Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 23:08:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/08_2023/7rav_24387_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/08_2023/7rav_24387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/08_2023/7rav_24387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/08_2023/7rav_24387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/08_2023/7rav_24387_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rav_24387/08_2023/7rav_24387_updated.pdb" } resolution = 3.3 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 40 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 39 5.16 5 C 3976 2.51 5 N 1046 2.21 5 O 1151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 60": "OE1" <-> "OE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ASP 551": "OD1" <-> "OD2" Residue "A ASP 588": "OD1" <-> "OD2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 631": "OD1" <-> "OD2" Residue "A ASP 634": "OD1" <-> "OD2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 764": "OD1" <-> "OD2" Residue "A TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 6215 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6215 Unusual residues: {'ATP': 1} Classifications: {'peptide': 773, 'undetermined': 1} Link IDs: {'PTRANS': 26, 'TRANS': 746, None: 1} Not linked: pdbres="ARG A 915 " pdbres="ATP A1501 " Chain breaks: 3 Time building chain proxies: 3.74, per 1000 atoms: 0.60 Number of scatterers: 6215 At special positions: 0 Unit cell: (74.858, 78.0662, 133.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 3 15.00 O 1151 8.00 N 1046 7.00 C 3976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 224 " 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 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 947.7 milliseconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 3 sheets defined 40.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 65 through 69 removed outlier: 4.092A pdb=" N THR A 69 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 178 through 184 removed outlier: 3.826A pdb=" N ALA A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 275 through 281 removed outlier: 4.022A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 333 through 339 Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 402 through 417 Processing helix chain 'A' and resid 455 through 461 removed outlier: 3.711A pdb=" N PHE A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 461' Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.803A pdb=" N ARG A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'A' and resid 532 through 541 Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 604 through 614 Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 642 through 653 Processing helix chain 'A' and resid 663 through 703 removed outlier: 3.880A pdb=" N LYS A 680 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) Proline residue: A 685 - end of helix removed outlier: 3.916A pdb=" N LEU A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 697 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 703 " --> pdb=" O THR A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 716 removed outlier: 3.749A pdb=" N ALA A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 715 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 727 Processing helix chain 'A' and resid 746 through 762 Processing helix chain 'A' and resid 766 through 777 removed outlier: 4.432A pdb=" N LEU A 771 " --> pdb=" O GLU A 767 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY A 772 " --> pdb=" O ASP A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 793 through 796 No H-bonds generated for 'chain 'A' and resid 793 through 796' Processing helix chain 'A' and resid 802 through 815 Proline residue: A 806 - end of helix removed outlier: 3.835A pdb=" N LEU A 815 " --> pdb=" O HIS A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 877 removed outlier: 3.993A pdb=" N THR A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 886 removed outlier: 4.224A pdb=" N ILE A 885 " --> pdb=" O CYS A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 913 No H-bonds generated for 'chain 'A' and resid 911 through 913' Processing sheet with id= A, first strand: chain 'A' and resid 86 through 88 Processing sheet with id= B, first strand: chain 'A' and resid 186 through 188 Processing sheet with id= C, first strand: chain 'A' and resid 466 through 468 removed outlier: 6.813A pdb=" N LEU A 500 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU A 549 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 502 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASP A 551 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 504 " --> pdb=" O ASP A 551 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 444 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: 1.53 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1961 1.34 - 1.46: 1377 1.46 - 1.58: 2962 1.58 - 1.70: 5 1.70 - 1.83: 52 Bond restraints: 6357 Sorted by residual: bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.24e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.79e+01 bond pdb=" C8 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.11e+01 bond pdb=" C5 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.387 1.342 0.045 1.00e-02 1.00e+04 2.01e+01 bond pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 1.374 1.331 0.043 1.00e-02 1.00e+04 1.89e+01 ... (remaining 6352 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.53: 158 106.53 - 113.91: 3493 113.91 - 121.28: 3388 121.28 - 128.66: 1506 128.66 - 136.04: 48 Bond angle restraints: 8593 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 119.24 20.63 1.00e+00 1.00e+00 4.26e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 118.98 17.85 1.00e+00 1.00e+00 3.19e+02 angle pdb=" N GLY A 175 " pdb=" CA GLY A 175 " pdb=" C GLY A 175 " ideal model delta sigma weight residual 112.73 100.90 11.83 1.20e+00 6.94e-01 9.72e+01 angle pdb=" C5 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N3 ATP A1501 " ideal model delta sigma weight residual 126.80 118.66 8.14 1.00e+00 1.00e+00 6.62e+01 angle pdb=" N3 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 127.04 134.79 -7.75 1.15e+00 7.59e-01 4.56e+01 ... (remaining 8588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3323 17.97 - 35.93: 366 35.93 - 53.90: 71 53.90 - 71.86: 15 71.86 - 89.83: 10 Dihedral angle restraints: 3785 sinusoidal: 1528 harmonic: 2257 Sorted by residual: dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 124 " pdb=" CB CYS A 124 " ideal model delta sinusoidal sigma weight residual 93.00 48.56 44.44 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CA HIS A 157 " pdb=" C HIS A 157 " pdb=" N GLU A 158 " pdb=" CA GLU A 158 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ILE A 135 " pdb=" C ILE A 135 " pdb=" N GLY A 136 " pdb=" CA GLY A 136 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 3782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 756 0.058 - 0.117: 170 0.117 - 0.175: 18 0.175 - 0.233: 2 0.233 - 0.292: 1 Chirality restraints: 947 Sorted by residual: chirality pdb=" CA PRO A 340 " pdb=" N PRO A 340 " pdb=" C PRO A 340 " pdb=" CB PRO A 340 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA HIS A 174 " pdb=" N HIS A 174 " pdb=" C HIS A 174 " pdb=" CB HIS A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA GLN A 766 " pdb=" N GLN A 766 " pdb=" C GLN A 766 " pdb=" CB GLN A 766 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 944 not shown) Planarity restraints: 1089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 339 " 0.061 5.00e-02 4.00e+02 9.20e-02 1.36e+01 pdb=" N PRO A 340 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 492 " -0.038 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 493 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 330 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO A 331 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.032 5.00e-02 4.00e+02 ... (remaining 1086 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1072 2.76 - 3.29: 6549 3.29 - 3.83: 9935 3.83 - 4.36: 11671 4.36 - 4.90: 18886 Nonbonded interactions: 48113 Sorted by model distance: nonbonded pdb=" OH TYR A 172 " pdb=" NH2 ARG A 261 " model vdw 2.224 2.520 nonbonded pdb=" NZ LYS A 723 " pdb=" OG1 THR A 725 " model vdw 2.224 2.520 nonbonded pdb=" NH1 ARG A 314 " pdb=" O THR A 430 " model vdw 2.242 2.520 nonbonded pdb=" OG SER A 554 " pdb=" OG SER A 558 " model vdw 2.247 2.440 nonbonded pdb=" O ASN A 900 " pdb=" ND2 ASN A 900 " model vdw 2.248 2.520 ... (remaining 48108 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=0.00 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 3.900 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 19.990 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 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 : 0.004 0.079 6357 Z= 0.275 Angle : 0.930 20.628 8593 Z= 0.590 Chirality : 0.049 0.292 947 Planarity : 0.005 0.092 1089 Dihedral : 15.842 89.826 2319 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.39 % Allowed : 16.73 % Favored : 82.88 % Rotamer Outliers : 1.17 % 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: -3.36 (0.29), residues: 765 helix: -0.98 (0.29), residues: 313 sheet: -1.74 (0.75), residues: 37 loop : -3.46 (0.29), residues: 415 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 225 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 228 average time/residue: 0.2150 time to fit residues: 61.8864 Evaluate side-chains 196 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.688 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.0020 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 570 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 6357 Z= 0.237 Angle : 0.770 10.786 8593 Z= 0.397 Chirality : 0.047 0.240 947 Planarity : 0.005 0.049 1089 Dihedral : 6.688 72.624 840 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.39 % Allowed : 17.12 % Favored : 82.48 % Rotamer Outliers : 1.76 % 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: -3.10 (0.30), residues: 765 helix: -0.67 (0.30), residues: 330 sheet: -1.80 (0.68), residues: 42 loop : -3.48 (0.29), residues: 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 209 time to evaluate : 0.719 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 213 average time/residue: 0.2234 time to fit residues: 59.7248 Evaluate side-chains 198 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 0.748 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0746 time to fit residues: 1.6533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6357 Z= 0.176 Angle : 0.717 10.180 8593 Z= 0.364 Chirality : 0.044 0.238 947 Planarity : 0.004 0.047 1089 Dihedral : 6.306 74.152 840 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.56 % Favored : 84.18 % Rotamer Outliers : 1.17 % 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: -2.90 (0.30), residues: 765 helix: -0.41 (0.31), residues: 315 sheet: -1.78 (0.70), residues: 37 loop : -3.35 (0.28), residues: 413 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 199 time to evaluate : 0.638 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 202 average time/residue: 0.2138 time to fit residues: 54.5102 Evaluate side-chains 193 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0625 time to fit residues: 1.3560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 6357 Z= 0.311 Angle : 0.769 9.887 8593 Z= 0.394 Chirality : 0.049 0.244 947 Planarity : 0.005 0.045 1089 Dihedral : 6.480 63.871 840 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.65 % Favored : 82.22 % Rotamer Outliers : 3.07 % 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: -2.96 (0.30), residues: 765 helix: -0.40 (0.31), residues: 319 sheet: -1.80 (0.67), residues: 42 loop : -3.48 (0.29), residues: 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 211 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 218 average time/residue: 0.2164 time to fit residues: 59.6806 Evaluate side-chains 211 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 201 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1536 time to fit residues: 3.0492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 695 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 6357 Z= 0.226 Angle : 0.759 11.697 8593 Z= 0.381 Chirality : 0.048 0.341 947 Planarity : 0.005 0.058 1089 Dihedral : 6.370 64.276 840 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.25 % Favored : 82.61 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.30), residues: 765 helix: -0.33 (0.31), residues: 316 sheet: -1.68 (0.73), residues: 37 loop : -3.45 (0.28), residues: 412 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 208 average time/residue: 0.2266 time to fit residues: 59.5337 Evaluate side-chains 205 residues out of total 683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1537 time to fit residues: 2.1745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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: 62.2875 > 50: distance: 14 - 37: 8.820 distance: 20 - 45: 23.008 distance: 33 - 37: 8.301 distance: 37 - 38: 9.389 distance: 38 - 39: 3.259 distance: 38 - 41: 27.427 distance: 39 - 40: 16.982 distance: 39 - 45: 26.101 distance: 41 - 42: 24.461 distance: 42 - 43: 10.166 distance: 42 - 44: 19.806 distance: 45 - 46: 46.014 distance: 46 - 47: 33.602 distance: 46 - 49: 46.214 distance: 47 - 48: 28.328 distance: 47 - 54: 25.133 distance: 49 - 50: 10.384 distance: 50 - 51: 29.968 distance: 51 - 52: 38.112 distance: 51 - 53: 40.250 distance: 54 - 55: 40.809 distance: 55 - 56: 36.804 distance: 55 - 58: 39.845 distance: 56 - 57: 14.638 distance: 56 - 62: 25.374 distance: 58 - 59: 29.668 distance: 59 - 60: 6.423 distance: 59 - 61: 37.114 distance: 62 - 63: 27.820 distance: 63 - 64: 39.222 distance: 63 - 66: 41.985 distance: 64 - 65: 62.287 distance: 64 - 69: 22.253 distance: 66 - 67: 45.222 distance: 66 - 68: 31.538 distance: 69 - 70: 6.650 distance: 70 - 71: 26.624 distance: 70 - 73: 22.007 distance: 71 - 72: 28.830 distance: 73 - 74: 11.914 distance: 74 - 75: 23.399 distance: 74 - 76: 14.511 distance: 77 - 78: 16.290 distance: 78 - 79: 4.974 distance: 78 - 81: 30.657 distance: 79 - 80: 27.187 distance: 79 - 83: 19.175 distance: 81 - 82: 26.500 distance: 83 - 84: 31.910 distance: 84 - 85: 27.114 distance: 84 - 87: 8.435 distance: 85 - 86: 41.859 distance: 85 - 89: 41.438 distance: 86 - 113: 28.378 distance: 87 - 88: 31.332 distance: 89 - 90: 36.936 distance: 90 - 91: 24.067 distance: 90 - 93: 21.459 distance: 91 - 92: 27.125 distance: 91 - 100: 54.930 distance: 92 - 122: 20.613 distance: 93 - 94: 17.417 distance: 94 - 95: 42.372 distance: 94 - 96: 38.003 distance: 95 - 97: 17.635 distance: 96 - 98: 27.656 distance: 97 - 99: 21.677 distance: 98 - 99: 15.566 distance: 100 - 101: 29.264 distance: 101 - 102: 49.462 distance: 101 - 104: 6.480 distance: 102 - 103: 16.379 distance: 102 - 107: 41.361 distance: 103 - 132: 18.591 distance: 104 - 105: 18.643 distance: 104 - 106: 22.741 distance: 107 - 108: 29.136 distance: 108 - 109: 28.098 distance: 108 - 111: 27.220 distance: 109 - 110: 32.852 distance: 109 - 113: 25.286 distance: 110 - 139: 29.549 distance: 111 - 112: 25.661