Starting phenix.real_space_refine on Thu Jun 27 20:52:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9j_15933/06_2024/8b9j_15933_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9j_15933/06_2024/8b9j_15933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9j_15933/06_2024/8b9j_15933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9j_15933/06_2024/8b9j_15933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9j_15933/06_2024/8b9j_15933_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9j_15933/06_2024/8b9j_15933_updated.pdb" } resolution = 3.45 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= 0.014 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 6846 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 1 5.21 5 S 46 5.16 5 C 4362 2.51 5 N 1186 2.21 5 O 1277 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 511": "OE1" <-> "OE2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 763": "OE1" <-> "OE2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A GLU 943": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 6879 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6846 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 864, 6843 Classifications: {'peptide': 864} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 821} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 864, 6843 Classifications: {'peptide': 864} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 821} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 6967 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.77, per 1000 atoms: 1.13 Number of scatterers: 6879 At special positions: 0 Unit cell: (73.158, 95.352, 101.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 46 16.00 P 2 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1277 8.00 N 1186 7.00 C 4362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 2.5 seconds 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 6 sheets defined 44.3% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 353 through 370 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.654A pdb=" N LYS A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 399 removed outlier: 3.701A pdb=" N MET A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 487 through 495 removed outlier: 4.313A pdb=" N GLU A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 584 through 599 removed outlier: 4.835A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLU A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 696 through 703 removed outlier: 3.927A pdb=" N LYS A 701 " --> pdb=" O ASP A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 759 through 767 Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 796 through 799 Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 830 through 841 Processing helix chain 'A' and resid 866 through 878 Processing helix chain 'A' and resid 881 through 891 Processing helix chain 'A' and resid 910 through 913 No H-bonds generated for 'chain 'A' and resid 910 through 913' Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 921 through 937 Processing helix chain 'A' and resid 940 through 949 Processing helix chain 'A' and resid 954 through 972 Processing helix chain 'A' and resid 978 through 980 No H-bonds generated for 'chain 'A' and resid 978 through 980' Processing helix chain 'A' and resid 995 through 1007 Processing helix chain 'A' and resid 1071 through 1076 Processing helix chain 'A' and resid 1086 through 1088 No H-bonds generated for 'chain 'A' and resid 1086 through 1088' Processing helix chain 'A' and resid 1102 through 1124 Proline residue: A1113 - end of helix Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1134 through 1146 Processing helix chain 'A' and resid 1149 through 1152 removed outlier: 4.416A pdb=" N GLY A1152 " --> pdb=" O LYS A1149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1149 through 1152' Processing sheet with id= A, first strand: chain 'A' and resid 555 through 559 removed outlier: 6.784A pdb=" N VAL A 535 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE A 405 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 537 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLY A 407 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER A 539 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA A 481 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL A 438 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 483 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLN A 440 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N CYS A 485 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 486 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 566 through 569 removed outlier: 7.300A pdb=" N GLY A 775 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N PHE A 569 " --> pdb=" O GLY A 775 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS A 777 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 714 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 737 through 740 Processing sheet with id= D, first strand: chain 'A' and resid 1066 through 1068 removed outlier: 6.971A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1054 through 1056 removed outlier: 3.628A pdb=" N GLU A1054 " --> pdb=" O LYS A1064 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1082 through 1085 removed outlier: 3.726A pdb=" N ILE A1089 " --> pdb=" O ALA A1085 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 807 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: 2.03 Time building geometry restraints manager: 3.22 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: 1693 1.33 - 1.45: 1230 1.45 - 1.57: 4007 1.57 - 1.69: 4 1.69 - 1.82: 74 Bond restraints: 7008 Sorted by residual: bond pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.684 1.783 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" F4 ALF A1202 " pdb="AL ALF A1202 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" N VAL A 772 " pdb=" CA VAL A 772 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 ... (remaining 7003 not shown) Histogram of bond angle deviations from ideal: 89.89 - 107.89: 318 107.89 - 125.89: 9079 125.89 - 143.89: 99 143.89 - 161.89: 0 161.89 - 179.89: 2 Bond angle restraints: 9498 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 179.89 -71.21 3.00e+00 1.11e-01 5.63e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 179.36 -69.73 3.00e+00 1.11e-01 5.40e+02 angle pdb=" CA PRO A 653 " pdb=" N PRO A 653 " pdb=" CD PRO A 653 " ideal model delta sigma weight residual 112.00 99.57 12.43 1.40e+00 5.10e-01 7.88e+01 angle pdb=" C GLN A 567 " pdb=" N GLN A 568 " pdb=" CA GLN A 568 " ideal model delta sigma weight residual 123.05 110.76 12.29 1.40e+00 5.10e-01 7.70e+01 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 110.21 90.00 20.21 3.00e+00 1.11e-01 4.54e+01 ... (remaining 9493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3638 17.69 - 35.38: 493 35.38 - 53.07: 134 53.07 - 70.76: 26 70.76 - 88.45: 6 Dihedral angle restraints: 4297 sinusoidal: 1766 harmonic: 2531 Sorted by residual: dihedral pdb=" CD ARG A 773 " pdb=" NE ARG A 773 " pdb=" CZ ARG A 773 " pdb=" NH1 ARG A 773 " ideal model delta sinusoidal sigma weight residual 0.00 60.89 -60.89 1 1.00e+01 1.00e-02 4.93e+01 dihedral pdb=" CA GLU A 842 " pdb=" C GLU A 842 " pdb=" N MET A 843 " pdb=" CA MET A 843 " ideal model delta harmonic sigma weight residual 180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CD ARG A 562 " pdb=" NE ARG A 562 " pdb=" CZ ARG A 562 " pdb=" NH1 ARG A 562 " ideal model delta sinusoidal sigma weight residual 0.00 33.69 -33.69 1 1.00e+01 1.00e-02 1.61e+01 ... (remaining 4294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 891 0.056 - 0.112: 169 0.112 - 0.168: 25 0.168 - 0.223: 3 0.223 - 0.279: 4 Chirality restraints: 1092 Sorted by residual: chirality pdb=" CA ARG A 773 " pdb=" N ARG A 773 " pdb=" C ARG A 773 " pdb=" CB ARG A 773 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA GLN A 567 " pdb=" N GLN A 567 " pdb=" C GLN A 567 " pdb=" CB GLN A 567 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA PHE A 564 " pdb=" N PHE A 564 " pdb=" C PHE A 564 " pdb=" CB PHE A 564 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1089 not shown) Planarity restraints: 1219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 773 " -0.962 9.50e-02 1.11e+02 4.31e-01 1.13e+02 pdb=" NE ARG A 773 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 773 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 773 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 773 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 562 " 0.598 9.50e-02 1.11e+02 2.68e-01 4.39e+01 pdb=" NE ARG A 562 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 562 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 562 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 562 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 652 " 0.071 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO A 653 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 653 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 653 " 0.056 5.00e-02 4.00e+02 ... (remaining 1216 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 65 2.60 - 3.17: 5972 3.17 - 3.75: 10839 3.75 - 4.32: 14328 4.32 - 4.90: 23925 Nonbonded interactions: 55129 Sorted by model distance: nonbonded pdb=" O ILE A 724 " pdb="MG MG A1203 " model vdw 2.019 2.170 nonbonded pdb=" OG1 THR A 676 " pdb=" O PHE A 679 " model vdw 2.153 2.440 nonbonded pdb=" O3B ADP A1201 " pdb=" F3 ALF A1202 " model vdw 2.193 2.390 nonbonded pdb=" NZ LYS A 413 " pdb=" F4 ALF A1202 " model vdw 2.196 2.470 nonbonded pdb=" OG SER A 448 " pdb=" N6 ADP A1201 " model vdw 2.225 2.520 ... (remaining 55124 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=0.50 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 3.550 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 28.840 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 7008 Z= 0.322 Angle : 1.365 71.213 9498 Z= 0.578 Chirality : 0.048 0.279 1092 Planarity : 0.016 0.431 1219 Dihedral : 17.470 88.445 2647 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.24 % Favored : 92.06 % Rotamer: Outliers : 1.18 % Allowed : 24.74 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.47 (0.29), residues: 857 helix: 0.70 (0.26), residues: 400 sheet: -1.05 (0.50), residues: 106 loop : -1.18 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 949 HIS 0.003 0.001 HIS A 941 PHE 0.031 0.002 PHE A 672 TYR 0.009 0.001 TYR A 550 ARG 0.013 0.001 ARG A 938 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 PHE cc_start: 0.6036 (m-80) cc_final: 0.5590 (m-10) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 0.2008 time to fit residues: 20.1296 Evaluate side-chains 48 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 902 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A 748 ASN ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN A1037 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 7008 Z= 0.198 Angle : 0.956 33.158 9498 Z= 0.399 Chirality : 0.043 0.155 1092 Planarity : 0.005 0.057 1219 Dihedral : 5.667 48.501 955 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.48 % Favored : 92.17 % Rotamer: Outliers : 2.09 % Allowed : 24.74 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.05 (0.30), residues: 857 helix: 1.21 (0.26), residues: 393 sheet: -0.91 (0.53), residues: 100 loop : -1.13 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 949 HIS 0.005 0.001 HIS A 984 PHE 0.017 0.001 PHE A 564 TYR 0.011 0.001 TYR A 619 ARG 0.007 0.001 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 884 MET cc_start: 0.8052 (mmm) cc_final: 0.7666 (mmp) outliers start: 15 outliers final: 3 residues processed: 59 average time/residue: 0.1630 time to fit residues: 14.4525 Evaluate side-chains 43 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.0170 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7008 Z= 0.219 Angle : 0.942 30.289 9498 Z= 0.389 Chirality : 0.044 0.243 1092 Planarity : 0.005 0.048 1219 Dihedral : 4.788 38.178 946 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.71 % Favored : 91.94 % Rotamer: Outliers : 1.70 % Allowed : 23.95 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.18 (0.30), residues: 857 helix: 1.47 (0.26), residues: 390 sheet: -0.76 (0.51), residues: 106 loop : -1.09 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 932 HIS 0.005 0.001 HIS A 984 PHE 0.013 0.001 PHE A 518 TYR 0.030 0.001 TYR A1009 ARG 0.005 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.836 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 54 average time/residue: 0.1370 time to fit residues: 11.6774 Evaluate side-chains 48 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 919 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7008 Z= 0.436 Angle : 1.019 30.899 9498 Z= 0.434 Chirality : 0.046 0.206 1092 Planarity : 0.005 0.047 1219 Dihedral : 5.244 39.152 946 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.53 % Favored : 91.12 % Rotamer: Outliers : 3.01 % Allowed : 23.17 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.21 (0.29), residues: 857 helix: 1.08 (0.26), residues: 397 sheet: -0.84 (0.51), residues: 102 loop : -1.31 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 932 HIS 0.005 0.002 HIS A 984 PHE 0.016 0.002 PHE A 659 TYR 0.014 0.002 TYR A 619 ARG 0.004 0.001 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 37 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 844 ARG cc_start: 0.4842 (OUTLIER) cc_final: 0.4492 (mtm-85) REVERT: A 965 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7388 (mt0) outliers start: 22 outliers final: 11 residues processed: 55 average time/residue: 0.1711 time to fit residues: 13.8202 Evaluate side-chains 48 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 35 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 919 CYS Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 965 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7008 Z= 0.293 Angle : 0.960 30.395 9498 Z= 0.399 Chirality : 0.044 0.224 1092 Planarity : 0.004 0.038 1219 Dihedral : 5.045 37.779 946 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.71 % Favored : 91.94 % Rotamer: Outliers : 2.62 % Allowed : 22.64 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.01 (0.30), residues: 857 helix: 1.31 (0.26), residues: 392 sheet: -0.72 (0.53), residues: 102 loop : -1.23 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 932 HIS 0.005 0.001 HIS A 984 PHE 0.011 0.001 PHE A 672 TYR 0.010 0.001 TYR A 619 ARG 0.007 0.000 ARG A1131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 35 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 844 ARG cc_start: 0.4562 (OUTLIER) cc_final: 0.4245 (mtm-85) REVERT: A 965 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7338 (mt0) outliers start: 19 outliers final: 10 residues processed: 51 average time/residue: 0.1516 time to fit residues: 11.7628 Evaluate side-chains 46 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 34 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 919 CYS Chi-restraints excluded: chain A residue 965 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7008 Z= 0.171 Angle : 0.932 30.015 9498 Z= 0.380 Chirality : 0.042 0.208 1092 Planarity : 0.004 0.040 1219 Dihedral : 4.787 37.327 946 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.89 % Favored : 92.76 % Rotamer: Outliers : 2.09 % Allowed : 23.30 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.31 (0.30), residues: 857 helix: 1.59 (0.26), residues: 391 sheet: -0.58 (0.54), residues: 98 loop : -1.09 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 949 HIS 0.005 0.001 HIS A 984 PHE 0.009 0.001 PHE A 672 TYR 0.012 0.001 TYR A1009 ARG 0.006 0.000 ARG A1131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 965 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7353 (mp10) outliers start: 15 outliers final: 9 residues processed: 50 average time/residue: 0.1619 time to fit residues: 12.0760 Evaluate side-chains 46 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 919 CYS Chi-restraints excluded: chain A residue 965 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.619 > 50: distance: 47 - 53: 28.999 distance: 53 - 54: 29.642 distance: 54 - 55: 45.941 distance: 54 - 57: 21.208 distance: 55 - 56: 10.991 distance: 55 - 60: 51.964 distance: 57 - 58: 10.892 distance: 60 - 61: 66.216 distance: 60 - 66: 6.694 distance: 61 - 64: 13.956 distance: 62 - 63: 3.963 distance: 62 - 67: 16.372 distance: 64 - 65: 38.431 distance: 65 - 66: 40.943 distance: 67 - 68: 37.540 distance: 68 - 69: 18.307 distance: 68 - 71: 21.351 distance: 69 - 76: 39.989 distance: 70 - 95: 40.245 distance: 71 - 72: 25.379 distance: 72 - 73: 22.539 distance: 73 - 74: 39.858 distance: 73 - 75: 58.016 distance: 76 - 77: 35.385 distance: 77 - 78: 4.452 distance: 77 - 80: 8.813 distance: 78 - 79: 8.856 distance: 78 - 84: 20.465 distance: 80 - 81: 41.119 distance: 81 - 82: 39.170 distance: 82 - 83: 56.022 distance: 84 - 85: 22.384 distance: 85 - 88: 12.426 distance: 86 - 87: 55.684 distance: 86 - 95: 68.257 distance: 88 - 89: 42.017 distance: 89 - 90: 21.947 distance: 89 - 91: 29.312 distance: 90 - 92: 9.850 distance: 91 - 93: 18.563 distance: 92 - 94: 41.872 distance: 93 - 94: 62.331 distance: 95 - 96: 43.422 distance: 96 - 97: 41.619 distance: 96 - 99: 41.901 distance: 97 - 98: 28.100 distance: 97 - 106: 26.247 distance: 99 - 100: 52.211 distance: 100 - 101: 44.206 distance: 101 - 102: 40.210 distance: 102 - 103: 40.049 distance: 106 - 107: 33.639 distance: 107 - 110: 36.561 distance: 108 - 109: 12.712 distance: 110 - 111: 39.076 distance: 110 - 112: 55.317 distance: 113 - 114: 39.698 distance: 113 - 119: 38.728 distance: 114 - 115: 56.990 distance: 114 - 117: 28.973 distance: 115 - 116: 8.203 distance: 115 - 120: 3.196 distance: 117 - 118: 31.191 distance: 118 - 119: 56.168 distance: 120 - 121: 37.771 distance: 121 - 122: 40.893 distance: 121 - 124: 39.492 distance: 124 - 125: 12.935 distance: 125 - 126: 56.444 distance: 125 - 127: 43.479 distance: 129 - 130: 31.985 distance: 129 - 132: 40.767 distance: 130 - 131: 48.425 distance: 130 - 138: 24.248 distance: 131 - 156: 33.703 distance: 132 - 133: 40.239 distance: 133 - 134: 40.016 distance: 133 - 135: 40.224 distance: 134 - 136: 31.525 distance: 135 - 137: 39.571 distance: 136 - 137: 57.348 distance: 141 - 163: 3.153