Starting phenix.real_space_refine on Thu Dec 7 23:16:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/12_2023/7yqm_34029.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/12_2023/7yqm_34029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/12_2023/7yqm_34029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/12_2023/7yqm_34029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/12_2023/7yqm_34029.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/12_2023/7yqm_34029.pdb" } resolution = 2.89 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= 0.036 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 29 5.16 5 C 3543 2.51 5 N 1015 2.21 5 O 1069 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 49": "OE1" <-> "OE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5656 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5656 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 31, 'TRANS': 691} Time building chain proxies: 3.52, per 1000 atoms: 0.62 Number of scatterers: 5656 At special positions: 0 Unit cell: (76.446, 81.378, 93.708, 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 29 16.00 O 1069 8.00 N 1015 7.00 C 3543 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: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 53.0% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 Processing helix chain 'A' and resid 31 through 71 Proline residue: A 48 - end of helix Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 159 through 178 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 279 through 296 Processing helix chain 'A' and resid 359 through 378 removed outlier: 4.224A pdb=" N TYR A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 414 removed outlier: 4.033A pdb=" N GLU A 398 " --> pdb=" O HIS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 434 through 440 Processing helix chain 'A' and resid 453 through 464 Processing helix chain 'A' and resid 465 through 468 removed outlier: 3.573A pdb=" N GLY A 468 " --> pdb=" O MET A 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.812A pdb=" N LYS A 477 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 496 removed outlier: 3.604A pdb=" N LYS A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 522 Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 537 through 551 removed outlier: 4.384A pdb=" N LEU A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 548 " --> pdb=" O HIS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 563 through 567 removed outlier: 5.878A pdb=" N ASN A 566 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 567 " --> pdb=" O GLU A 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 567' Processing helix chain 'A' and resid 568 through 577 Processing helix chain 'A' and resid 588 through 613 removed outlier: 4.039A pdb=" N ARG A 609 " --> pdb=" O GLY A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 648 Processing helix chain 'A' and resid 652 through 671 Processing helix chain 'A' and resid 683 through 686 Processing helix chain 'A' and resid 687 through 699 Processing helix chain 'A' and resid 700 through 707 Proline residue: A 704 - end of helix Processing helix chain 'A' and resid 708 through 723 removed outlier: 3.540A pdb=" N HIS A 723 " --> pdb=" O GLU A 719 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 8.214A pdb=" N VAL A 348 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE A 349 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 503 through 505 removed outlier: 6.809A pdb=" N ALA A 447 " --> pdb=" O GLN A 503 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLY A 505 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 449 " --> pdb=" O GLY A 505 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA A 447 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N MET A 422 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 449 " --> pdb=" O MET A 422 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A 424 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 451 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP A 426 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 386 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY A 423 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 388 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N MET A 425 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LYS A 390 " --> pdb=" O MET A 425 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU A 335 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N VAL A 389 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 337 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR A 267 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG A 338 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 269 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN A 116 " --> pdb=" O VAL A 535 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 137 removed outlier: 3.540A pdb=" N ASP A 258 " --> pdb=" O GLN A 241 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N HIS A 237 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR A 227 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N CYS A 228 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS A 232 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE A 216 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY A 221 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 11.966A pdb=" N HIS A 318 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 194 removed outlier: 6.648A pdb=" N GLN A 201 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE A 191 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG A 199 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL A 193 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA6, first strand: chain 'A' and resid 620 through 621 289 hydrogen bonds defined for protein. 834 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: 1.82 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 983 1.30 - 1.42: 1403 1.42 - 1.55: 3289 1.55 - 1.68: 37 1.68 - 1.81: 52 Bond restraints: 5764 Sorted by residual: bond pdb=" C SER A 437 " pdb=" O SER A 437 " ideal model delta sigma weight residual 1.237 1.169 0.067 1.17e-02 7.31e+03 3.32e+01 bond pdb=" C GLU A 49 " pdb=" O GLU A 49 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.29e-02 6.01e+03 1.80e+01 bond pdb=" CA ILE A 642 " pdb=" CB ILE A 642 " ideal model delta sigma weight residual 1.540 1.589 -0.050 1.29e-02 6.01e+03 1.49e+01 bond pdb=" CA THR A 209 " pdb=" CB THR A 209 " ideal model delta sigma weight residual 1.532 1.587 -0.056 1.45e-02 4.76e+03 1.47e+01 bond pdb=" C ILE A 642 " pdb=" O ILE A 642 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.19e-02 7.06e+03 1.05e+01 ... (remaining 5759 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.10: 187 107.10 - 113.83: 3196 113.83 - 120.57: 2255 120.57 - 127.30: 2106 127.30 - 134.04: 68 Bond angle restraints: 7812 Sorted by residual: angle pdb=" N GLU A 49 " pdb=" CA GLU A 49 " pdb=" C GLU A 49 " ideal model delta sigma weight residual 112.23 106.86 5.37 1.26e+00 6.30e-01 1.82e+01 angle pdb=" CA LEU A 491 " pdb=" C LEU A 491 " pdb=" N SER A 492 " ideal model delta sigma weight residual 117.63 122.73 -5.10 1.25e+00 6.40e-01 1.66e+01 angle pdb=" N ASP A 668 " pdb=" CA ASP A 668 " pdb=" C ASP A 668 " ideal model delta sigma weight residual 111.07 106.73 4.34 1.07e+00 8.73e-01 1.65e+01 angle pdb=" N ILE A 642 " pdb=" CA ILE A 642 " pdb=" CB ILE A 642 " ideal model delta sigma weight residual 110.58 116.35 -5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" C ASP A 668 " pdb=" CA ASP A 668 " pdb=" CB ASP A 668 " ideal model delta sigma weight residual 110.88 104.99 5.89 1.57e+00 4.06e-01 1.41e+01 ... (remaining 7807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 3286 16.84 - 33.68: 168 33.68 - 50.51: 26 50.51 - 67.35: 11 67.35 - 84.19: 8 Dihedral angle restraints: 3499 sinusoidal: 1415 harmonic: 2084 Sorted by residual: dihedral pdb=" CA LEU A 343 " pdb=" C LEU A 343 " pdb=" N MET A 344 " pdb=" CA MET A 344 " ideal model delta harmonic sigma weight residual -180.00 -162.90 -17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CB MET A 470 " pdb=" CG MET A 470 " pdb=" SD MET A 470 " pdb=" CE MET A 470 " ideal model delta sinusoidal sigma weight residual 60.00 109.11 -49.11 3 1.50e+01 4.44e-03 8.73e+00 dihedral pdb=" CA GLN A 186 " pdb=" CB GLN A 186 " pdb=" CG GLN A 186 " pdb=" CD GLN A 186 " ideal model delta sinusoidal sigma weight residual 180.00 133.88 46.12 3 1.50e+01 4.44e-03 8.28e+00 ... (remaining 3496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 712 0.050 - 0.100: 108 0.100 - 0.150: 35 0.150 - 0.201: 4 0.201 - 0.251: 5 Chirality restraints: 864 Sorted by residual: chirality pdb=" CG LEU A 210 " pdb=" CB LEU A 210 " pdb=" CD1 LEU A 210 " pdb=" CD2 LEU A 210 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 118 " pdb=" CA VAL A 118 " pdb=" CG1 VAL A 118 " pdb=" CG2 VAL A 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.86 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU A 491 " pdb=" CB LEU A 491 " pdb=" CD1 LEU A 491 " pdb=" CD2 LEU A 491 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 861 not shown) Planarity restraints: 1034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 197 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C GLN A 197 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN A 197 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 198 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 490 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.31e+00 pdb=" C VAL A 490 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 490 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 491 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 569 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C PHE A 569 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE A 569 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 570 " 0.010 2.00e-02 2.50e+03 ... (remaining 1031 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1550 2.82 - 3.34: 5621 3.34 - 3.86: 9547 3.86 - 4.38: 11823 4.38 - 4.90: 20105 Nonbonded interactions: 48646 Sorted by model distance: nonbonded pdb=" O GLY A 104 " pdb=" OG SER A 385 " model vdw 2.294 2.440 nonbonded pdb=" O PHE A 453 " pdb=" OG1 THR A 457 " model vdw 2.339 2.440 nonbonded pdb=" OD2 ASP A 106 " pdb=" OG SER A 381 " model vdw 2.341 2.440 nonbonded pdb=" O ASP A 426 " pdb=" OH TYR A 485 " model vdw 2.346 2.440 nonbonded pdb=" OG1 THR A 451 " pdb=" OE1 GLU A 486 " model vdw 2.349 2.440 ... (remaining 48641 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: 2.080 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: 7.000 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.550 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: 0.000 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 0.080 5764 Z= 0.339 Angle : 0.581 6.059 7812 Z= 0.361 Chirality : 0.045 0.251 864 Planarity : 0.004 0.036 1034 Dihedral : 11.882 84.188 2155 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.17 % Allowed : 0.83 % Favored : 99.00 % 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: -0.02 (0.31), residues: 721 helix: 1.12 (0.28), residues: 352 sheet: -1.77 (0.56), residues: 69 loop : -0.89 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 169 HIS 0.004 0.001 HIS A 544 PHE 0.008 0.001 PHE A 191 TYR 0.017 0.001 TYR A 485 ARG 0.003 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.633 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 1.3863 time to fit residues: 136.9093 Evaluate side-chains 63 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.572 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 378 GLN A 593 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5764 Z= 0.359 Angle : 0.592 7.486 7812 Z= 0.315 Chirality : 0.046 0.150 864 Planarity : 0.005 0.036 1034 Dihedral : 4.382 18.449 784 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.33 % Allowed : 10.00 % Favored : 88.67 % 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: -0.03 (0.31), residues: 721 helix: 1.10 (0.28), residues: 357 sheet: -1.62 (0.56), residues: 71 loop : -0.93 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 169 HIS 0.006 0.001 HIS A 648 PHE 0.010 0.002 PHE A 448 TYR 0.018 0.002 TYR A 485 ARG 0.004 0.001 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.680 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 71 average time/residue: 1.2891 time to fit residues: 95.8550 Evaluate side-chains 65 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.8806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 0.0070 chunk 64 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5764 Z= 0.192 Angle : 0.481 6.363 7812 Z= 0.256 Chirality : 0.041 0.143 864 Planarity : 0.004 0.034 1034 Dihedral : 4.076 17.254 784 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.17 % Allowed : 11.83 % Favored : 87.00 % 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: 0.36 (0.31), residues: 721 helix: 1.41 (0.28), residues: 358 sheet: -1.29 (0.57), residues: 68 loop : -0.80 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 36 HIS 0.003 0.001 HIS A 648 PHE 0.012 0.001 PHE A 453 TYR 0.015 0.001 TYR A 485 ARG 0.004 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.619 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 72 average time/residue: 1.1849 time to fit residues: 89.8773 Evaluate side-chains 62 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.9300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 52.9621 > 50: distance: 62 - 69: 20.120 distance: 69 - 70: 11.961 distance: 69 - 132: 23.064 distance: 70 - 71: 14.898 distance: 70 - 73: 18.372 distance: 71 - 72: 8.962 distance: 71 - 76: 10.717 distance: 72 - 129: 23.809 distance: 73 - 74: 43.335 distance: 73 - 75: 13.874 distance: 76 - 77: 7.541 distance: 76 - 82: 10.137 distance: 77 - 78: 11.209 distance: 77 - 80: 14.362 distance: 78 - 79: 27.021 distance: 78 - 83: 11.972 distance: 80 - 81: 22.534 distance: 81 - 82: 32.260 distance: 83 - 84: 13.076 distance: 84 - 85: 29.408 distance: 84 - 87: 11.134 distance: 85 - 86: 13.457 distance: 85 - 91: 20.681 distance: 87 - 88: 5.982 distance: 88 - 89: 12.933 distance: 91 - 92: 19.950 distance: 92 - 93: 18.731 distance: 92 - 95: 17.508 distance: 93 - 99: 20.067 distance: 95 - 96: 13.011 distance: 95 - 97: 20.294 distance: 96 - 98: 12.541 distance: 99 - 100: 4.683 distance: 100 - 101: 16.218 distance: 100 - 103: 18.480 distance: 101 - 102: 9.504 distance: 101 - 109: 13.222 distance: 103 - 104: 12.752 distance: 104 - 105: 10.721 distance: 104 - 106: 26.223 distance: 105 - 107: 11.123 distance: 107 - 108: 12.393 distance: 109 - 110: 5.491 distance: 110 - 111: 4.781 distance: 110 - 113: 9.854 distance: 111 - 112: 8.323 distance: 111 - 117: 12.897 distance: 113 - 114: 8.158 distance: 114 - 115: 13.074 distance: 114 - 116: 17.438 distance: 117 - 118: 14.532 distance: 118 - 119: 8.509 distance: 118 - 121: 11.937 distance: 119 - 120: 10.730 distance: 121 - 122: 10.651 distance: 121 - 123: 27.030 distance: 124 - 125: 3.681 distance: 125 - 126: 17.419 distance: 125 - 128: 4.549 distance: 126 - 127: 21.488 distance: 126 - 129: 27.729 distance: 129 - 130: 8.667 distance: 130 - 131: 16.739 distance: 130 - 133: 16.647 distance: 131 - 132: 10.219 distance: 131 - 137: 8.757 distance: 133 - 134: 16.637 distance: 134 - 135: 25.258 distance: 134 - 136: 26.654 distance: 137 - 138: 12.490 distance: 138 - 139: 21.679 distance: 138 - 141: 5.971 distance: 139 - 140: 22.741 distance: 139 - 145: 22.758 distance: 141 - 142: 14.513 distance: 142 - 143: 9.395 distance: 143 - 144: 37.401