Starting phenix.real_space_refine on Mon Mar 11 01:43:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sy0_25512/03_2024/7sy0_25512.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sy0_25512/03_2024/7sy0_25512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sy0_25512/03_2024/7sy0_25512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sy0_25512/03_2024/7sy0_25512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sy0_25512/03_2024/7sy0_25512.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sy0_25512/03_2024/7sy0_25512.pdb" } resolution = 3.0 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= -0.001 sd= 0.029 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 4186 2.51 5 N 1081 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6553 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1593 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.23, per 1000 atoms: 0.65 Number of scatterers: 6553 At special positions: 0 Unit cell: (79, 84, 121, 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 1249 8.00 N 1081 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.4 seconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 57.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.708A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.162A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.781A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.028A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 3.933A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.725A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.669A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.784A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.541A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.701A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.235A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.310A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.726A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.458A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.931A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.911A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.620A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.966A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.313A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 918 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: 1.77 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2086 1.35 - 1.47: 1795 1.47 - 1.60: 2796 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6735 Sorted by residual: bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C1 NAG E 704 " pdb=" O5 NAG E 704 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 NAG E 705 " pdb=" O5 NAG E 705 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.35e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.95e+00 bond pdb=" C SER E 611 " pdb=" N PRO E 612 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.73e+00 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 98.55 - 105.66: 170 105.66 - 112.77: 3385 112.77 - 119.88: 2455 119.88 - 127.00: 3025 127.00 - 134.11: 117 Bond angle restraints: 9152 Sorted by residual: angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 128.96 -6.14 1.42e+00 4.96e-01 1.87e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.65 -9.25 2.30e+00 1.89e-01 1.62e+01 angle pdb=" CB MET E 323 " pdb=" CG MET E 323 " pdb=" SD MET E 323 " ideal model delta sigma weight residual 112.70 122.94 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CA ASN E 437 " pdb=" CB ASN E 437 " pdb=" CG ASN E 437 " ideal model delta sigma weight residual 112.60 115.96 -3.36 1.00e+00 1.00e+00 1.13e+01 angle pdb=" N LYS E 234 " pdb=" CA LYS E 234 " pdb=" C LYS E 234 " ideal model delta sigma weight residual 113.16 117.68 -4.52 1.42e+00 4.96e-01 1.01e+01 ... (remaining 9147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 3688 17.12 - 34.25: 314 34.25 - 51.37: 43 51.37 - 68.50: 11 68.50 - 85.62: 12 Dihedral angle restraints: 4068 sinusoidal: 1730 harmonic: 2338 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -42.93 -43.07 1 1.00e+01 1.00e-02 2.59e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 17.52 61.48 1 2.00e+01 2.50e-03 1.25e+01 dihedral pdb=" C ASN B 360 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual -122.60 -130.76 8.16 0 2.50e+00 1.60e-01 1.06e+01 ... (remaining 4065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 724 0.055 - 0.109: 197 0.109 - 0.164: 46 0.164 - 0.218: 7 0.218 - 0.273: 3 Chirality restraints: 977 Sorted by residual: chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " 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=" CB VAL E 581 " pdb=" CA VAL E 581 " pdb=" CG1 VAL E 581 " pdb=" CG2 VAL E 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL E 318 " pdb=" CA VAL E 318 " pdb=" CG1 VAL E 318 " pdb=" CG2 VAL E 318 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 974 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 36 " 0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ALA E 36 " -0.086 2.00e-02 2.50e+03 pdb=" O ALA E 36 " 0.032 2.00e-02 2.50e+03 pdb=" N GLU E 37 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C ARG E 169 " -0.060 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.022 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 32 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C PHE E 32 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE E 32 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN E 33 " 0.018 2.00e-02 2.50e+03 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1834 2.82 - 3.34: 5957 3.34 - 3.86: 11435 3.86 - 4.38: 12999 4.38 - 4.90: 22431 Nonbonded interactions: 54656 Sorted by model distance: nonbonded pdb=" OG1 THR B 500 " pdb=" OH TYR E 41 " model vdw 2.295 2.440 nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.322 2.440 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.335 2.440 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.335 2.440 nonbonded pdb=" OD1 ASN B 487 " pdb=" OH TYR E 83 " model vdw 2.338 2.440 ... (remaining 54651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.430 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.100 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.005 0.057 6735 Z= 0.327 Angle : 0.843 10.244 9152 Z= 0.460 Chirality : 0.055 0.273 977 Planarity : 0.007 0.065 1178 Dihedral : 13.353 85.622 2550 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.49 (0.26), residues: 793 helix: -0.06 (0.23), residues: 387 sheet: 0.55 (0.66), residues: 52 loop : -0.63 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 165 HIS 0.004 0.001 HIS E 374 PHE 0.030 0.003 PHE E 369 TYR 0.032 0.002 TYR E 385 ARG 0.011 0.001 ARG E 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: E 142 LEU cc_start: 0.9130 (mt) cc_final: 0.8923 (mt) REVERT: E 149 ASN cc_start: 0.9200 (m-40) cc_final: 0.8949 (m-40) REVERT: E 249 MET cc_start: 0.9324 (ttm) cc_final: 0.9031 (ttp) REVERT: E 290 ASN cc_start: 0.8984 (t0) cc_final: 0.8685 (t0) REVERT: E 347 THR cc_start: 0.8821 (m) cc_final: 0.8354 (p) REVERT: E 371 THR cc_start: 0.9207 (m) cc_final: 0.8930 (p) REVERT: E 441 LYS cc_start: 0.8993 (tttp) cc_final: 0.8572 (ttmm) REVERT: E 455 MET cc_start: 0.8781 (tmm) cc_final: 0.8460 (tmm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 1.3443 time to fit residues: 178.8019 Evaluate side-chains 59 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN B 501 ASN E 154 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6735 Z= 0.274 Angle : 0.578 9.315 9152 Z= 0.301 Chirality : 0.042 0.148 977 Planarity : 0.005 0.037 1178 Dihedral : 5.258 55.121 1013 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.86 % Allowed : 9.57 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.90 (0.28), residues: 793 helix: 1.20 (0.25), residues: 392 sheet: 0.96 (0.75), residues: 43 loop : -0.02 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.016 0.001 PHE E 400 TYR 0.011 0.001 TYR E 516 ARG 0.006 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 53 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: E 55 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8675 (p) REVERT: E 149 ASN cc_start: 0.9254 (m-40) cc_final: 0.8952 (m110) REVERT: E 249 MET cc_start: 0.9341 (ttm) cc_final: 0.9009 (ttp) REVERT: E 347 THR cc_start: 0.8881 (m) cc_final: 0.8422 (p) REVERT: E 366 MET cc_start: 0.8509 (ttp) cc_final: 0.8242 (ttm) REVERT: E 441 LYS cc_start: 0.8946 (tttp) cc_final: 0.8548 (ttmm) REVERT: E 455 MET cc_start: 0.8904 (tmm) cc_final: 0.8639 (tmm) REVERT: E 474 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7551 (mmt) outliers start: 20 outliers final: 8 residues processed: 67 average time/residue: 1.1924 time to fit residues: 84.6099 Evaluate side-chains 57 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6735 Z= 0.259 Angle : 0.530 6.342 9152 Z= 0.275 Chirality : 0.041 0.147 977 Planarity : 0.004 0.040 1178 Dihedral : 4.930 55.475 1013 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.29 % Allowed : 10.29 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.48 (0.30), residues: 793 helix: 1.62 (0.26), residues: 391 sheet: 1.03 (0.77), residues: 43 loop : 0.39 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.015 0.001 PHE E 400 TYR 0.012 0.001 TYR E 385 ARG 0.006 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: B 428 ASP cc_start: 0.8870 (p0) cc_final: 0.8622 (p0) REVERT: B 523 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8269 (t) REVERT: E 149 ASN cc_start: 0.9259 (m-40) cc_final: 0.8864 (m110) REVERT: E 249 MET cc_start: 0.9294 (ttm) cc_final: 0.8890 (ttp) REVERT: E 347 THR cc_start: 0.8888 (m) cc_final: 0.8450 (p) REVERT: E 441 LYS cc_start: 0.9022 (tttp) cc_final: 0.8581 (ttmm) outliers start: 16 outliers final: 8 residues processed: 63 average time/residue: 1.1505 time to fit residues: 76.9351 Evaluate side-chains 58 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 506 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.4316 > 50: distance: 20 - 42: 30.997 distance: 25 - 50: 18.772 distance: 33 - 58: 9.673 distance: 36 - 42: 29.324 distance: 37 - 66: 21.164 distance: 42 - 43: 42.950 distance: 43 - 44: 18.953 distance: 43 - 46: 20.343 distance: 44 - 45: 29.887 distance: 44 - 50: 12.920 distance: 45 - 71: 21.588 distance: 46 - 47: 16.491 distance: 47 - 48: 14.048 distance: 47 - 49: 11.056 distance: 50 - 51: 22.934 distance: 51 - 52: 18.163 distance: 51 - 54: 17.385 distance: 52 - 53: 16.119 distance: 52 - 58: 16.616 distance: 54 - 55: 4.508 distance: 55 - 56: 8.401 distance: 56 - 57: 9.198 distance: 58 - 59: 27.130 distance: 59 - 60: 17.642 distance: 59 - 62: 45.715 distance: 60 - 61: 28.337 distance: 60 - 66: 29.064 distance: 62 - 63: 20.280 distance: 63 - 64: 23.448 distance: 63 - 65: 17.002 distance: 66 - 67: 45.839 distance: 67 - 68: 31.095 distance: 67 - 70: 43.097 distance: 68 - 69: 23.569 distance: 68 - 71: 44.629 distance: 71 - 72: 47.001 distance: 72 - 73: 41.643 distance: 72 - 75: 38.414 distance: 73 - 74: 32.139 distance: 73 - 83: 42.178 distance: 75 - 76: 7.508 distance: 76 - 77: 17.931 distance: 76 - 78: 4.834 distance: 77 - 79: 10.362 distance: 78 - 80: 9.006 distance: 79 - 81: 4.590 distance: 80 - 81: 13.519 distance: 81 - 82: 10.392 distance: 83 - 84: 38.599 distance: 83 - 89: 30.634 distance: 84 - 85: 31.391 distance: 84 - 87: 22.262 distance: 85 - 86: 21.298 distance: 85 - 90: 32.852 distance: 87 - 88: 6.512 distance: 88 - 89: 9.625 distance: 90 - 91: 25.261 distance: 91 - 92: 8.830 distance: 91 - 94: 11.177 distance: 92 - 93: 21.134 distance: 92 - 96: 28.653 distance: 94 - 95: 18.837 distance: 96 - 97: 36.985 distance: 97 - 98: 37.431 distance: 97 - 100: 51.505 distance: 98 - 99: 12.692 distance: 98 - 108: 16.587 distance: 100 - 101: 33.200 distance: 101 - 102: 9.102 distance: 101 - 103: 7.550 distance: 102 - 104: 9.604 distance: 103 - 105: 12.698 distance: 105 - 106: 8.280 distance: 106 - 107: 6.779 distance: 108 - 109: 17.128 distance: 109 - 110: 14.190 distance: 109 - 112: 20.143 distance: 110 - 111: 29.135 distance: 110 - 116: 48.663 distance: 112 - 113: 26.407 distance: 112 - 114: 15.973 distance: 113 - 115: 14.685 distance: 116 - 117: 18.874 distance: 117 - 118: 24.508 distance: 117 - 120: 23.625 distance: 118 - 119: 31.889 distance: 118 - 122: 19.611 distance: 120 - 121: 3.218