Starting phenix.real_space_refine on Sun Jul 27 18:26:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqc_60382/07_2025/8zqc_60382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqc_60382/07_2025/8zqc_60382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zqc_60382/07_2025/8zqc_60382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqc_60382/07_2025/8zqc_60382.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqc_60382/07_2025/8zqc_60382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqc_60382/07_2025/8zqc_60382.cif" } resolution = 3.4 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= 0.000 sd= 0.007 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 P 99 5.49 5 S 27 5.16 5 C 5784 2.51 5 N 1703 2.21 5 O 2067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9680 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7612 Classifications: {'peptide': 930} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 907} Chain breaks: 3 Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1167 Classifications: {'RNA': 55} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 20, 'rna3p_pyr': 20} Link IDs: {'rna2p': 15, 'rna3p': 39} Chain: "C" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 542 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 7.95, per 1000 atoms: 0.82 Number of scatterers: 9680 At special positions: 0 Unit cell: (84.48, 104.94, 126.06, 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 27 16.00 P 99 15.00 O 2067 8.00 N 1703 7.00 C 5784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 51.1% alpha, 10.2% beta 20 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 15 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 64 through 76 removed outlier: 4.171A pdb=" N SER A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N CYS A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 106 through 115 removed outlier: 3.741A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 171 removed outlier: 4.232A pdb=" N ALA A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 186 through 229 removed outlier: 3.519A pdb=" N LEU A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.991A pdb=" N LEU A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 272 removed outlier: 3.654A pdb=" N ALA A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 272 " --> pdb=" O TRP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.727A pdb=" N HIS A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.758A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 452 through 458 Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.866A pdb=" N THR A 462 " --> pdb=" O LEU A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 537 through 565 removed outlier: 3.806A pdb=" N LYS A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.531A pdb=" N GLY A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.574A pdb=" N PHE A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 635 Processing helix chain 'A' and resid 638 through 657 removed outlier: 3.517A pdb=" N PHE A 642 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 657 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 679 through 700 Processing helix chain 'A' and resid 715 through 743 removed outlier: 3.668A pdb=" N GLN A 719 " --> pdb=" O PHE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 removed outlier: 4.115A pdb=" N ARG A 769 " --> pdb=" O ASP A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 removed outlier: 3.815A pdb=" N GLU A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.536A pdb=" N GLN A 804 " --> pdb=" O HIS A 801 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 805 " --> pdb=" O SER A 802 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 801 through 805' Processing helix chain 'A' and resid 835 through 850 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 908 through 916 removed outlier: 3.608A pdb=" N LEU A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 951 removed outlier: 4.089A pdb=" N ARG A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N THR A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN A 949 " --> pdb=" O GLY A 945 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 950 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 951 " --> pdb=" O ARG A 947 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 339 removed outlier: 4.921A pdb=" N PHE A 439 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 13 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 372 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 383 Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 510 removed outlier: 6.955A pdb=" N ILE A 497 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU A 529 " --> pdb=" O MET A 495 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET A 495 " --> pdb=" O GLU A 529 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 748 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU A 752 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 814 through 815 Processing sheet with id=AA5, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA6, first strand: chain 'A' and resid 861 through 863 removed outlier: 3.653A pdb=" N GLY A 920 " --> pdb=" O LEU A 862 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2276 1.33 - 1.45: 2497 1.45 - 1.57: 5065 1.57 - 1.69: 195 1.69 - 1.81: 39 Bond restraints: 10072 Sorted by residual: bond pdb=" N PHE A 670 " pdb=" CA PHE A 670 " ideal model delta sigma weight residual 1.462 1.481 -0.019 1.36e-02 5.41e+03 2.02e+00 bond pdb=" CA VAL A 580 " pdb=" CB VAL A 580 " ideal model delta sigma weight residual 1.540 1.558 -0.018 1.36e-02 5.41e+03 1.81e+00 bond pdb=" O5' A B -8 " pdb=" C5' A B -8 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.55e+00 bond pdb=" CB GLU A 317 " pdb=" CG GLU A 317 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.48e+00 bond pdb=" C LEU A 567 " pdb=" N GLU A 568 " ideal model delta sigma weight residual 1.332 1.316 0.017 1.40e-02 5.10e+03 1.44e+00 ... (remaining 10067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 13636 1.72 - 3.44: 311 3.44 - 5.17: 46 5.17 - 6.89: 18 6.89 - 8.61: 4 Bond angle restraints: 14015 Sorted by residual: angle pdb=" CA LYS A 180 " pdb=" CB LYS A 180 " pdb=" CG LYS A 180 " ideal model delta sigma weight residual 114.10 120.80 -6.70 2.00e+00 2.50e-01 1.12e+01 angle pdb=" N LYS A 674 " pdb=" CA LYS A 674 " pdb=" C LYS A 674 " ideal model delta sigma weight residual 110.80 117.66 -6.86 2.13e+00 2.20e-01 1.04e+01 angle pdb=" C4' A B -8 " pdb=" C3' A B -8 " pdb=" O3' A B -8 " ideal model delta sigma weight residual 113.00 108.51 4.49 1.50e+00 4.44e-01 8.98e+00 angle pdb=" N LEU A 98 " pdb=" CA LEU A 98 " pdb=" C LEU A 98 " ideal model delta sigma weight residual 110.35 106.23 4.12 1.38e+00 5.25e-01 8.92e+00 angle pdb=" N VAL A 580 " pdb=" CA VAL A 580 " pdb=" C VAL A 580 " ideal model delta sigma weight residual 109.34 115.29 -5.95 2.08e+00 2.31e-01 8.19e+00 ... (remaining 14010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 5502 34.84 - 69.68: 501 69.68 - 104.52: 40 104.52 - 139.36: 4 139.36 - 174.21: 2 Dihedral angle restraints: 6049 sinusoidal: 3314 harmonic: 2735 Sorted by residual: dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual -128.00 46.21 -174.21 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual 70.00 -2.59 72.59 1 2.00e+01 2.50e-03 1.68e+01 dihedral pdb=" O4' A B -18 " pdb=" C1' A B -18 " pdb=" N9 A B -18 " pdb=" C4 A B -18 " ideal model delta sinusoidal sigma weight residual 70.00 -1.28 71.28 1 2.00e+01 2.50e-03 1.63e+01 ... (remaining 6046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1237 0.046 - 0.092: 291 0.092 - 0.138: 42 0.138 - 0.184: 6 0.184 - 0.229: 3 Chirality restraints: 1579 Sorted by residual: chirality pdb=" C3' A B -8 " pdb=" C4' A B -8 " pdb=" O3' A B -8 " pdb=" C2' A B -8 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C1' U B 5 " pdb=" O4' U B 5 " pdb=" C2' U B 5 " pdb=" N1 U B 5 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" C1' G B -36 " pdb=" O4' G B -36 " pdb=" C2' G B -36 " pdb=" N9 G B -36 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 1576 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 806 " 0.065 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO A 807 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 807 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 807 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B -31 " 0.035 2.00e-02 2.50e+03 1.61e-02 7.12e+00 pdb=" N9 A B -31 " -0.037 2.00e-02 2.50e+03 pdb=" C8 A B -31 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B -31 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A B -31 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A B -31 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A B -31 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A B -31 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A B -31 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B -31 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A B -31 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 1 " 0.028 2.00e-02 2.50e+03 1.54e-02 5.31e+00 pdb=" N1 C B 1 " -0.036 2.00e-02 2.50e+03 pdb=" C2 C B 1 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C B 1 " 0.000 2.00e-02 2.50e+03 pdb=" N3 C B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C B 1 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C B 1 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C B 1 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C B 1 " -0.004 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1030 2.74 - 3.28: 9166 3.28 - 3.82: 17008 3.82 - 4.36: 18905 4.36 - 4.90: 30721 Nonbonded interactions: 76830 Sorted by model distance: nonbonded pdb=" OG SER A 125 " pdb=" N4 DC D 1 " model vdw 2.198 3.120 nonbonded pdb=" OD1 ASN A 124 " pdb=" N SER A 125 " model vdw 2.210 3.120 nonbonded pdb=" OH TYR A 107 " pdb=" NZ LYS A 144 " model vdw 2.221 3.120 nonbonded pdb=" O SER A 892 " pdb=" OG SER A 892 " model vdw 2.237 3.040 nonbonded pdb=" OP2 G B -15 " pdb=" N2 G B -15 " model vdw 2.245 3.120 ... (remaining 76825 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: 3.060 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 31.400 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 0.051 10072 Z= 0.198 Angle : 0.659 8.609 14015 Z= 0.353 Chirality : 0.040 0.229 1579 Planarity : 0.004 0.098 1438 Dihedral : 22.960 174.205 4275 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.29 % Favored : 93.60 % Rotamer: Outliers : 0.83 % Allowed : 33.06 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.28), residues: 922 helix: 1.86 (0.26), residues: 425 sheet: 0.44 (0.46), residues: 126 loop : -1.84 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 382 HIS 0.012 0.001 HIS A 376 PHE 0.017 0.002 PHE A 325 TYR 0.011 0.001 TYR A 92 ARG 0.005 0.000 ARG A 668 Details of bonding type rmsd hydrogen bonds : bond 0.11553 ( 433) hydrogen bonds : angle 4.65810 ( 1196) covalent geometry : bond 0.00424 (10072) covalent geometry : angle 0.65917 (14015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 138 average time/residue: 0.2994 time to fit residues: 54.9854 Evaluate side-chains 67 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 886 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/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-5711/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-5711/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-5711/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-5711/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-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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-5711/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-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.0185 > 50: distance: 35 - 36: 13.008 distance: 36 - 37: 3.575 distance: 36 - 39: 19.770 distance: 37 - 38: 13.061 distance: 37 - 43: 13.522 distance: 39 - 40: 8.451 distance: 40 - 41: 7.463 distance: 40 - 42: 7.091 distance: 43 - 44: 5.039 distance: 44 - 45: 10.249 distance: 44 - 47: 15.974 distance: 45 - 46: 12.596 distance: 45 - 49: 23.070 distance: 47 - 48: 7.469 distance: 49 - 50: 9.241 distance: 50 - 51: 6.031 distance: 50 - 53: 3.669 distance: 51 - 52: 11.333 distance: 51 - 58: 9.760 distance: 53 - 54: 10.676 distance: 54 - 55: 5.812 distance: 55 - 56: 5.120 distance: 56 - 57: 30.017 distance: 58 - 59: 13.154 distance: 59 - 60: 8.761 distance: 59 - 62: 15.010 distance: 60 - 61: 25.990 distance: 60 - 66: 17.462 distance: 62 - 63: 17.182 distance: 63 - 64: 11.911 distance: 63 - 65: 26.126 distance: 66 - 67: 3.335 distance: 67 - 68: 13.387 distance: 67 - 70: 28.327 distance: 68 - 69: 17.368 distance: 68 - 75: 8.786 distance: 69 - 94: 46.688 distance: 70 - 71: 9.180 distance: 71 - 72: 10.417 distance: 72 - 73: 23.423 distance: 73 - 74: 10.822 distance: 75 - 76: 13.507 distance: 76 - 77: 30.720 distance: 76 - 79: 15.116 distance: 77 - 78: 13.764 distance: 77 - 83: 12.837 distance: 79 - 80: 8.255 distance: 80 - 81: 18.670 distance: 80 - 82: 7.694 distance: 83 - 84: 13.304 distance: 84 - 85: 7.195 distance: 84 - 87: 13.523 distance: 85 - 86: 22.836 distance: 85 - 94: 57.234 distance: 87 - 88: 16.333 distance: 88 - 89: 9.696 distance: 89 - 90: 6.568 distance: 90 - 91: 16.971 distance: 91 - 92: 12.558 distance: 91 - 93: 26.115 distance: 94 - 95: 50.486 distance: 95 - 96: 19.167 distance: 95 - 98: 21.584 distance: 96 - 97: 16.105 distance: 96 - 102: 26.128 distance: 98 - 99: 40.427 distance: 99 - 100: 19.659 distance: 99 - 101: 21.293 distance: 102 - 103: 21.305 distance: 103 - 104: 13.681 distance: 103 - 106: 12.828 distance: 104 - 110: 13.785 distance: 106 - 107: 18.005 distance: 107 - 108: 25.594 distance: 107 - 109: 27.422 distance: 110 - 111: 31.321 distance: 111 - 112: 25.036 distance: 111 - 114: 26.834 distance: 112 - 113: 51.172 distance: 112 - 116: 33.979