Starting phenix.real_space_refine on Mon Sep 23 23:14:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urc_26708/09_2024/7urc_26708.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urc_26708/09_2024/7urc_26708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urc_26708/09_2024/7urc_26708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urc_26708/09_2024/7urc_26708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urc_26708/09_2024/7urc_26708.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urc_26708/09_2024/7urc_26708.cif" } resolution = 3.14 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= 0.008 sd= 0.068 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 Zn 1 6.06 5 S 31 5.16 5 C 3718 2.51 5 N 868 2.21 5 O 943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5561 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3449 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 357 Unusual residues: {' ZN': 1, 'AJP': 1, 'CLR': 9, 'O50': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2833 SG CYS A 370 54.567 29.769 19.702 1.00119.07 S ATOM 2880 SG CYS A 376 53.579 28.925 23.636 1.00124.43 S ATOM 2908 SG CYS A 380 57.213 30.122 21.402 1.00134.93 S Time building chain proxies: 4.35, per 1000 atoms: 0.78 Number of scatterers: 5561 At special positions: 0 Unit cell: (97.11, 73.04, 93.79, 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) Zn 1 29.99 S 31 16.00 O 943 8.00 N 868 7.00 C 3718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 209 " distance=2.02 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 783.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 512 " pdb="ZN ZN A 512 " - pdb=" ND1 HIS A 382 " pdb="ZN ZN A 512 " - pdb=" SG CYS A 380 " pdb="ZN ZN A 512 " - pdb=" SG CYS A 370 " pdb="ZN ZN A 512 " - pdb=" SG CYS A 376 " Number of angles added : 3 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 7 sheets defined 52.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 removed outlier: 3.988A pdb=" N GLN A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 43 removed outlier: 3.744A pdb=" N ALA A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 34 " --> pdb=" O TRP A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 68 Processing helix chain 'A' and resid 72 through 89 removed outlier: 4.400A pdb=" N LEU A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 116 through 141 removed outlier: 4.567A pdb=" N LYS A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 124 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ALA A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 172 through 181 removed outlier: 4.017A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 removed outlier: 3.926A pdb=" N LEU A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.833A pdb=" N TYR A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 264 removed outlier: 3.531A pdb=" N ALA A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.661A pdb=" N ASN A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 320 through 336 removed outlier: 3.661A pdb=" N VAL A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 368 removed outlier: 3.961A pdb=" N ALA A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 409 Processing helix chain 'A' and resid 410 through 413 removed outlier: 4.061A pdb=" N ASP A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 455 removed outlier: 3.886A pdb=" N PHE A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 84 removed outlier: 3.663A pdb=" N THR H 84 " --> pdb=" O GLN H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.975A pdb=" N SER H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA2, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AA3, first strand: chain 'L' and resid 30 through 32 removed outlier: 6.970A pdb=" N LEU L 31 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP L 55 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.417A pdb=" N GLU H 29 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET H 53 " --> pdb=" O ASN H 69 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.417A pdb=" N GLU H 29 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) 299 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: 1.69 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.19: 5 1.19 - 1.39: 2276 1.39 - 1.58: 3413 1.58 - 1.78: 8 1.78 - 1.98: 48 Bond restraints: 5750 Sorted by residual: bond pdb=" C07 AJP A 511 " pdb=" C08 AJP A 511 " ideal model delta sigma weight residual 1.550 1.978 -0.428 2.00e-02 2.50e+03 4.59e+02 bond pdb=" C01 AJP A 511 " pdb=" C02 AJP A 511 " ideal model delta sigma weight residual 1.521 1.943 -0.422 2.00e-02 2.50e+03 4.46e+02 bond pdb=" C08 AJP A 511 " pdb=" O09 AJP A 511 " ideal model delta sigma weight residual 1.410 0.995 0.415 2.00e-02 2.50e+03 4.31e+02 bond pdb=" C02 AJP A 511 " pdb=" C03 AJP A 511 " ideal model delta sigma weight residual 1.525 1.136 0.389 2.00e-02 2.50e+03 3.78e+02 bond pdb=" C05 AJP A 511 " pdb=" O09 AJP A 511 " ideal model delta sigma weight residual 1.407 1.794 -0.387 2.00e-02 2.50e+03 3.74e+02 ... (remaining 5745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 7603 2.49 - 4.98: 217 4.98 - 7.47: 50 7.47 - 9.96: 11 9.96 - 12.44: 5 Bond angle restraints: 7886 Sorted by residual: angle pdb=" C03 AJP A 511 " pdb=" C02 AJP A 511 " pdb=" C85 AJP A 511 " ideal model delta sigma weight residual 109.14 121.58 -12.44 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C07 AJP A 511 " pdb=" C12 AJP A 511 " pdb=" C13 AJP A 511 " ideal model delta sigma weight residual 114.18 126.51 -12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C10 AJP A 511 " pdb=" C08 AJP A 511 " pdb=" O09 AJP A 511 " ideal model delta sigma weight residual 114.16 124.94 -10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C11 AJP A 511 " pdb=" C12 AJP A 511 " pdb=" C13 AJP A 511 " ideal model delta sigma weight residual 106.34 116.70 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C11 AJP A 511 " pdb=" C12 AJP A 511 " pdb=" C81 AJP A 511 " ideal model delta sigma weight residual 114.35 104.10 10.25 3.00e+00 1.11e-01 1.17e+01 ... (remaining 7881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 3688 35.39 - 70.77: 71 70.77 - 106.16: 33 106.16 - 141.54: 51 141.54 - 176.93: 8 Dihedral angle restraints: 3851 sinusoidal: 1944 harmonic: 1907 Sorted by residual: dihedral pdb=" CB CYS A 17 " pdb=" SG CYS A 17 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual -86.00 -158.72 72.72 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CA TYR H 74 " pdb=" C TYR H 74 " pdb=" N VAL H 75 " pdb=" CA VAL H 75 " ideal model delta harmonic sigma weight residual -180.00 -151.87 -28.13 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" C06 AJP A 511 " pdb=" C07 AJP A 511 " pdb=" C12 AJP A 511 " pdb=" C13 AJP A 511 " ideal model delta sinusoidal sigma weight residual 109.15 -67.78 176.93 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 3848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.097: 883 1.097 - 2.193: 0 2.193 - 3.290: 0 3.290 - 4.386: 2 4.386 - 5.483: 27 Chirality restraints: 912 Sorted by residual: chirality pdb=" C20 AJP A 511 " pdb=" C15 AJP A 511 " pdb=" C19 AJP A 511 " pdb=" C21 AJP A 511 " both_signs ideal model delta sigma weight residual False 2.96 -2.53 5.48 2.00e-01 2.50e+01 7.52e+02 chirality pdb=" C16 AJP A 511 " pdb=" C11 AJP A 511 " pdb=" C15 AJP A 511 " pdb=" C17 AJP A 511 " both_signs ideal model delta sigma weight residual False -2.70 2.76 -5.46 2.00e-01 2.50e+01 7.47e+02 chirality pdb=" C15 AJP A 511 " pdb=" C14 AJP A 511 " pdb=" C16 AJP A 511 " pdb=" C20 AJP A 511 " both_signs ideal model delta sigma weight residual False -2.42 2.85 -5.27 2.00e-01 2.50e+01 6.95e+02 ... (remaining 909 not shown) Planarity restraints: 898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 376 " 0.017 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C CYS A 376 " -0.056 2.00e-02 2.50e+03 pdb=" O CYS A 376 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO A 377 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 219 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 220 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 375 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C ARG A 375 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG A 375 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 376 " -0.010 2.00e-02 2.50e+03 ... (remaining 895 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1288 2.78 - 3.31: 5100 3.31 - 3.84: 9015 3.84 - 4.37: 10719 4.37 - 4.90: 18577 Nonbonded interactions: 44699 Sorted by model distance: nonbonded pdb=" O62 AJP A 511 " pdb=" O63 AJP A 511 " model vdw 2.248 3.040 nonbonded pdb=" O42 AJP A 511 " pdb=" O43 AJP A 511 " model vdw 2.263 3.040 nonbonded pdb=" NH1 ARG A 183 " pdb=" OE1 GLU A 270 " model vdw 2.306 3.120 nonbonded pdb=" NH1 ARG A 360 " pdb=" O LEU A 372 " model vdw 2.334 3.120 nonbonded pdb=" O SER H 138 " pdb=" OG SER H 138 " model vdw 2.350 3.040 ... (remaining 44694 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: 1.470 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.120 Find NCS groups from input model: 0.060 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.018 0.428 5750 Z= 0.899 Angle : 1.001 12.444 7886 Z= 0.407 Chirality : 0.881 5.483 912 Planarity : 0.005 0.047 898 Dihedral : 25.593 176.927 2624 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -3.02 (0.29), residues: 648 helix: -1.25 (0.26), residues: 324 sheet: -2.18 (0.43), residues: 105 loop : -2.85 (0.35), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 300 HIS 0.004 0.001 HIS A 341 PHE 0.012 0.001 PHE A 167 TYR 0.013 0.001 TYR A 83 ARG 0.002 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.551 Fit side-chains REVERT: A 191 GLN cc_start: 0.7938 (tt0) cc_final: 0.7545 (mt0) REVERT: A 235 ARG cc_start: 0.6878 (mmt180) cc_final: 0.5742 (mtm-85) REVERT: A 386 LEU cc_start: 0.9003 (pt) cc_final: 0.8725 (mp) REVERT: A 453 ARG cc_start: 0.7686 (ttt90) cc_final: 0.7377 (ttt180) REVERT: L 65 GLN cc_start: 0.7427 (mt0) cc_final: 0.6843 (mm-40) REVERT: L 72 LYS cc_start: 0.9082 (ptpt) cc_final: 0.8712 (ptmm) REVERT: L 81 ARG cc_start: 0.8592 (ptt-90) cc_final: 0.8042 (ptt-90) REVERT: H 38 LYS cc_start: 0.9157 (tttt) cc_final: 0.8893 (tttp) REVERT: H 62 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8261 (mmmm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2419 time to fit residues: 33.8155 Evaluate side-chains 97 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 10.0000 chunk 48 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 121 HIS A 247 HIS L 111 HIS H 24 GLN H 52 ASN H 78 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5750 Z= 0.284 Angle : 1.156 33.536 7886 Z= 0.438 Chirality : 0.120 2.238 912 Planarity : 0.004 0.046 898 Dihedral : 17.964 176.706 1501 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.25 % Allowed : 10.02 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.32), residues: 648 helix: 0.23 (0.28), residues: 332 sheet: -2.04 (0.43), residues: 111 loop : -2.10 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 300 HIS 0.006 0.001 HIS A 53 PHE 0.012 0.001 PHE A 68 TYR 0.021 0.001 TYR A 83 ARG 0.005 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.597 Fit side-chains REVERT: A 112 MET cc_start: 0.7928 (ptp) cc_final: 0.7532 (ptt) REVERT: A 156 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8411 (mmp) REVERT: A 191 GLN cc_start: 0.7963 (tt0) cc_final: 0.7649 (mt0) REVERT: A 386 LEU cc_start: 0.8978 (pt) cc_final: 0.8601 (mp) REVERT: A 453 ARG cc_start: 0.7712 (ttt90) cc_final: 0.7340 (ttt180) REVERT: L 56 TYR cc_start: 0.9281 (m-80) cc_final: 0.9012 (m-80) REVERT: L 72 LYS cc_start: 0.9112 (ptpt) cc_final: 0.8707 (ptmm) REVERT: L 81 ARG cc_start: 0.8766 (ptt-90) cc_final: 0.8382 (ptt-90) REVERT: L 98 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7566 (mp) REVERT: H 38 LYS cc_start: 0.9109 (tttt) cc_final: 0.8851 (tttp) REVERT: H 62 LYS cc_start: 0.8643 (mmtm) cc_final: 0.8227 (mmmm) outliers start: 7 outliers final: 2 residues processed: 93 average time/residue: 0.2275 time to fit residues: 26.2945 Evaluate side-chains 92 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 61.8339 > 50: distance: 40 - 56: 14.635 distance: 44 - 64: 24.041 distance: 48 - 72: 19.923 distance: 53 - 56: 12.509 distance: 56 - 57: 16.476 distance: 57 - 58: 10.681 distance: 57 - 60: 7.294 distance: 58 - 59: 4.243 distance: 58 - 64: 28.002 distance: 60 - 61: 12.035 distance: 61 - 62: 12.749 distance: 61 - 63: 12.883 distance: 64 - 65: 4.464 distance: 65 - 66: 11.254 distance: 65 - 68: 18.432 distance: 66 - 67: 12.592 distance: 66 - 72: 7.915 distance: 68 - 69: 26.705 distance: 69 - 70: 6.521 distance: 69 - 71: 10.560 distance: 72 - 73: 17.476 distance: 73 - 74: 7.767 distance: 74 - 75: 11.185 distance: 74 - 82: 14.294 distance: 76 - 77: 23.164 distance: 77 - 78: 6.999 distance: 77 - 79: 37.552 distance: 78 - 80: 24.227 distance: 79 - 81: 48.829 distance: 80 - 81: 34.394 distance: 82 - 83: 13.805 distance: 83 - 84: 13.730 distance: 84 - 85: 9.416 distance: 84 - 86: 8.528 distance: 86 - 87: 3.205 distance: 87 - 88: 16.199 distance: 87 - 90: 17.970 distance: 88 - 89: 16.201 distance: 88 - 97: 19.498 distance: 90 - 91: 6.088 distance: 91 - 92: 11.862 distance: 91 - 93: 9.055 distance: 92 - 94: 9.701 distance: 93 - 95: 5.079 distance: 94 - 96: 8.772 distance: 95 - 96: 12.753 distance: 97 - 98: 37.079 distance: 98 - 99: 42.358 distance: 98 - 101: 17.991 distance: 100 - 132: 30.179 distance: 101 - 102: 17.202 distance: 103 - 104: 22.096 distance: 104 - 105: 20.400 distance: 104 - 107: 40.378 distance: 105 - 106: 25.460 distance: 105 - 114: 18.338 distance: 106 - 137: 32.814 distance: 107 - 108: 11.992 distance: 108 - 109: 26.449 distance: 108 - 110: 25.725 distance: 109 - 111: 9.898 distance: 110 - 112: 46.796 distance: 111 - 113: 44.812 distance: 112 - 113: 15.885 distance: 114 - 115: 6.989 distance: 115 - 116: 20.757 distance: 115 - 118: 18.518 distance: 116 - 117: 5.634 distance: 116 - 124: 20.618 distance: 117 - 142: 25.574 distance: 118 - 119: 17.153 distance: 119 - 120: 21.299 distance: 119 - 121: 18.591 distance: 120 - 122: 16.508 distance: 121 - 123: 17.801 distance: 122 - 123: 23.503 distance: 124 - 125: 8.904 distance: 125 - 126: 26.999 distance: 125 - 128: 9.448 distance: 126 - 127: 18.723 distance: 126 - 132: 9.812 distance: 127 - 149: 21.722 distance: 128 - 129: 28.813 distance: 129 - 130: 16.596 distance: 129 - 131: 22.265 distance: 132 - 133: 19.451 distance: 133 - 134: 14.014 distance: 133 - 136: 31.551 distance: 134 - 135: 12.677 distance: 134 - 137: 17.955 distance: 135 - 157: 20.861