Starting phenix.real_space_refine on Sat Aug 23 01:06:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j6j_61174/08_2025/9j6j_61174.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j6j_61174/08_2025/9j6j_61174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j6j_61174/08_2025/9j6j_61174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j6j_61174/08_2025/9j6j_61174.map" model { file = "/net/cci-nas-00/data/ceres_data/9j6j_61174/08_2025/9j6j_61174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j6j_61174/08_2025/9j6j_61174.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5602 2.51 5 N 1486 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8834 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1127, 8834 Classifications: {'peptide': 1127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 1084} Chain breaks: 5 Time building chain proxies: 1.75, per 1000 atoms: 0.20 Number of scatterers: 8834 At special positions: 0 Unit cell: (103.85, 103.85, 107.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1697 8.00 N 1486 7.00 C 5602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 496 " distance=2.06 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: 0.60 Conformation dependent library (CDL) restraints added in 223.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 22 sheets defined 7.7% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.538A pdb=" N LEU A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.770A pdb=" N GLN A 438 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.741A pdb=" N SER A 528 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1243 removed outlier: 3.644A pdb=" N TYR A1231 " --> pdb=" O SER A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1257 Processing helix chain 'A' and resid 1274 through 1279 Processing helix chain 'A' and resid 1280 through 1283 removed outlier: 3.746A pdb=" N ILE A1283 " --> pdb=" O PHE A1280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1280 through 1283' Processing helix chain 'A' and resid 1284 through 1291 Processing helix chain 'A' and resid 1308 through 1321 removed outlier: 3.665A pdb=" N LEU A1312 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A1315 " --> pdb=" O ASP A1311 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A1321 " --> pdb=" O GLU A1317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1187 through 1192 removed outlier: 6.755A pdb=" N GLY A1214 " --> pdb=" O ASN A1188 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE A1190 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A1212 " --> pdb=" O PHE A1190 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N HIS A1192 " --> pdb=" O SER A1210 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N SER A1210 " --> pdb=" O HIS A1192 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLY A1209 " --> pdb=" O SER A1225 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER A1225 " --> pdb=" O GLY A1209 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A1220 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 204 removed outlier: 3.660A pdb=" N GLY A 200 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 236 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL A 226 " --> pdb=" O PRO A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 250 removed outlier: 3.933A pdb=" N ASN A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 287 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU A 273 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N THR A 285 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 275 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE A 283 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 307 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.703A pdb=" N VAL A 364 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 350 " --> pdb=" O CYS A 362 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS A 362 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE A 352 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR A 360 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 373 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 404 Processing sheet with id=AA7, first strand: chain 'A' and resid 441 through 446 removed outlier: 6.888A pdb=" N GLY A 457 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N HIS A 444 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 455 " --> pdb=" O HIS A 444 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ARG A 446 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ARG A 453 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ARG A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 463 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU A 487 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET A 465 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL A 485 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 467 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU A 483 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU A 469 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 496 through 499 removed outlier: 5.703A pdb=" N LYS A 518 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA A 532 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 542 through 548 removed outlier: 4.184A pdb=" N ASP A 544 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 592 through 595 Processing sheet with id=AB2, first strand: chain 'A' and resid 640 through 642 removed outlier: 3.941A pdb=" N PHE A 642 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 653 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 658 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 661 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER A 671 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 681 through 686 removed outlier: 3.826A pdb=" N VAL A 683 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 699 " --> pdb=" O HIS A 714 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS A 714 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR A 701 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 710 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS A 705 " --> pdb=" O GLU A 708 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 721 through 725 removed outlier: 6.497A pdb=" N GLY A 742 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU A 724 " --> pdb=" O ALA A 740 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA A 740 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 743 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER A 748 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 771 through 778 removed outlier: 6.569A pdb=" N ALA A 788 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE A 774 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 786 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET A 776 " --> pdb=" O TYR A 784 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR A 784 " --> pdb=" O MET A 776 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 783 " --> pdb=" O LEU A 799 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 820 through 823 removed outlier: 3.540A pdb=" N VAL A 832 " --> pdb=" O ILE A 842 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 861 through 865 removed outlier: 3.811A pdb=" N TYR A 861 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 903 through 910 removed outlier: 6.491A pdb=" N LEU A 919 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A 907 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY A 917 " --> pdb=" O ILE A 907 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TYR A 909 " --> pdb=" O CYS A 915 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS A 915 " --> pdb=" O TYR A 909 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP A 978 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 984 " --> pdb=" O ASP A 978 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER A 945 " --> pdb=" O ALA A 987 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLN A 989 " --> pdb=" O SER A 945 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER A 947 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 994 through 1002 removed outlier: 6.657A pdb=" N GLY A1015 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU A 999 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A1013 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER A1001 " --> pdb=" O TYR A1011 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR A1011 " --> pdb=" O SER A1001 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A1033 " --> pdb=" O VAL A1044 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A1035 " --> pdb=" O GLN A1042 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1057 through 1058 removed outlier: 4.061A pdb=" N CYS A1086 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU A1075 " --> pdb=" O THR A1084 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR A1084 " --> pdb=" O GLU A1075 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1100 removed outlier: 6.463A pdb=" N ALA A1117 " --> pdb=" O GLU A1127 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU A1127 " --> pdb=" O ALA A1117 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS A1119 " --> pdb=" O PHE A1125 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE A1125 " --> pdb=" O LYS A1119 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1137 through 1142 removed outlier: 6.827A pdb=" N ALA A1151 " --> pdb=" O SER A1138 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A1140 " --> pdb=" O LEU A1149 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU A1149 " --> pdb=" O VAL A1140 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE A1142 " --> pdb=" O ASN A1147 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASN A1147 " --> pdb=" O ILE A1142 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN A1161 " --> pdb=" O GLU A1177 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU A1177 " --> pdb=" O GLN A1161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1259 through 1261 267 hydrogen bonds defined for protein. 702 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: 1.86 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2831 1.34 - 1.46: 1436 1.46 - 1.58: 4649 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 8992 Sorted by residual: bond pdb=" N VAL A1292 " pdb=" CA VAL A1292 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.34e+01 bond pdb=" N ARG A1285 " pdb=" CA ARG A1285 " ideal model delta sigma weight residual 1.462 1.495 -0.034 9.50e-03 1.11e+04 1.26e+01 bond pdb=" N MET A1110 " pdb=" CA MET A1110 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.00e-02 1.00e+04 1.05e+01 bond pdb=" N LEU A 497 " pdb=" CA LEU A 497 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.21e-02 6.83e+03 9.75e+00 bond pdb=" N VAL A1291 " pdb=" CA VAL A1291 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.67e+00 ... (remaining 8987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11304 1.71 - 3.43: 731 3.43 - 5.14: 108 5.14 - 6.86: 28 6.86 - 8.57: 6 Bond angle restraints: 12177 Sorted by residual: angle pdb=" C SER A1112 " pdb=" CA SER A1112 " pdb=" CB SER A1112 " ideal model delta sigma weight residual 116.54 107.97 8.57 1.15e+00 7.56e-01 5.56e+01 angle pdb=" N GLU A1290 " pdb=" CA GLU A1290 " pdb=" C GLU A1290 " ideal model delta sigma weight residual 111.28 103.21 8.07 1.09e+00 8.42e-01 5.48e+01 angle pdb=" N ASP A 837 " pdb=" CA ASP A 837 " pdb=" C ASP A 837 " ideal model delta sigma weight residual 111.28 103.84 7.44 1.09e+00 8.42e-01 4.66e+01 angle pdb=" N VAL A1113 " pdb=" CA VAL A1113 " pdb=" C VAL A1113 " ideal model delta sigma weight residual 108.96 115.66 -6.70 1.42e+00 4.96e-01 2.23e+01 angle pdb=" N GLU A 495 " pdb=" CA GLU A 495 " pdb=" C GLU A 495 " ideal model delta sigma weight residual 112.04 105.85 6.19 1.44e+00 4.82e-01 1.85e+01 ... (remaining 12172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.20: 4715 18.20 - 36.40: 580 36.40 - 54.60: 104 54.60 - 72.79: 25 72.79 - 90.99: 15 Dihedral angle restraints: 5439 sinusoidal: 2183 harmonic: 3256 Sorted by residual: dihedral pdb=" CA ALA A 564 " pdb=" C ALA A 564 " pdb=" N PHE A 565 " pdb=" CA PHE A 565 " ideal model delta harmonic sigma weight residual -180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PRO A 406 " pdb=" C PRO A 406 " pdb=" N GLU A 407 " pdb=" CA GLU A 407 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA HIS A 648 " pdb=" C HIS A 648 " pdb=" N GLN A 649 " pdb=" CA GLN A 649 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 5436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1202 0.084 - 0.167: 194 0.167 - 0.251: 10 0.251 - 0.335: 2 0.335 - 0.418: 2 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CB VAL A1292 " pdb=" CA VAL A1292 " pdb=" CG1 VAL A1292 " pdb=" CG2 VAL A1292 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CA CYS A 496 " pdb=" N CYS A 496 " pdb=" C CYS A 496 " pdb=" CB CYS A 496 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CB ILE A 747 " pdb=" CA ILE A 747 " pdb=" CG1 ILE A 747 " pdb=" CG2 ILE A 747 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1407 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1007 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO A1008 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A1008 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1008 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 594 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.10e+00 pdb=" N PRO A 595 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1109 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" C LEU A1109 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU A1109 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A1110 " -0.013 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 360 2.70 - 3.25: 8102 3.25 - 3.80: 12852 3.80 - 4.35: 17032 4.35 - 4.90: 29152 Nonbonded interactions: 67498 Sorted by model distance: nonbonded pdb=" O SER A 880 " pdb=" OG1 THR A 881 " model vdw 2.145 3.040 nonbonded pdb=" O LEU A1276 " pdb=" OG SER A1279 " model vdw 2.152 3.040 nonbonded pdb=" OD1 ASP A1038 " pdb=" N GLY A1039 " model vdw 2.154 3.120 nonbonded pdb=" NH2 ARG A 822 " pdb=" O THR A 823 " model vdw 2.154 3.120 nonbonded pdb=" OD1 ASN A 853 " pdb=" NZ LYS A 892 " model vdw 2.158 3.120 ... (remaining 67493 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=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: 1.800 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.830 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:5.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.010 0.071 8993 Z= 0.415 Angle : 0.966 8.574 12179 Z= 0.554 Chirality : 0.060 0.418 1410 Planarity : 0.006 0.062 1568 Dihedral : 16.852 90.993 3336 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.23), residues: 1115 helix: -1.68 (0.48), residues: 82 sheet: -0.71 (0.24), residues: 473 loop : -3.15 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1083 TYR 0.033 0.003 TYR A1089 PHE 0.029 0.003 PHE A1158 TRP 0.022 0.004 TRP A1076 HIS 0.008 0.002 HIS A1174 Details of bonding type rmsd covalent geometry : bond 0.00950 ( 8992) covalent geometry : angle 0.96519 (12177) SS BOND : bond 0.02520 ( 1) SS BOND : angle 3.81510 ( 2) hydrogen bonds : bond 0.17035 ( 267) hydrogen bonds : angle 8.08228 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.337 Fit side-chains REVERT: A 482 ASP cc_start: 0.7846 (p0) cc_final: 0.7617 (t0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.7121 time to fit residues: 64.3104 Evaluate side-chains 62 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.2980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 GLN A 515 GLN A 615 GLN A 719 HIS ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.173892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.101228 restraints weight = 13167.021| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.42 r_work: 0.2863 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8993 Z= 0.169 Angle : 0.698 7.426 12179 Z= 0.369 Chirality : 0.049 0.220 1410 Planarity : 0.005 0.055 1568 Dihedral : 5.832 22.031 1204 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.02 % Allowed : 11.40 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.23), residues: 1115 helix: -1.17 (0.53), residues: 86 sheet: -0.42 (0.24), residues: 476 loop : -3.11 (0.21), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 312 TYR 0.013 0.002 TYR A1096 PHE 0.017 0.002 PHE A 779 TRP 0.014 0.002 TRP A1256 HIS 0.005 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8992) covalent geometry : angle 0.69658 (12177) SS BOND : bond 0.02840 ( 1) SS BOND : angle 3.50993 ( 2) hydrogen bonds : bond 0.04763 ( 267) hydrogen bonds : angle 6.55733 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.281 Fit side-chains REVERT: A 1089 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.8069 (p90) REVERT: A 1171 GLU cc_start: 0.8054 (mp0) cc_final: 0.7413 (pp20) outliers start: 20 outliers final: 9 residues processed: 82 average time/residue: 0.6630 time to fit residues: 57.1422 Evaluate side-chains 72 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 1089 TYR Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1322 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.0010 chunk 96 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 86 optimal weight: 0.0020 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 GLN A 800 ASN A1068 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.174741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101721 restraints weight = 13043.300| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.85 r_work: 0.2865 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8993 Z= 0.147 Angle : 0.654 15.807 12179 Z= 0.343 Chirality : 0.047 0.204 1410 Planarity : 0.005 0.055 1568 Dihedral : 5.419 20.713 1204 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.02 % Allowed : 15.74 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.24), residues: 1115 helix: -0.82 (0.55), residues: 86 sheet: -0.19 (0.24), residues: 465 loop : -3.02 (0.21), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1111 TYR 0.013 0.001 TYR A1096 PHE 0.015 0.002 PHE A 779 TRP 0.013 0.002 TRP A1256 HIS 0.004 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8992) covalent geometry : angle 0.64883 (12177) SS BOND : bond 0.02403 ( 1) SS BOND : angle 6.57906 ( 2) hydrogen bonds : bond 0.04239 ( 267) hydrogen bonds : angle 6.10521 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.322 Fit side-chains REVERT: A 490 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8130 (tp30) REVERT: A 1089 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8118 (p90) REVERT: A 1152 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8280 (pt0) outliers start: 20 outliers final: 9 residues processed: 74 average time/residue: 0.6149 time to fit residues: 48.2173 Evaluate side-chains 71 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 1089 TYR Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1322 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 0.0060 chunk 51 optimal weight: 0.3980 chunk 25 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 77 optimal weight: 0.0030 chunk 86 optimal weight: 0.0980 overall best weight: 0.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 346 HIS A 866 ASN A1088 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.180756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108532 restraints weight = 13302.488| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.62 r_work: 0.3001 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8993 Z= 0.100 Angle : 0.579 13.012 12179 Z= 0.302 Chirality : 0.045 0.168 1410 Planarity : 0.004 0.052 1568 Dihedral : 4.772 19.323 1204 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.51 % Allowed : 17.66 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.24), residues: 1115 helix: -0.23 (0.59), residues: 85 sheet: -0.03 (0.25), residues: 456 loop : -2.85 (0.22), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 381 TYR 0.009 0.001 TYR A 861 PHE 0.011 0.001 PHE A 779 TRP 0.010 0.001 TRP A 673 HIS 0.005 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8992) covalent geometry : angle 0.57292 (12177) SS BOND : bond 0.01198 ( 1) SS BOND : angle 6.50626 ( 2) hydrogen bonds : bond 0.02959 ( 267) hydrogen bonds : angle 5.63677 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.214 Fit side-chains REVERT: A 490 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8144 (tp30) REVERT: A 862 MET cc_start: 0.1692 (OUTLIER) cc_final: 0.1372 (mtt) REVERT: A 1152 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8104 (pt0) outliers start: 15 outliers final: 5 residues processed: 80 average time/residue: 0.6196 time to fit residues: 52.4039 Evaluate side-chains 72 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 1152 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 69 optimal weight: 0.4980 chunk 77 optimal weight: 0.0970 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.176128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.102782 restraints weight = 13093.929| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.92 r_work: 0.2881 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8993 Z= 0.160 Angle : 0.641 15.088 12179 Z= 0.332 Chirality : 0.046 0.177 1410 Planarity : 0.004 0.057 1568 Dihedral : 4.988 18.612 1204 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.62 % Allowed : 18.06 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.24), residues: 1115 helix: -0.38 (0.58), residues: 86 sheet: -0.15 (0.24), residues: 475 loop : -2.91 (0.22), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1111 TYR 0.013 0.001 TYR A 188 PHE 0.015 0.002 PHE A1132 TRP 0.012 0.002 TRP A1256 HIS 0.003 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8992) covalent geometry : angle 0.63515 (12177) SS BOND : bond 0.01454 ( 1) SS BOND : angle 7.04182 ( 2) hydrogen bonds : bond 0.04223 ( 267) hydrogen bonds : angle 5.69783 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.274 Fit side-chains REVERT: A 437 LYS cc_start: 0.8706 (tptt) cc_final: 0.8437 (tppt) REVERT: A 490 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8168 (tp30) REVERT: A 496 CYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6861 (p) REVERT: A 593 LEU cc_start: -0.2161 (OUTLIER) cc_final: -0.3598 (mt) REVERT: A 833 PHE cc_start: 0.3678 (OUTLIER) cc_final: 0.2632 (t80) outliers start: 26 outliers final: 11 residues processed: 77 average time/residue: 0.5762 time to fit residues: 47.2512 Evaluate side-chains 74 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1322 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.157 > 50: distance: 53 - 54: 17.642 distance: 54 - 55: 9.202 distance: 54 - 57: 14.232 distance: 55 - 56: 13.118 distance: 55 - 60: 27.926 distance: 57 - 58: 8.823 distance: 57 - 59: 9.190 distance: 60 - 61: 3.488 distance: 61 - 62: 34.998 distance: 61 - 64: 17.070 distance: 62 - 63: 18.935 distance: 62 - 67: 35.605 distance: 64 - 65: 29.762 distance: 64 - 66: 20.785 distance: 67 - 68: 20.349 distance: 68 - 69: 28.061 distance: 68 - 71: 30.441 distance: 69 - 70: 15.188 distance: 69 - 72: 24.557 distance: 72 - 73: 31.452 distance: 73 - 74: 19.782 distance: 73 - 76: 40.527 distance: 74 - 75: 25.233 distance: 74 - 80: 12.108 distance: 76 - 77: 15.649 distance: 77 - 78: 27.512 distance: 77 - 79: 21.249 distance: 80 - 81: 21.721 distance: 81 - 82: 21.123 distance: 81 - 84: 24.332 distance: 82 - 83: 17.689 distance: 82 - 91: 44.786 distance: 84 - 85: 9.833 distance: 85 - 86: 8.797 distance: 86 - 87: 27.062 distance: 87 - 88: 7.789 distance: 88 - 89: 8.068 distance: 88 - 90: 3.841 distance: 91 - 92: 11.628 distance: 91 - 97: 21.765 distance: 92 - 93: 16.485 distance: 92 - 95: 21.796 distance: 93 - 98: 12.903 distance: 95 - 96: 28.866 distance: 96 - 97: 20.048 distance: 98 - 99: 32.312 distance: 99 - 100: 12.681 distance: 99 - 102: 5.292 distance: 100 - 101: 6.093 distance: 100 - 104: 47.286 distance: 102 - 103: 13.094 distance: 104 - 105: 20.040 distance: 105 - 106: 16.898 distance: 105 - 108: 24.244 distance: 106 - 107: 17.261 distance: 106 - 109: 5.665 distance: 110 - 111: 15.979 distance: 110 - 113: 11.111 distance: 111 - 112: 9.698 distance: 111 - 115: 8.387 distance: 113 - 114: 8.259 distance: 115 - 116: 9.521 distance: 117 - 118: 9.413 distance: 117 - 122: 3.435 distance: 119 - 120: 3.267 distance: 119 - 121: 5.513