Starting phenix.real_space_refine on Wed Jan 17 18:01:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/01_2024/8csw_26973.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/01_2024/8csw_26973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/01_2024/8csw_26973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/01_2024/8csw_26973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/01_2024/8csw_26973.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/01_2024/8csw_26973.pdb" } resolution = 2.5 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= 0.272 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 23 5.16 5 C 3278 2.51 5 N 915 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 5332 Number of models: 1 Model: "" Number of chains: 1 Chain: "X" Number of atoms: 5332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 5332 Inner-chain residues flagged as termini: ['pdbres="ALA X 691 "'] Classifications: {'peptide': 657, 'water': 165} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 626, None: 165} Not linked: pdbres="ALA X 691 " pdbres="HOH X 701 " Not linked: pdbres="HOH X 701 " pdbres="HOH X 702 " Not linked: pdbres="HOH X 702 " pdbres="HOH X 703 " Not linked: pdbres="HOH X 703 " pdbres="HOH X 704 " Not linked: pdbres="HOH X 704 " pdbres="HOH X 705 " ... (remaining 160 not shown) Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 3.40, per 1000 atoms: 0.64 Number of scatterers: 5332 At special positions: 0 Unit cell: (95.45, 102.92, 71.795, 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 23 16.00 O 1116 8.00 N 915 7.00 C 3278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 891.6 milliseconds 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1232 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 10 sheets defined 21.2% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 51 through 58 removed outlier: 3.658A pdb=" N ALA X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 159 Processing helix chain 'X' and resid 187 through 197 Processing helix chain 'X' and resid 201 through 206 removed outlier: 3.998A pdb=" N SER X 206 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 227 Processing helix chain 'X' and resid 247 through 258 removed outlier: 4.118A pdb=" N ILE X 251 " --> pdb=" O GLY X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 268 Processing helix chain 'X' and resid 269 through 283 removed outlier: 4.363A pdb=" N ALA X 273 " --> pdb=" O TRP X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 373 Processing helix chain 'X' and resid 381 through 389 removed outlier: 3.745A pdb=" N ILE X 389 " --> pdb=" O LEU X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 436 removed outlier: 3.869A pdb=" N TYR X 435 " --> pdb=" O ILE X 431 " (cutoff:3.500A) Processing helix chain 'X' and resid 441 through 459 Processing helix chain 'X' and resid 550 through 552 No H-bonds generated for 'chain 'X' and resid 550 through 552' Processing sheet with id=AA1, first strand: chain 'X' and resid 7 through 11 removed outlier: 3.509A pdb=" N GLU X 96 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER X 105 " --> pdb=" O VAL X 94 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL X 94 " --> pdb=" O SER X 105 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR X 107 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ALA X 92 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 31 through 34 removed outlier: 4.693A pdb=" N LEU X 31 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU X 130 " --> pdb=" O LEU X 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU X 121 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY X 132 " --> pdb=" O LEU X 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 163 through 169 Processing sheet with id=AA4, first strand: chain 'X' and resid 322 through 327 removed outlier: 6.303A pdb=" N PHE X 326 " --> pdb=" O PHE X 292 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE X 292 " --> pdb=" O PHE X 326 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR X 330 " --> pdb=" O LEU X 349 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER X 362 " --> pdb=" O SER X 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 322 through 327 removed outlier: 6.303A pdb=" N PHE X 326 " --> pdb=" O PHE X 292 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE X 292 " --> pdb=" O PHE X 326 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL X 288 " --> pdb=" O LYS X 421 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS X 421 " --> pdb=" O VAL X 288 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE X 292 " --> pdb=" O ASN X 417 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN X 417 " --> pdb=" O PHE X 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 303 through 308 removed outlier: 6.068A pdb=" N ILE X 304 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TRP X 396 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU X 306 " --> pdb=" O TRP X 396 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N CYS X 398 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR X 308 " --> pdb=" O CYS X 398 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N CYS X 393 " --> pdb=" O SER X 409 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N SER X 409 " --> pdb=" O CYS X 393 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL X 395 " --> pdb=" O THR X 407 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER X 576 " --> pdb=" O LEU X 406 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU X 485 " --> pdb=" O CYS X 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 303 through 308 removed outlier: 6.068A pdb=" N ILE X 304 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TRP X 396 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU X 306 " --> pdb=" O TRP X 396 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N CYS X 398 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR X 308 " --> pdb=" O CYS X 398 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N CYS X 393 " --> pdb=" O SER X 409 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N SER X 409 " --> pdb=" O CYS X 393 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL X 395 " --> pdb=" O THR X 407 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER X 576 " --> pdb=" O LEU X 406 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS X 505 " --> pdb=" O LEU X 533 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU X 533 " --> pdb=" O LYS X 505 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL X 507 " --> pdb=" O LEU X 531 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU X 531 " --> pdb=" O VAL X 507 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU X 509 " --> pdb=" O LYS X 529 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS X 529 " --> pdb=" O LEU X 509 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE X 511 " --> pdb=" O TRP X 527 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TRP X 527 " --> pdb=" O ILE X 511 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL X 513 " --> pdb=" O LYS X 525 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LYS X 525 " --> pdb=" O VAL X 513 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA X 515 " --> pdb=" O ALA X 523 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 475 through 480 Processing sheet with id=AA9, first strand: chain 'X' and resid 590 through 593 Processing sheet with id=AB1, first strand: chain 'X' and resid 597 through 599 removed outlier: 6.536A pdb=" N ALA X 598 " --> pdb=" O VAL X 685 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 899 1.32 - 1.44: 1339 1.44 - 1.57: 3004 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 5273 Sorted by residual: bond pdb=" N TRP X 89 " pdb=" CA TRP X 89 " ideal model delta sigma weight residual 1.454 1.493 -0.040 1.17e-02 7.31e+03 1.14e+01 bond pdb=" N GLU X 405 " pdb=" CA GLU X 405 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.21e-02 6.83e+03 1.06e+01 bond pdb=" N ILE X 104 " pdb=" CA ILE X 104 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA SER X 105 " pdb=" CB SER X 105 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.43e-02 4.89e+03 9.52e+00 bond pdb=" N VAL X 211 " pdb=" CA VAL X 211 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.17e+00 ... (remaining 5268 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.63: 164 106.63 - 113.57: 2909 113.57 - 120.51: 2000 120.51 - 127.45: 2013 127.45 - 134.39: 67 Bond angle restraints: 7153 Sorted by residual: angle pdb=" N ASP X 408 " pdb=" CA ASP X 408 " pdb=" C ASP X 408 " ideal model delta sigma weight residual 109.96 101.96 8.00 1.50e+00 4.44e-01 2.85e+01 angle pdb=" C THR X 403 " pdb=" N LEU X 404 " pdb=" CA LEU X 404 " ideal model delta sigma weight residual 123.11 117.38 5.73 1.42e+00 4.96e-01 1.63e+01 angle pdb=" C GLY X 85 " pdb=" N ASP X 86 " pdb=" CA ASP X 86 " ideal model delta sigma weight residual 121.99 116.05 5.94 1.49e+00 4.50e-01 1.59e+01 angle pdb=" CA LEU X 404 " pdb=" C LEU X 404 " pdb=" O LEU X 404 " ideal model delta sigma weight residual 120.46 116.22 4.24 1.07e+00 8.73e-01 1.57e+01 angle pdb=" CB ARG X 287 " pdb=" CG ARG X 287 " pdb=" CD ARG X 287 " ideal model delta sigma weight residual 111.30 102.41 8.89 2.30e+00 1.89e-01 1.49e+01 ... (remaining 7148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 2890 17.21 - 34.42: 199 34.42 - 51.63: 59 51.63 - 68.84: 21 68.84 - 86.04: 7 Dihedral angle restraints: 3176 sinusoidal: 1276 harmonic: 1900 Sorted by residual: dihedral pdb=" CA GLU X 185 " pdb=" C GLU X 185 " pdb=" N GLY X 186 " pdb=" CA GLY X 186 " ideal model delta harmonic sigma weight residual -180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ILE X 418 " pdb=" C ILE X 418 " pdb=" N SER X 419 " pdb=" CA SER X 419 " ideal model delta harmonic sigma weight residual -180.00 -163.11 -16.89 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" C ILE X 431 " pdb=" N ILE X 431 " pdb=" CA ILE X 431 " pdb=" CB ILE X 431 " ideal model delta harmonic sigma weight residual -122.00 -129.86 7.86 0 2.50e+00 1.60e-01 9.88e+00 ... (remaining 3173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 577 0.050 - 0.100: 168 0.100 - 0.150: 39 0.150 - 0.199: 17 0.199 - 0.249: 8 Chirality restraints: 809 Sorted by residual: chirality pdb=" CB VAL X 106 " pdb=" CA VAL X 106 " pdb=" CG1 VAL X 106 " pdb=" CG2 VAL X 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA LEU X 349 " pdb=" N LEU X 349 " pdb=" C LEU X 349 " pdb=" CB LEU X 349 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA SER X 329 " pdb=" N SER X 329 " pdb=" C SER X 329 " pdb=" CB SER X 329 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 806 not shown) Planarity restraints: 921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP X 364 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C ASP X 364 " 0.057 2.00e-02 2.50e+03 pdb=" O ASP X 364 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU X 365 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER X 576 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C SER X 576 " -0.052 2.00e-02 2.50e+03 pdb=" O SER X 576 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS X 577 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP X 89 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C TRP X 89 " -0.046 2.00e-02 2.50e+03 pdb=" O TRP X 89 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP X 90 " 0.016 2.00e-02 2.50e+03 ... (remaining 918 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 691 2.76 - 3.29: 4879 3.29 - 3.83: 9713 3.83 - 4.36: 11710 4.36 - 4.90: 19288 Nonbonded interactions: 46281 Sorted by model distance: nonbonded pdb=" O HOH X 738 " pdb=" O HOH X 851 " model vdw 2.219 2.440 nonbonded pdb=" O HOH X 768 " pdb=" O HOH X 798 " model vdw 2.236 2.440 nonbonded pdb=" O HOH X 792 " pdb=" O HOH X 838 " model vdw 2.261 2.440 nonbonded pdb=" O HOH X 755 " pdb=" O HOH X 839 " model vdw 2.271 2.440 nonbonded pdb=" O ASP X 426 " pdb=" O HOH X 701 " model vdw 2.283 2.440 ... (remaining 46276 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: 1.350 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: 5.680 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 19.420 Find NCS groups from input model: 0.150 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 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 : 0.007 0.047 5273 Z= 0.429 Angle : 0.862 8.892 7153 Z= 0.555 Chirality : 0.057 0.249 809 Planarity : 0.006 0.038 921 Dihedral : 14.462 86.044 1944 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.33 % Allowed : 8.24 % Favored : 89.43 % 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: 0.83 (0.31), residues: 647 helix: 0.80 (0.45), residues: 116 sheet: 0.87 (0.31), residues: 250 loop : 0.30 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 90 HIS 0.005 0.001 HIS X 632 PHE 0.022 0.002 PHE X 639 TYR 0.017 0.002 TYR X 167 ARG 0.003 0.001 ARG X 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.642 Fit side-chains REVERT: X 16 ARG cc_start: 0.7419 (ttm170) cc_final: 0.7217 (tmm-80) REVERT: X 88 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7557 (mmpt) REVERT: X 143 ARG cc_start: 0.8201 (ttp-170) cc_final: 0.7961 (ttm-80) REVERT: X 194 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7695 (ttp-110) REVERT: X 442 LEU cc_start: 0.8074 (mp) cc_final: 0.7733 (mm) REVERT: X 445 LYS cc_start: 0.8096 (tmtt) cc_final: 0.7647 (ttpp) REVERT: X 446 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7537 (tm-30) REVERT: X 452 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6893 (mt-10) REVERT: X 483 SER cc_start: 0.8344 (p) cc_final: 0.8047 (m) REVERT: X 508 GLN cc_start: 0.7339 (tt0) cc_final: 0.6839 (mt0) REVERT: X 593 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8154 (tppt) REVERT: X 638 ARG cc_start: 0.7856 (mpt90) cc_final: 0.6170 (mtm110) REVERT: X 647 THR cc_start: 0.8417 (m) cc_final: 0.8179 (p) REVERT: X 651 LYS cc_start: 0.7522 (mptt) cc_final: 0.7244 (pttp) outliers start: 13 outliers final: 6 residues processed: 130 average time/residue: 1.4185 time to fit residues: 191.2938 Evaluate side-chains 111 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 404 LEU Chi-restraints excluded: chain X residue 406 LEU Chi-restraints excluded: chain X residue 549 PHE Chi-restraints excluded: chain X residue 576 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 50.0000 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 50.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 64 GLN X 76 GLN X 133 GLN X 154 GLN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 433 GLN X 570 HIS ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5273 Z= 0.274 Angle : 0.567 5.538 7153 Z= 0.294 Chirality : 0.043 0.150 809 Planarity : 0.005 0.043 921 Dihedral : 6.756 59.902 719 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.87 % Allowed : 11.47 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.31), residues: 647 helix: 1.65 (0.45), residues: 114 sheet: 0.60 (0.31), residues: 247 loop : 0.38 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 90 HIS 0.005 0.001 HIS X 570 PHE 0.014 0.002 PHE X 639 TYR 0.017 0.002 TYR X 167 ARG 0.008 0.001 ARG X 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.579 Fit side-chains REVERT: X 127 LYS cc_start: 0.6402 (ttpp) cc_final: 0.5935 (ttpt) REVERT: X 133 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7712 (mm110) REVERT: X 143 ARG cc_start: 0.8208 (ttp-170) cc_final: 0.7966 (ttm-80) REVERT: X 194 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7690 (ttp-110) REVERT: X 199 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8382 (t70) REVERT: X 442 LEU cc_start: 0.7969 (mp) cc_final: 0.7660 (mm) REVERT: X 445 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7676 (ttpp) REVERT: X 452 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6889 (mt-10) REVERT: X 483 SER cc_start: 0.8319 (p) cc_final: 0.8038 (m) REVERT: X 593 LYS cc_start: 0.8386 (ttmm) cc_final: 0.8138 (tppt) REVERT: X 638 ARG cc_start: 0.7836 (mpt90) cc_final: 0.6030 (mtm110) REVERT: X 651 LYS cc_start: 0.7488 (mptt) cc_final: 0.7173 (ptmm) outliers start: 16 outliers final: 7 residues processed: 113 average time/residue: 1.2960 time to fit residues: 152.1545 Evaluate side-chains 108 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 199 ASP Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 549 PHE Chi-restraints excluded: chain X residue 576 SER Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 50.0000 chunk 80 optimal weight: 50.0000 chunk 66 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 133 GLN X 154 GLN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5273 Z= 0.180 Angle : 0.504 5.431 7153 Z= 0.259 Chirality : 0.041 0.133 809 Planarity : 0.004 0.035 921 Dihedral : 5.677 59.410 715 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.69 % Allowed : 12.01 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.32), residues: 647 helix: 1.88 (0.46), residues: 116 sheet: 0.54 (0.31), residues: 254 loop : 0.60 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 90 HIS 0.003 0.001 HIS X 22 PHE 0.010 0.001 PHE X 639 TYR 0.014 0.001 TYR X 167 ARG 0.009 0.000 ARG X 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.567 Fit side-chains REVERT: X 127 LYS cc_start: 0.6383 (ttpp) cc_final: 0.5939 (ttpt) REVERT: X 133 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7547 (mm110) REVERT: X 143 ARG cc_start: 0.8201 (ttp-170) cc_final: 0.7971 (ttm-80) REVERT: X 442 LEU cc_start: 0.7936 (mp) cc_final: 0.7660 (mm) REVERT: X 445 LYS cc_start: 0.8078 (tmtt) cc_final: 0.7688 (ttpp) REVERT: X 446 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7665 (tm-30) REVERT: X 452 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6853 (mt-10) REVERT: X 483 SER cc_start: 0.8281 (p) cc_final: 0.8040 (m) REVERT: X 593 LYS cc_start: 0.8341 (ttmm) cc_final: 0.8060 (ttmt) REVERT: X 638 ARG cc_start: 0.7802 (mpt90) cc_final: 0.5984 (mtm110) REVERT: X 651 LYS cc_start: 0.7456 (mptt) cc_final: 0.7149 (ptmm) REVERT: X 672 MET cc_start: 0.8533 (mmp) cc_final: 0.8204 (mmm) outliers start: 15 outliers final: 7 residues processed: 109 average time/residue: 1.4004 time to fit residues: 158.2416 Evaluate side-chains 106 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 404 LEU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 576 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 62.6004 > 50: distance: 5 - 9: 10.117 distance: 9 - 10: 19.032 distance: 10 - 11: 11.505 distance: 10 - 13: 5.013 distance: 11 - 12: 10.416 distance: 11 - 17: 25.070 distance: 13 - 14: 24.487 distance: 14 - 15: 19.811 distance: 15 - 16: 9.081 distance: 17 - 18: 8.041 distance: 17 - 23: 19.485 distance: 18 - 19: 18.357 distance: 18 - 21: 9.023 distance: 19 - 24: 13.832 distance: 21 - 22: 9.356 distance: 22 - 23: 22.708 distance: 24 - 25: 18.260 distance: 25 - 26: 17.600 distance: 25 - 28: 8.171 distance: 26 - 27: 15.468 distance: 26 - 33: 14.980 distance: 29 - 30: 8.819 distance: 30 - 31: 3.477 distance: 30 - 32: 4.368 distance: 33 - 34: 4.869 distance: 34 - 35: 6.935 distance: 34 - 37: 10.421 distance: 35 - 36: 6.471 distance: 35 - 42: 9.630 distance: 37 - 38: 11.029 distance: 38 - 39: 8.176 distance: 39 - 40: 6.577 distance: 40 - 41: 10.313 distance: 42 - 43: 17.929 distance: 43 - 44: 14.013 distance: 43 - 46: 22.790 distance: 44 - 45: 15.636 distance: 44 - 47: 21.715 distance: 47 - 48: 9.778 distance: 48 - 49: 24.122 distance: 48 - 51: 10.701 distance: 49 - 50: 20.839 distance: 49 - 56: 25.464 distance: 51 - 52: 6.025 distance: 52 - 53: 11.589 distance: 53 - 54: 9.519 distance: 53 - 55: 14.504 distance: 56 - 57: 9.446 distance: 57 - 58: 8.583 distance: 57 - 60: 35.637 distance: 58 - 59: 10.854 distance: 58 - 65: 21.808 distance: 60 - 61: 7.571 distance: 61 - 62: 27.754 distance: 62 - 63: 12.176 distance: 62 - 64: 8.629 distance: 65 - 66: 10.915 distance: 66 - 67: 16.836 distance: 66 - 69: 12.779 distance: 67 - 68: 32.407 distance: 67 - 77: 13.933 distance: 69 - 70: 3.043 distance: 70 - 71: 20.035 distance: 70 - 72: 32.086 distance: 71 - 73: 4.844 distance: 72 - 74: 9.625 distance: 73 - 75: 22.757 distance: 74 - 75: 29.929 distance: 75 - 76: 9.392 distance: 77 - 78: 10.530 distance: 78 - 79: 18.183 distance: 78 - 81: 30.169 distance: 79 - 80: 7.335 distance: 79 - 86: 16.743 distance: 81 - 82: 28.707 distance: 82 - 83: 31.306 distance: 83 - 84: 23.101 distance: 83 - 85: 13.738 distance: 86 - 87: 24.047 distance: 87 - 88: 19.843 distance: 87 - 90: 18.579 distance: 88 - 89: 20.013 distance: 88 - 93: 20.493 distance: 90 - 91: 9.039 distance: 91 - 92: 33.732