6.553 9004 Z= 0.284 Chirality : 0.041 0.125 934 Planarity : 0.004 0.030 1167 Dihedral : 4.903 45.839 867 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.02 % Allowed : 8.33 % Favored : 88.65 % 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: 0.08 (0.29), residues: 788 helix: 1.47 (0.27), residues: 391 sheet: 1.63 (0.78), residues: 45 loop : -1.91 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 436 HIS 0.004 0.001 HIS B 374 PHE 0.018 0.002 PHE A 375 TYR 0.019 0.001 TYR B 385 ARG 0.005 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8773 (t0) cc_final: 0.8409 (p0) REVERT: B 190 MET cc_start: 0.9261 (ttp) cc_final: 0.8996 (tmm) REVERT: B 199 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8601 (t80) REVERT: B 497 TYR cc_start: 0.7686 (m-10) cc_final: 0.7447 (m-80) outliers start: 21 outliers final: 13 residues processed: 86 average time/residue: 0.1891 time to fit residues: 21.9385 Evaluate side-chains 87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.047112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.040411 restraints weight = 20142.681| |-----------------------------------------------------------------------------| r_work (start): 0.2444 rms_B_bonded: 1.84 r_work: 0.2362 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6625 Z= 0.242 Angle : 0.552 6.909 9004 Z= 0.293 Chirality : 0.042 0.130 934 Planarity : 0.004 0.030 1167 Dihedral : 5.097 51.291 867 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.16 % Allowed : 9.48 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 788 helix: 1.52 (0.27), residues: 392 sheet: 1.61 (0.76), residues: 45 loop : -1.75 (0.28), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.004 0.001 HIS B 374 PHE 0.011 0.002 PHE B 438 TYR 0.019 0.001 TYR B 385 ARG 0.003 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8762 (t0) cc_final: 0.8432 (p0) REVERT: B 190 MET cc_start: 0.9250 (ttp) cc_final: 0.8970 (tmm) REVERT: B 199 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.8645 (t80) REVERT: B 497 TYR cc_start: 0.7919 (m-80) cc_final: 0.7652 (m-80) REVERT: B 512 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8661 (m-80) outliers start: 22 outliers final: 15 residues processed: 87 average time/residue: 0.2079 time to fit residues: 23.8152 Evaluate side-chains 91 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.047865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.041198 restraints weight = 19958.509| |-----------------------------------------------------------------------------| r_work (start): 0.2467 rms_B_bonded: 1.82 r_work: 0.2386 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2299 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6625 Z= 0.203 Angle : 0.523 6.267 9004 Z= 0.276 Chirality : 0.041 0.131 934 Planarity : 0.004 0.028 1167 Dihedral : 4.947 51.278 867 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.87 % Allowed : 10.49 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.30), residues: 788 helix: 1.60 (0.27), residues: 399 sheet: 1.57 (0.77), residues: 45 loop : -1.61 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.003 0.001 HIS B 374 PHE 0.021 0.001 PHE A 375 TYR 0.018 0.001 TYR B 158 ARG 0.003 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8753 (t0) cc_final: 0.8437 (p0) REVERT: B 199 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8776 (t80) outliers start: 20 outliers final: 12 residues processed: 86 average time/residue: 0.2141 time to fit residues: 24.8198 Evaluate side-chains 86 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN B 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.044335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.037827 restraints weight = 20308.740| |-----------------------------------------------------------------------------| r_work (start): 0.2367 rms_B_bonded: 1.83 r_work: 0.2282 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2195 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6625 Z= 0.374 Angle : 0.648 7.335 9004 Z= 0.347 Chirality : 0.045 0.137 934 Planarity : 0.004 0.032 1167 Dihedral : 5.467 54.645 867 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.02 % Allowed : 11.64 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.05 (0.29), residues: 788 helix: 1.38 (0.27), residues: 389 sheet: 1.38 (0.74), residues: 45 loop : -1.79 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.006 0.001 HIS B 239 PHE 0.021 0.002 PHE A 375 TYR 0.034 0.002 TYR B 158 ARG 0.006 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8728 (t0) cc_final: 0.8498 (p0) REVERT: B 190 MET cc_start: 0.9264 (ttp) cc_final: 0.8937 (tmm) REVERT: B 255 TYR cc_start: 0.8854 (m-10) cc_final: 0.8648 (m-10) outliers start: 21 outliers final: 17 residues processed: 86 average time/residue: 0.2184 time to fit residues: 25.1192 Evaluate side-chains 89 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.048419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.041794 restraints weight = 19973.168| |-----------------------------------------------------------------------------| r_work (start): 0.2484 rms_B_bonded: 1.84 r_work: 0.2403 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2317 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6625 Z= 0.175 Angle : 0.521 6.407 9004 Z= 0.275 Chirality : 0.040 0.132 934 Planarity : 0.004 0.033 1167 Dihedral : 4.657 54.840 865 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.16 % Allowed : 13.07 % Favored : 84.77 % 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: 0.53 (0.30), residues: 788 helix: 1.69 (0.27), residues: 400 sheet: 1.67 (0.78), residues: 45 loop : -1.55 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.003 0.001 HIS B 374 PHE 0.019 0.001 PHE A 375 TYR 0.020 0.001 TYR B 158 ARG 0.002 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8761 (t0) cc_final: 0.8539 (p0) REVERT: B 255 TYR cc_start: 0.8767 (m-10) cc_final: 0.8562 (m-10) REVERT: B 512 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8602 (m-80) outliers start: 15 outliers final: 11 residues processed: 83 average time/residue: 0.2092 time to fit residues: 22.9060 Evaluate side-chains 85 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 601 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.7182 > 50: distance: 84 - 108: 12.322 distance: 91 - 116: 20.090 distance: 102 - 108: 12.191 distance: 108 - 109: 21.490 distance: 109 - 110: 26.258 distance: 109 - 112: 39.393 distance: 110 - 111: 12.804 distance: 110 - 116: 39.554 distance: 112 - 113: 39.152 distance: 113 - 114: 13.264 distance: 113 - 115: 4.035 distance: 116 - 117: 24.735 distance: 117 - 118: 31.491 distance: 117 - 120: 11.589 distance: 118 - 119: 42.527 distance: 118 - 127: 25.734 distance: 120 - 121: 36.844 distance: 122 - 123: 7.867 distance: 123 - 124: 22.430 distance: 124 - 125: 20.366 distance: 124 - 126: 19.839 distance: 127 - 128: 15.971 distance: 128 - 129: 28.618 distance: 128 - 131: 32.775 distance: 129 - 130: 27.429 distance: 129 - 135: 9.526 distance: 131 - 132: 17.054 distance: 132 - 133: 13.899 distance: 132 - 134: 18.858 distance: 135 - 136: 14.407 distance: 136 - 137: 16.571 distance: 137 - 138: 21.386 distance: 137 - 139: 10.484 distance: 139 - 140: 7.610 distance: 140 - 141: 5.950 distance: 140 - 143: 14.181 distance: 141 - 142: 26.304 distance: 141 - 148: 22.921 distance: 143 - 144: 4.284 distance: 144 - 145: 11.346 distance: 145 - 146: 8.632 distance: 146 - 147: 5.867 distance: 148 - 149: 35.011 distance: 149 - 150: 15.790 distance: 149 - 152: 19.182 distance: 150 - 151: 21.364 distance: 150 - 154: 31.214 distance: 152 - 153: 9.688 distance: 154 - 155: 19.252 distance: 155 - 156: 35.700 distance: 155 - 158: 21.663 distance: 156 - 157: 23.924 distance: 156 - 163: 37.275 distance: 158 - 159: 22.537 distance: 159 - 160: 15.569 distance: 160 - 161: 9.620 distance: 160 - 162: 28.808 distance: 163 - 164: 34.639 distance: 163 - 169: 27.468 distance: 164 - 165: 29.698 distance: 164 - 167: 18.242 distance: 165 - 166: 17.916 distance: 165 - 170: 20.124 distance: 166 - 198: 19.747 distance: 167 - 168: 19.219 distance: 168 - 169: 10.311 distance: 170 - 171: 10.429 distance: 171 - 172: 9.834 distance: 171 - 174: 5.122 distance: 172 - 173: 9.545 distance: 172 - 184: 7.537 distance: 173 - 203: 26.479 distance: 174 - 175: 13.413 distance: 175 - 176: 12.737 distance: 175 - 177: 10.775 distance: 176 - 178: 9.782 distance: 177 - 179: 13.247 distance: 177 - 180: 8.195 distance: 178 - 179: 10.816 distance: 179 - 181: 19.322 distance: 180 - 182: 9.946 distance: 181 - 183: 9.589 distance: 182 - 183: 11.330 distance: 184 - 185: 13.277 distance: 185 - 186: 12.641 distance: 185 - 188: 13.820 distance: 186 - 187: 8.807 distance: 186 - 191: 11.411 distance: 187 - 210: 17.519 distance: 188 - 189: 13.877 distance: 188 - 190: 11.303