Starting phenix.real_space_refine on Sat Aug 3 10:50:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emr_28262/08_2024/8emr_28262.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emr_28262/08_2024/8emr_28262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emr_28262/08_2024/8emr_28262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emr_28262/08_2024/8emr_28262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emr_28262/08_2024/8emr_28262.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emr_28262/08_2024/8emr_28262.cif" } resolution = 2.92 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= 0.030 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 35 5.16 5 C 4880 2.51 5 N 1329 2.21 5 O 1439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7685 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6930 Classifications: {'peptide': 859} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 798} Chain breaks: 2 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 703 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.64, per 1000 atoms: 0.60 Number of scatterers: 7685 At special positions: 0 Unit cell: (70.2, 87.48, 122.04, 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) Ca 2 19.99 S 35 16.00 O 1439 8.00 N 1329 7.00 C 4880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 116 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG D 1 " - " ASN A 97 " Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.4 seconds 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 22.0% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.530A pdb=" N ASN A 37 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.873A pdb=" N VAL A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.662A pdb=" N LYS A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 removed outlier: 3.900A pdb=" N GLU A 481 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.674A pdb=" N ARG A 610 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 638 removed outlier: 4.580A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 656 through 668 Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.661A pdb=" N ASP A 695 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'A' and resid 728 through 733 removed outlier: 4.434A pdb=" N GLN A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.804A pdb=" N ASN A 741 " --> pdb=" O THR A 738 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 742 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 852 through 857 removed outlier: 3.572A pdb=" N THR A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 10.464A pdb=" N LEU A 64 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 11.898A pdb=" N ILE A 79 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 66 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 77 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY A 93 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 69 removed outlier: 10.464A pdb=" N LEU A 64 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 11.898A pdb=" N ILE A 79 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 66 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 77 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS A 255 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.559A pdb=" N SER A 129 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A 139 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG A 133 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.559A pdb=" N SER A 129 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A 139 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG A 133 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA6, first strand: chain 'A' and resid 537 through 540 removed outlier: 7.299A pdb=" N HIS A 397 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 727 removed outlier: 3.876A pdb=" N LEU A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 764 through 769 Processing sheet with id=AA9, first strand: chain 'A' and resid 808 through 812 removed outlier: 6.081A pdb=" N ILE A 828 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 891 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N TRP A 888 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY A 932 " --> pdb=" O TRP A 888 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU A 890 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 839 through 846 Processing sheet with id=AB2, first strand: chain 'B' and resid 74 through 76 277 hydrogen bonds defined for protein. 732 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: 2.75 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1278 1.32 - 1.44: 2277 1.44 - 1.57: 4299 1.57 - 1.69: 0 1.69 - 1.82: 53 Bond restraints: 7907 Sorted by residual: bond pdb=" CA ARG A 818 " pdb=" C ARG A 818 " ideal model delta sigma weight residual 1.523 1.441 0.082 1.30e-02 5.92e+03 4.02e+01 bond pdb=" C ARG A 817 " pdb=" N ARG A 818 " ideal model delta sigma weight residual 1.335 1.405 -0.070 1.31e-02 5.83e+03 2.83e+01 bond pdb=" CA SER A 819 " pdb=" C SER A 819 " ideal model delta sigma weight residual 1.525 1.459 0.066 1.25e-02 6.40e+03 2.82e+01 bond pdb=" C SER A 819 " pdb=" O SER A 819 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.08e-02 8.57e+03 1.64e+01 bond pdb=" C ARG A 818 " pdb=" O ARG A 818 " ideal model delta sigma weight residual 1.237 1.191 0.045 1.17e-02 7.31e+03 1.51e+01 ... (remaining 7902 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.09: 343 107.09 - 113.85: 4230 113.85 - 120.60: 3083 120.60 - 127.35: 2979 127.35 - 134.11: 133 Bond angle restraints: 10768 Sorted by residual: angle pdb=" N GLY A 612 " pdb=" CA GLY A 612 " pdb=" C GLY A 612 " ideal model delta sigma weight residual 110.20 115.31 -5.11 1.32e+00 5.74e-01 1.50e+01 angle pdb=" N ARG A 817 " pdb=" CA ARG A 817 " pdb=" C ARG A 817 " ideal model delta sigma weight residual 109.41 103.74 5.67 1.52e+00 4.33e-01 1.39e+01 angle pdb=" C ARG A 817 " pdb=" N ARG A 818 " pdb=" CA ARG A 818 " ideal model delta sigma weight residual 120.28 125.13 -4.85 1.34e+00 5.57e-01 1.31e+01 angle pdb=" C MET A 814 " pdb=" N ARG A 815 " pdb=" CA ARG A 815 " ideal model delta sigma weight residual 123.05 118.19 4.86 1.40e+00 5.10e-01 1.20e+01 angle pdb=" CA ARG A 817 " pdb=" C ARG A 817 " pdb=" N ARG A 818 " ideal model delta sigma weight residual 115.42 121.07 -5.65 1.64e+00 3.72e-01 1.19e+01 ... (remaining 10763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 4394 21.81 - 43.62: 277 43.62 - 65.43: 24 65.43 - 87.24: 14 87.24 - 109.05: 9 Dihedral angle restraints: 4718 sinusoidal: 1972 harmonic: 2746 Sorted by residual: dihedral pdb=" CB CYS B 100 " pdb=" SG CYS B 100 " pdb=" SG CYS B 116 " pdb=" CB CYS B 116 " ideal model delta sinusoidal sigma weight residual -86.00 -156.29 70.29 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS B 77 " pdb=" SG CYS B 77 " pdb=" SG CYS B 99 " pdb=" CB CYS B 99 " ideal model delta sinusoidal sigma weight residual 93.00 60.24 32.76 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" C MET A 814 " pdb=" N MET A 814 " pdb=" CA MET A 814 " pdb=" CB MET A 814 " ideal model delta harmonic sigma weight residual -122.60 -132.11 9.51 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 4715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1066 0.090 - 0.181: 75 0.181 - 0.271: 0 0.271 - 0.362: 1 0.362 - 0.452: 1 Chirality restraints: 1143 Sorted by residual: chirality pdb=" CA MET A 814 " pdb=" N MET A 814 " pdb=" C MET A 814 " pdb=" CB MET A 814 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA TRP A 503 " pdb=" N TRP A 503 " pdb=" C TRP A 503 " pdb=" CB TRP A 503 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 1140 not shown) Planarity restraints: 1413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 489 " 0.020 2.00e-02 2.50e+03 1.70e-02 5.75e+00 pdb=" CG TYR A 489 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 489 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 489 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 489 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 489 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 489 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 489 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 87 " 0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO B 88 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 306 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 307 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " 0.023 5.00e-02 4.00e+02 ... (remaining 1410 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1713 2.79 - 3.32: 6617 3.32 - 3.84: 12673 3.84 - 4.37: 15067 4.37 - 4.90: 26466 Nonbonded interactions: 62536 Sorted by model distance: nonbonded pdb=" OH TYR A 257 " pdb=" O PHE A 740 " model vdw 2.263 3.040 nonbonded pdb=" O ARG B 91 " pdb="CA CA B 601 " model vdw 2.275 2.510 nonbonded pdb=" OD2 ASP A 848 " pdb=" OG1 THR A 851 " model vdw 2.284 3.040 nonbonded pdb=" O VAL B 96 " pdb="CA CA B 601 " model vdw 2.303 2.510 nonbonded pdb=" OD2 ASP B 104 " pdb="CA CA B 601 " model vdw 2.316 2.510 ... (remaining 62531 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 0.003 0.082 7907 Z= 0.226 Angle : 0.624 7.221 10768 Z= 0.331 Chirality : 0.046 0.452 1143 Planarity : 0.005 0.046 1412 Dihedral : 14.915 109.049 2948 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.58 (0.27), residues: 944 helix: 1.26 (0.42), residues: 153 sheet: 0.46 (0.36), residues: 241 loop : -1.32 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 503 HIS 0.004 0.001 HIS A 480 PHE 0.014 0.001 PHE A 673 TYR 0.042 0.001 TYR A 489 ARG 0.004 0.000 ARG A 817 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.832 Fit side-chains REVERT: A 416 PHE cc_start: 0.7537 (m-80) cc_final: 0.7329 (m-10) REVERT: A 524 MET cc_start: 0.8008 (tpp) cc_final: 0.7781 (tpp) REVERT: A 543 MET cc_start: 0.8380 (mtp) cc_final: 0.8090 (mtp) REVERT: A 699 ASP cc_start: 0.8455 (t0) cc_final: 0.8222 (t0) REVERT: A 882 HIS cc_start: 0.7791 (m-70) cc_final: 0.6588 (p90) REVERT: A 908 LYS cc_start: 0.8374 (mmtm) cc_final: 0.8086 (mmmt) REVERT: A 942 HIS cc_start: 0.6925 (m-70) cc_final: 0.6307 (t-90) REVERT: B 63 ASP cc_start: 0.6869 (p0) cc_final: 0.6656 (p0) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 1.1801 time to fit residues: 166.3246 Evaluate side-chains 85 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 69.6279 > 50: distance: 15 - 124: 20.184 distance: 18 - 121: 3.837 distance: 77 - 132: 27.834 distance: 80 - 129: 26.705 distance: 88 - 113: 28.009 distance: 91 - 110: 31.277 distance: 105 - 110: 32.579 distance: 110 - 111: 50.355 distance: 111 - 112: 57.230 distance: 111 - 114: 33.398 distance: 112 - 113: 19.716 distance: 112 - 121: 32.924 distance: 114 - 115: 6.517 distance: 115 - 116: 4.398 distance: 115 - 117: 6.715 distance: 116 - 118: 32.050 distance: 117 - 119: 29.148 distance: 118 - 120: 18.113 distance: 119 - 120: 13.473 distance: 121 - 122: 39.163 distance: 122 - 123: 26.190 distance: 122 - 125: 4.003 distance: 123 - 124: 17.002 distance: 123 - 129: 18.894 distance: 125 - 126: 35.937 distance: 126 - 127: 37.470 distance: 126 - 128: 35.465 distance: 129 - 130: 29.170 distance: 130 - 131: 22.222 distance: 131 - 132: 32.724 distance: 131 - 137: 28.302 distance: 133 - 134: 35.586 distance: 134 - 135: 24.428 distance: 134 - 136: 20.310 distance: 137 - 138: 14.895 distance: 138 - 139: 48.598 distance: 138 - 141: 30.784 distance: 139 - 140: 31.306 distance: 139 - 145: 11.885 distance: 141 - 142: 21.285 distance: 142 - 143: 31.526 distance: 142 - 144: 47.515 distance: 145 - 146: 36.897 distance: 146 - 147: 36.707 distance: 147 - 148: 32.476 distance: 147 - 149: 35.217 distance: 149 - 150: 42.700 distance: 149 - 155: 34.600 distance: 150 - 151: 41.971 distance: 150 - 153: 41.849 distance: 151 - 152: 52.521 distance: 151 - 156: 65.907 distance: 153 - 154: 43.640 distance: 154 - 155: 42.161 distance: 156 - 157: 34.036 distance: 157 - 158: 49.581 distance: 157 - 160: 9.232 distance: 158 - 159: 8.520 distance: 158 - 162: 51.890 distance: 159 - 184: 36.120 distance: 160 - 161: 42.536 distance: 162 - 163: 37.057 distance: 163 - 164: 23.560 distance: 163 - 166: 24.657 distance: 164 - 165: 29.561 distance: 164 - 170: 34.690 distance: 165 - 191: 32.077 distance: 166 - 167: 38.071 distance: 166 - 168: 6.448 distance: 167 - 169: 17.176 distance: 170 - 171: 22.837 distance: 171 - 172: 9.699 distance: 171 - 174: 7.510 distance: 172 - 173: 29.074 distance: 172 - 176: 37.584 distance: 173 - 202: 17.038 distance: 174 - 175: 37.837 distance: 176 - 177: 14.753 distance: 177 - 178: 8.794 distance: 177 - 180: 28.041 distance: 178 - 179: 19.406 distance: 178 - 184: 18.004 distance: 179 - 213: 33.073 distance: 180 - 181: 23.135 distance: 181 - 182: 28.029 distance: 181 - 183: 23.051