Starting phenix.real_space_refine on Sat Jan 20 12:44:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg0_31103/01_2024/7eg0_31103_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg0_31103/01_2024/7eg0_31103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg0_31103/01_2024/7eg0_31103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg0_31103/01_2024/7eg0_31103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg0_31103/01_2024/7eg0_31103_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg0_31103/01_2024/7eg0_31103_trim_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 4 5.21 5 S 98 5.16 5 Cl 4 4.86 5 C 9754 2.51 5 N 2582 2.21 5 O 2802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 687": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 935": "OE1" <-> "OE2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A GLU 1091": "OE1" <-> "OE2" Residue "A GLU 1093": "OE1" <-> "OE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "C GLU 687": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C ARG 705": "NH1" <-> "NH2" Residue "C ARG 709": "NH1" <-> "NH2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C GLU 726": "OE1" <-> "OE2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C GLU 743": "OE1" <-> "OE2" Residue "C GLU 903": "OE1" <-> "OE2" Residue "C GLU 935": "OE1" <-> "OE2" Residue "C GLU 1028": "OE1" <-> "OE2" Residue "C GLU 1091": "OE1" <-> "OE2" Residue "C GLU 1093": "OE1" <-> "OE2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D GLU 161": "OE1" <-> "OE2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D GLU 354": "OE1" <-> "OE2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ARG 426": "NH1" <-> "NH2" Residue "D GLU 464": "OE1" <-> "OE2" Residue "D GLU 503": "OE1" <-> "OE2" Residue "D GLU 520": "OE1" <-> "OE2" Residue "D ARG 527": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15246 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3004 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain breaks: 2 Chain: "B" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3004 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain breaks: 2 Chain: "D" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' MG': 2, 'J33': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {' MG': 2, 'J33': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5222 SG CYS B 277 24.263 58.587 74.568 1.00 72.83 S ATOM 5495 SG CYS B 311 24.842 57.312 77.759 1.00 65.90 S ATOM 5501 SG CYS B 312 27.488 59.772 76.145 1.00 64.10 S ATOM 12826 SG CYS D 277 74.559 72.486 74.857 1.00 72.83 S ATOM 13099 SG CYS D 311 73.979 73.759 78.049 1.00 65.90 S ATOM 13105 SG CYS D 312 71.335 71.299 76.434 1.00 64.10 S Time building chain proxies: 7.94, per 1000 atoms: 0.52 Number of scatterers: 15246 At special positions: 0 Unit cell: (99.9006, 132.127, 127.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Cl 4 17.00 S 98 16.00 Mg 4 11.99 O 2802 8.00 N 2582 7.00 C 9754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 411 " distance=2.03 Simple disulfide: pdb=" SG CYS D 381 " - pdb=" SG CYS D 411 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.86 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 275 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 312 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 277 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 311 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 275 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 312 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 277 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 311 " Number of angles added : 6 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 8 sheets defined 41.6% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 686 through 689 Processing helix chain 'A' and resid 696 through 702 Processing helix chain 'A' and resid 710 through 722 Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'A' and resid 732 through 745 Processing helix chain 'A' and resid 754 through 768 Processing helix chain 'A' and resid 817 through 819 No H-bonds generated for 'chain 'A' and resid 817 through 819' Processing helix chain 'A' and resid 823 through 834 Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 854 through 857 No H-bonds generated for 'chain 'A' and resid 854 through 857' Processing helix chain 'A' and resid 864 through 879 Processing helix chain 'A' and resid 891 through 908 removed outlier: 3.885A pdb=" N THR A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 922 removed outlier: 4.801A pdb=" N PHE A 914 " --> pdb=" O LYS A 911 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 915 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 950 Processing helix chain 'A' and resid 953 through 955 No H-bonds generated for 'chain 'A' and resid 953 through 955' Processing helix chain 'A' and resid 958 through 981 removed outlier: 3.521A pdb=" N SER A 981 " --> pdb=" O ASP A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1007 Processing helix chain 'A' and resid 1009 through 1018 Processing helix chain 'A' and resid 1074 through 1101 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 34 through 53 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 215 through 230 removed outlier: 3.738A pdb=" N GLU B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 257 through 270 Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 351 through 360 removed outlier: 4.819A pdb=" N ASN B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 404 through 413 removed outlier: 3.983A pdb=" N GLN B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 467 through 483 Processing helix chain 'B' and resid 520 through 523 removed outlier: 3.961A pdb=" N TYR B 523 " --> pdb=" O GLU B 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 523' Processing helix chain 'B' and resid 529 through 541 Processing helix chain 'B' and resid 553 through 558 removed outlier: 3.517A pdb=" N ILE B 557 " --> pdb=" O ASN B 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 689 Processing helix chain 'C' and resid 696 through 702 Processing helix chain 'C' and resid 710 through 722 Processing helix chain 'C' and resid 724 through 727 No H-bonds generated for 'chain 'C' and resid 724 through 727' Processing helix chain 'C' and resid 732 through 745 Processing helix chain 'C' and resid 754 through 768 Processing helix chain 'C' and resid 817 through 819 No H-bonds generated for 'chain 'C' and resid 817 through 819' Processing helix chain 'C' and resid 823 through 834 Processing helix chain 'C' and resid 845 through 850 Processing helix chain 'C' and resid 854 through 857 No H-bonds generated for 'chain 'C' and resid 854 through 857' Processing helix chain 'C' and resid 864 through 879 Processing helix chain 'C' and resid 891 through 908 removed outlier: 3.885A pdb=" N THR C 908 " --> pdb=" O ALA C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 922 removed outlier: 4.800A pdb=" N PHE C 914 " --> pdb=" O LYS C 911 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP C 915 " --> pdb=" O LYS C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 950 Processing helix chain 'C' and resid 953 through 955 No H-bonds generated for 'chain 'C' and resid 953 through 955' Processing helix chain 'C' and resid 958 through 981 removed outlier: 3.520A pdb=" N SER C 981 " --> pdb=" O ASP C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1007 Processing helix chain 'C' and resid 1009 through 1018 Processing helix chain 'C' and resid 1074 through 1101 Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 34 through 53 Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 174 through 185 Processing helix chain 'D' and resid 215 through 230 removed outlier: 3.738A pdb=" N GLU D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 257 through 270 Processing helix chain 'D' and resid 334 through 342 Processing helix chain 'D' and resid 351 through 360 removed outlier: 4.818A pdb=" N ASN D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 404 through 413 removed outlier: 3.985A pdb=" N GLN D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 432 Processing helix chain 'D' and resid 467 through 483 Processing helix chain 'D' and resid 520 through 523 removed outlier: 3.962A pdb=" N TYR D 523 " --> pdb=" O GLU D 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 523' Processing helix chain 'D' and resid 529 through 541 Processing helix chain 'D' and resid 553 through 558 removed outlier: 3.517A pdb=" N ILE D 557 " --> pdb=" O ASN D 553 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 15 through 17 removed outlier: 6.809A pdb=" N VAL B 58 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 127 through 129 Processing sheet with id= C, first strand: chain 'B' and resid 204 through 207 removed outlier: 6.437A pdb=" N TYR B 236 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LYS B 207 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE B 238 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 454 through 459 removed outlier: 7.299A pdb=" N MET B 494 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N THR B 457 " --> pdb=" O MET B 494 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS B 496 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N HIS B 459 " --> pdb=" O LYS B 496 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE B 498 " --> pdb=" O HIS B 459 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.808A pdb=" N VAL D 58 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 127 through 129 Processing sheet with id= G, first strand: chain 'D' and resid 204 through 207 removed outlier: 6.437A pdb=" N TYR D 236 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LYS D 207 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE D 238 " --> pdb=" O LYS D 207 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 454 through 459 removed outlier: 7.300A pdb=" N MET D 494 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N THR D 457 " --> pdb=" O MET D 494 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS D 496 " --> pdb=" O THR D 457 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N HIS D 459 " --> pdb=" O LYS D 496 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE D 498 " --> pdb=" O HIS D 459 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 536 hydrogen bonds defined for protein. 1542 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: 4.16 Time building geometry restraints manager: 6.32 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: 4923 1.34 - 1.46: 3482 1.46 - 1.58: 7023 1.58 - 1.70: 0 1.70 - 1.82: 154 Bond restraints: 15582 Sorted by residual: bond pdb=" C GLU B 393 " pdb=" N ASN B 394 " ideal model delta sigma weight residual 1.329 1.288 0.041 1.79e-02 3.12e+03 5.26e+00 bond pdb=" C GLU D 393 " pdb=" N ASN D 394 " ideal model delta sigma weight residual 1.329 1.288 0.041 1.79e-02 3.12e+03 5.16e+00 bond pdb=" N LYS A1088 " pdb=" CA LYS A1088 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.19e-02 7.06e+03 4.45e+00 bond pdb=" N LYS C1088 " pdb=" CA LYS C1088 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.19e-02 7.06e+03 4.29e+00 bond pdb=" N GLU D 345 " pdb=" CA GLU D 345 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.44e-02 4.82e+03 3.85e+00 ... (remaining 15577 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.39: 369 106.39 - 113.32: 8633 113.32 - 120.24: 5790 120.24 - 127.17: 6081 127.17 - 134.10: 167 Bond angle restraints: 21040 Sorted by residual: angle pdb=" C GLY B 55 " pdb=" N GLY B 56 " pdb=" CA GLY B 56 " ideal model delta sigma weight residual 122.55 119.00 3.55 1.10e+00 8.26e-01 1.04e+01 angle pdb=" C GLY D 55 " pdb=" N GLY D 56 " pdb=" CA GLY D 56 " ideal model delta sigma weight residual 122.55 119.03 3.52 1.10e+00 8.26e-01 1.02e+01 angle pdb=" O ALA D 344 " pdb=" C ALA D 344 " pdb=" N GLU D 345 " ideal model delta sigma weight residual 122.84 119.13 3.71 1.16e+00 7.43e-01 1.02e+01 angle pdb=" N THR D 391 " pdb=" CA THR D 391 " pdb=" C THR D 391 " ideal model delta sigma weight residual 109.81 116.85 -7.04 2.21e+00 2.05e-01 1.01e+01 angle pdb=" N THR B 391 " pdb=" CA THR B 391 " pdb=" C THR B 391 " ideal model delta sigma weight residual 109.81 116.84 -7.03 2.21e+00 2.05e-01 1.01e+01 ... (remaining 21035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 8322 17.72 - 35.43: 852 35.43 - 53.14: 172 53.14 - 70.86: 26 70.86 - 88.57: 18 Dihedral angle restraints: 9390 sinusoidal: 3874 harmonic: 5516 Sorted by residual: dihedral pdb=" CB CYS B 381 " pdb=" SG CYS B 381 " pdb=" SG CYS B 411 " pdb=" CB CYS B 411 " ideal model delta sinusoidal sigma weight residual 93.00 163.74 -70.74 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CB CYS D 381 " pdb=" SG CYS D 381 " pdb=" SG CYS D 411 " pdb=" CB CYS D 411 " ideal model delta sinusoidal sigma weight residual 93.00 163.71 -70.71 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CA TYR B 390 " pdb=" C TYR B 390 " pdb=" N THR B 391 " pdb=" CA THR B 391 " ideal model delta harmonic sigma weight residual 180.00 -154.21 -25.79 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 9387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1490 0.040 - 0.080: 592 0.080 - 0.120: 168 0.120 - 0.159: 28 0.159 - 0.199: 8 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CA THR B 391 " pdb=" N THR B 391 " pdb=" C THR B 391 " pdb=" CB THR B 391 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA THR D 391 " pdb=" N THR D 391 " pdb=" C THR D 391 " pdb=" CB THR D 391 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA PHE B 550 " pdb=" N PHE B 550 " pdb=" C PHE B 550 " pdb=" CB PHE B 550 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-01 ... (remaining 2283 not shown) Planarity restraints: 2688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 344 " -0.021 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ALA D 344 " 0.070 2.00e-02 2.50e+03 pdb=" O ALA D 344 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU D 345 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 344 " -0.021 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C ALA B 344 " 0.070 2.00e-02 2.50e+03 pdb=" O ALA B 344 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU B 345 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C1087 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C LYS C1087 " 0.058 2.00e-02 2.50e+03 pdb=" O LYS C1087 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS C1088 " -0.019 2.00e-02 2.50e+03 ... (remaining 2685 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 152 2.56 - 3.15: 13383 3.15 - 3.73: 22349 3.73 - 4.32: 32478 4.32 - 4.90: 54850 Nonbonded interactions: 123212 Sorted by model distance: nonbonded pdb=" OD1 ASP A 950 " pdb="MG MG A1202 " model vdw 1.975 2.170 nonbonded pdb=" OD1 ASP C 950 " pdb="MG MG C1202 " model vdw 1.976 2.170 nonbonded pdb=" OD2 ASP A 837 " pdb="MG MG A1202 " model vdw 1.996 2.170 nonbonded pdb=" OD2 ASP C 837 " pdb="MG MG C1202 " model vdw 1.996 2.170 nonbonded pdb=" OD2 ASP A 861 " pdb=" NH1 ARG C 898 " model vdw 2.173 2.520 ... (remaining 123207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.450 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: 2.650 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 44.330 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.009 0.075 15582 Z= 0.563 Angle : 0.783 7.501 21040 Z= 0.445 Chirality : 0.046 0.199 2286 Planarity : 0.004 0.051 2688 Dihedral : 14.943 88.574 5816 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.91 % Favored : 85.98 % Rotamer: Outliers : 0.12 % Allowed : 6.34 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.18), residues: 1862 helix: -0.66 (0.16), residues: 868 sheet: -2.06 (0.37), residues: 166 loop : -3.50 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 110 HIS 0.005 0.001 HIS C 836 PHE 0.026 0.002 PHE B 145 TYR 0.020 0.002 TYR A 807 ARG 0.009 0.001 ARG C 717 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 324 time to evaluate : 1.722 Fit side-chains REVERT: A 675 GLU cc_start: 0.7199 (mp0) cc_final: 0.6870 (mp0) REVERT: A 717 ARG cc_start: 0.7175 (mmt-90) cc_final: 0.6531 (mmm160) REVERT: A 722 MET cc_start: 0.9197 (mmm) cc_final: 0.8946 (mmm) REVERT: A 736 MET cc_start: 0.8403 (mmm) cc_final: 0.8186 (mmm) REVERT: A 887 ILE cc_start: 0.8683 (tp) cc_final: 0.8463 (tt) REVERT: A 895 LYS cc_start: 0.8170 (tptt) cc_final: 0.7889 (ttpt) REVERT: A 1091 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6452 (mt-10) REVERT: B 144 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8218 (tm-30) REVERT: B 194 GLU cc_start: 0.6404 (pt0) cc_final: 0.6151 (tp30) REVERT: B 219 LYS cc_start: 0.7415 (ttmt) cc_final: 0.7182 (tptp) REVERT: B 270 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7517 (mtmm) REVERT: B 293 TYR cc_start: 0.7024 (m-80) cc_final: 0.6670 (m-80) REVERT: B 299 CYS cc_start: 0.7426 (m) cc_final: 0.7161 (m) REVERT: B 369 TRP cc_start: 0.7215 (m-90) cc_final: 0.6982 (m-10) REVERT: B 483 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8104 (mmtt) REVERT: C 736 MET cc_start: 0.7936 (mmm) cc_final: 0.7316 (mmm) REVERT: C 820 ASN cc_start: 0.8543 (m110) cc_final: 0.8240 (m-40) REVERT: C 835 MET cc_start: 0.8003 (ptt) cc_final: 0.7783 (ptp) REVERT: C 880 ARG cc_start: 0.7670 (mmt90) cc_final: 0.7317 (mmm160) REVERT: C 884 ASN cc_start: 0.7928 (t0) cc_final: 0.7239 (p0) REVERT: C 1084 LYS cc_start: 0.7625 (mtmt) cc_final: 0.7154 (tttt) REVERT: C 1091 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6542 (mt-10) REVERT: D 37 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7647 (ttp80) REVERT: D 194 GLU cc_start: 0.6484 (pt0) cc_final: 0.6136 (tp30) REVERT: D 401 LEU cc_start: 0.8064 (tp) cc_final: 0.7691 (tt) REVERT: D 409 LEU cc_start: 0.8713 (tp) cc_final: 0.8486 (tp) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.3818 time to fit residues: 166.9860 Evaluate side-chains 185 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 168 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 ASN A 888 ASN A 943 GLN ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 GLN B 125 ASN B 172 GLN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN C 860 ASN ** C 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 ASN C 943 GLN ** C1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1081 GLN D 26 ASN D 125 ASN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15582 Z= 0.174 Angle : 0.535 7.258 21040 Z= 0.277 Chirality : 0.041 0.154 2286 Planarity : 0.004 0.059 2688 Dihedral : 4.521 23.901 2036 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 2.15 % Allowed : 11.06 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.20), residues: 1862 helix: 0.88 (0.18), residues: 862 sheet: -1.20 (0.40), residues: 162 loop : -2.84 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1086 HIS 0.008 0.001 HIS D 367 PHE 0.033 0.001 PHE D 550 TYR 0.020 0.001 TYR B 70 ARG 0.004 0.000 ARG C 733 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 1.737 Fit side-chains REVERT: A 675 GLU cc_start: 0.6933 (mp0) cc_final: 0.6572 (mp0) REVERT: A 895 LYS cc_start: 0.8084 (tptt) cc_final: 0.7848 (ttpp) REVERT: A 1091 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6569 (mt-10) REVERT: B 37 ARG cc_start: 0.8137 (ttm170) cc_final: 0.7716 (ttp80) REVERT: B 144 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8182 (tm-30) REVERT: B 194 GLU cc_start: 0.6724 (pt0) cc_final: 0.6181 (tp30) REVERT: B 379 HIS cc_start: 0.7310 (t70) cc_final: 0.6843 (t-90) REVERT: B 483 LYS cc_start: 0.8393 (mtpt) cc_final: 0.8059 (mmtt) REVERT: B 561 ASP cc_start: 0.5591 (OUTLIER) cc_final: 0.4764 (t0) REVERT: B 566 ASN cc_start: 0.1586 (OUTLIER) cc_final: 0.1309 (m110) REVERT: C 682 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6857 (pt) REVERT: C 880 ARG cc_start: 0.7356 (mmt90) cc_final: 0.7072 (mmm160) REVERT: C 893 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6499 (mm-30) REVERT: C 1084 LYS cc_start: 0.7680 (mtmt) cc_final: 0.7085 (tttt) REVERT: C 1091 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6557 (mt-10) REVERT: D 37 ARG cc_start: 0.8175 (ttm170) cc_final: 0.7689 (ttp80) REVERT: D 194 GLU cc_start: 0.6803 (pt0) cc_final: 0.6171 (tp30) REVERT: D 378 ARG cc_start: 0.7204 (mtp85) cc_final: 0.6546 (mtt-85) REVERT: D 479 GLN cc_start: 0.8188 (mt0) cc_final: 0.7986 (mt0) REVERT: D 561 ASP cc_start: 0.5459 (OUTLIER) cc_final: 0.4952 (t0) outliers start: 36 outliers final: 18 residues processed: 260 average time/residue: 0.2979 time to fit residues: 111.5513 Evaluate side-chains 210 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 0.0970 chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN A 925 ASN ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN C 867 ASN C 913 HIS C 925 ASN ** C1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1078 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15582 Z= 0.180 Angle : 0.503 7.218 21040 Z= 0.261 Chirality : 0.040 0.153 2286 Planarity : 0.004 0.048 2688 Dihedral : 4.192 22.237 2036 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.81 % Allowed : 13.16 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1862 helix: 1.27 (0.18), residues: 864 sheet: -0.55 (0.42), residues: 162 loop : -2.59 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1086 HIS 0.004 0.001 HIS B 367 PHE 0.030 0.001 PHE D 550 TYR 0.011 0.001 TYR D 70 ARG 0.003 0.000 ARG D 540 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 199 time to evaluate : 1.668 Fit side-chains REVERT: A 675 GLU cc_start: 0.6885 (mp0) cc_final: 0.6528 (mp0) REVERT: A 736 MET cc_start: 0.8613 (mmm) cc_final: 0.8379 (mmp) REVERT: A 881 PRO cc_start: 0.8157 (Cg_endo) cc_final: 0.7888 (Cg_exo) REVERT: A 1091 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6577 (mt-10) REVERT: B 37 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7828 (ttp80) REVERT: B 144 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8224 (tm-30) REVERT: B 158 LEU cc_start: 0.3086 (OUTLIER) cc_final: 0.2141 (pt) REVERT: B 194 GLU cc_start: 0.6852 (pt0) cc_final: 0.6268 (tp30) REVERT: B 379 HIS cc_start: 0.7374 (t70) cc_final: 0.6836 (t-90) REVERT: B 483 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8141 (mmtt) REVERT: B 561 ASP cc_start: 0.5825 (OUTLIER) cc_final: 0.5154 (t0) REVERT: C 736 MET cc_start: 0.8327 (mmm) cc_final: 0.8078 (mmm) REVERT: C 893 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6444 (mm-30) REVERT: C 930 ILE cc_start: 0.7210 (mm) cc_final: 0.6788 (tt) REVERT: C 931 ASP cc_start: 0.7075 (t70) cc_final: 0.6574 (t70) REVERT: C 1084 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7153 (tttt) REVERT: C 1091 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6517 (mt-10) REVERT: D 37 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7827 (ttp80) REVERT: D 158 LEU cc_start: 0.2373 (OUTLIER) cc_final: 0.1319 (pp) REVERT: D 175 ASN cc_start: 0.8379 (m-40) cc_final: 0.8127 (m-40) REVERT: D 191 ASP cc_start: 0.8045 (m-30) cc_final: 0.7723 (m-30) REVERT: D 194 GLU cc_start: 0.6741 (pt0) cc_final: 0.6199 (tp30) REVERT: D 378 ARG cc_start: 0.7385 (mtp85) cc_final: 0.6831 (mtt-85) REVERT: D 388 ILE cc_start: 0.9000 (mt) cc_final: 0.8677 (tt) REVERT: D 506 THR cc_start: 0.6094 (OUTLIER) cc_final: 0.5840 (p) REVERT: D 561 ASP cc_start: 0.5569 (OUTLIER) cc_final: 0.5025 (t0) outliers start: 47 outliers final: 32 residues processed: 236 average time/residue: 0.2686 time to fit residues: 94.0435 Evaluate side-chains 217 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain C residue 690 ASN Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 160 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1001 GLN ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 HIS B 509 GLN C1001 GLN ** C1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 HIS D 403 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15582 Z= 0.382 Angle : 0.622 7.935 21040 Z= 0.324 Chirality : 0.044 0.174 2286 Planarity : 0.004 0.048 2688 Dihedral : 4.869 27.044 2036 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 3.77 % Allowed : 14.17 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1862 helix: 0.88 (0.18), residues: 868 sheet: -0.52 (0.43), residues: 162 loop : -2.56 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 322 HIS 0.007 0.001 HIS B 323 PHE 0.029 0.002 PHE B 550 TYR 0.018 0.002 TYR D 70 ARG 0.005 0.001 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 179 time to evaluate : 1.988 Fit side-chains REVERT: A 675 GLU cc_start: 0.6756 (mp0) cc_final: 0.6536 (mp0) REVERT: A 881 PRO cc_start: 0.8228 (Cg_endo) cc_final: 0.7958 (Cg_exo) REVERT: A 930 ILE cc_start: 0.7490 (mm) cc_final: 0.7219 (tt) REVERT: A 1084 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7550 (tttt) REVERT: A 1091 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6513 (mt-10) REVERT: A 1093 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: B 144 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7978 (tt0) REVERT: B 158 LEU cc_start: 0.3148 (OUTLIER) cc_final: 0.2356 (pt) REVERT: B 194 GLU cc_start: 0.6919 (pt0) cc_final: 0.6119 (tp30) REVERT: B 221 ILE cc_start: 0.7787 (tt) cc_final: 0.7513 (tt) REVERT: B 299 CYS cc_start: 0.7521 (m) cc_final: 0.7071 (m) REVERT: B 379 HIS cc_start: 0.7392 (t70) cc_final: 0.6760 (t-90) REVERT: B 483 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8420 (mtpp) REVERT: C 736 MET cc_start: 0.8421 (mmm) cc_final: 0.8212 (mmp) REVERT: C 887 ILE cc_start: 0.8457 (tp) cc_final: 0.8234 (tt) REVERT: C 930 ILE cc_start: 0.7521 (mm) cc_final: 0.7256 (tt) REVERT: C 1084 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7424 (tttt) REVERT: C 1091 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6718 (mt-10) REVERT: D 37 ARG cc_start: 0.8433 (ttm170) cc_final: 0.8187 (ttp80) REVERT: D 158 LEU cc_start: 0.3204 (OUTLIER) cc_final: 0.1927 (pt) REVERT: D 175 ASN cc_start: 0.8445 (m-40) cc_final: 0.8219 (m-40) REVERT: D 194 GLU cc_start: 0.6912 (pt0) cc_final: 0.6020 (tp30) REVERT: D 299 CYS cc_start: 0.7612 (m) cc_final: 0.7081 (m) REVERT: D 378 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7258 (mtt-85) REVERT: D 526 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.6951 (mtm180) REVERT: D 566 ASN cc_start: 0.1739 (OUTLIER) cc_final: 0.1400 (m-40) outliers start: 63 outliers final: 40 residues processed: 231 average time/residue: 0.2722 time to fit residues: 94.3686 Evaluate side-chains 215 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 170 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 506 THR Chi-restraints excluded: chain D residue 526 ARG Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 566 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.0980 chunk 161 optimal weight: 0.0270 chunk 45 optimal weight: 2.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15582 Z= 0.148 Angle : 0.490 8.847 21040 Z= 0.252 Chirality : 0.039 0.154 2286 Planarity : 0.003 0.044 2688 Dihedral : 4.241 24.517 2036 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.39 % Allowed : 16.33 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.20), residues: 1862 helix: 1.32 (0.18), residues: 866 sheet: -0.23 (0.44), residues: 162 loop : -2.40 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1086 HIS 0.007 0.001 HIS B 380 PHE 0.032 0.001 PHE D 550 TYR 0.011 0.001 TYR D 301 ARG 0.002 0.000 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 198 time to evaluate : 1.842 Fit side-chains REVERT: A 881 PRO cc_start: 0.8092 (Cg_endo) cc_final: 0.7814 (Cg_exo) REVERT: A 930 ILE cc_start: 0.7542 (mm) cc_final: 0.7255 (tt) REVERT: A 1084 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7455 (tttt) REVERT: A 1091 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6602 (mt-10) REVERT: B 37 ARG cc_start: 0.8316 (ttm170) cc_final: 0.7921 (ttp80) REVERT: B 144 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7906 (tm-30) REVERT: B 194 GLU cc_start: 0.6936 (pt0) cc_final: 0.6109 (tp30) REVERT: B 221 ILE cc_start: 0.7695 (tt) cc_final: 0.7432 (tt) REVERT: B 276 PHE cc_start: 0.8024 (m-80) cc_final: 0.7554 (m-80) REVERT: B 299 CYS cc_start: 0.7391 (m) cc_final: 0.7138 (m) REVERT: B 379 HIS cc_start: 0.7324 (t70) cc_final: 0.6787 (t-90) REVERT: B 483 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8403 (mtpp) REVERT: B 520 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7432 (tp30) REVERT: B 526 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6572 (mtt180) REVERT: C 736 MET cc_start: 0.8267 (mmm) cc_final: 0.7940 (mmm) REVERT: C 893 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6654 (mm-30) REVERT: C 930 ILE cc_start: 0.7443 (mm) cc_final: 0.7222 (tt) REVERT: C 1084 LYS cc_start: 0.7773 (mtmt) cc_final: 0.7362 (tttt) REVERT: C 1091 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6325 (mt-10) REVERT: D 37 ARG cc_start: 0.8274 (ttm170) cc_final: 0.8063 (ttp80) REVERT: D 48 MET cc_start: 0.8302 (ttt) cc_final: 0.7913 (ttm) REVERT: D 158 LEU cc_start: 0.2993 (OUTLIER) cc_final: 0.1922 (pt) REVERT: D 194 GLU cc_start: 0.6893 (pt0) cc_final: 0.6033 (tp30) REVERT: D 213 ARG cc_start: 0.1803 (OUTLIER) cc_final: 0.1477 (tpm170) REVERT: D 299 CYS cc_start: 0.7448 (m) cc_final: 0.7128 (m) REVERT: D 378 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7178 (mtt-85) REVERT: D 566 ASN cc_start: 0.1383 (OUTLIER) cc_final: 0.1069 (m-40) outliers start: 40 outliers final: 30 residues processed: 232 average time/residue: 0.2632 time to fit residues: 91.4273 Evaluate side-chains 207 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 526 ARG Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 566 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 9.9990 chunk 161 optimal weight: 0.0370 chunk 35 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 overall best weight: 1.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 ASN ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN B 360 ASN ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 HIS B 449 GLN C 860 ASN ** C1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1078 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15582 Z= 0.247 Angle : 0.542 9.552 21040 Z= 0.275 Chirality : 0.041 0.153 2286 Planarity : 0.004 0.046 2688 Dihedral : 4.317 23.756 2036 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 3.17 % Allowed : 17.34 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1862 helix: 1.30 (0.18), residues: 866 sheet: -0.24 (0.43), residues: 162 loop : -2.34 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1086 HIS 0.004 0.001 HIS D 380 PHE 0.028 0.002 PHE D 550 TYR 0.022 0.001 TYR D 301 ARG 0.003 0.000 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 171 time to evaluate : 1.710 Fit side-chains REVERT: A 881 PRO cc_start: 0.8190 (Cg_endo) cc_final: 0.7902 (Cg_exo) REVERT: A 882 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7920 (pt0) REVERT: A 930 ILE cc_start: 0.7516 (mm) cc_final: 0.7222 (tt) REVERT: A 1084 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7519 (tttt) REVERT: A 1091 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6628 (mt-10) REVERT: B 37 ARG cc_start: 0.8333 (ttm170) cc_final: 0.7920 (ttp80) REVERT: B 144 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 194 GLU cc_start: 0.6990 (pt0) cc_final: 0.6207 (tp30) REVERT: B 221 ILE cc_start: 0.7735 (tt) cc_final: 0.7461 (tt) REVERT: B 276 PHE cc_start: 0.8031 (m-80) cc_final: 0.7599 (m-80) REVERT: B 299 CYS cc_start: 0.7490 (m) cc_final: 0.7182 (m) REVERT: B 379 HIS cc_start: 0.7465 (t70) cc_final: 0.6812 (t-90) REVERT: B 483 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8386 (mtpp) REVERT: B 526 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6871 (mtt180) REVERT: B 561 ASP cc_start: 0.6289 (OUTLIER) cc_final: 0.5073 (t0) REVERT: C 736 MET cc_start: 0.8323 (mmm) cc_final: 0.8038 (mmm) REVERT: C 930 ILE cc_start: 0.7513 (mm) cc_final: 0.7221 (tt) REVERT: C 1084 LYS cc_start: 0.7806 (mtmt) cc_final: 0.7385 (tttt) REVERT: C 1091 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6413 (mt-10) REVERT: D 37 ARG cc_start: 0.8296 (ttm170) cc_final: 0.8057 (ttp80) REVERT: D 158 LEU cc_start: 0.3246 (OUTLIER) cc_final: 0.2098 (pt) REVERT: D 194 GLU cc_start: 0.7008 (pt0) cc_final: 0.6012 (tp30) REVERT: D 213 ARG cc_start: 0.1741 (OUTLIER) cc_final: 0.1463 (tpm170) REVERT: D 299 CYS cc_start: 0.7424 (m) cc_final: 0.6978 (m) REVERT: D 378 ARG cc_start: 0.7554 (mtp85) cc_final: 0.7203 (mtt-85) REVERT: D 526 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6608 (mtm180) REVERT: D 561 ASP cc_start: 0.6149 (OUTLIER) cc_final: 0.5173 (t0) REVERT: D 566 ASN cc_start: 0.1526 (OUTLIER) cc_final: 0.1202 (m-40) outliers start: 53 outliers final: 37 residues processed: 217 average time/residue: 0.2834 time to fit residues: 91.4820 Evaluate side-chains 214 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 169 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 526 ARG Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 526 ARG Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 566 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 HIS ** C1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1078 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15582 Z= 0.238 Angle : 0.542 9.738 21040 Z= 0.274 Chirality : 0.041 0.156 2286 Planarity : 0.004 0.042 2688 Dihedral : 4.341 23.961 2036 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.65 % Allowed : 17.64 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1862 helix: 1.32 (0.18), residues: 866 sheet: -0.35 (0.43), residues: 166 loop : -2.31 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1086 HIS 0.004 0.001 HIS B 323 PHE 0.029 0.001 PHE B 550 TYR 0.042 0.001 TYR D 70 ARG 0.003 0.000 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 168 time to evaluate : 1.766 Fit side-chains REVERT: A 881 PRO cc_start: 0.8131 (Cg_endo) cc_final: 0.7852 (Cg_exo) REVERT: A 882 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7923 (pt0) REVERT: A 930 ILE cc_start: 0.7590 (mm) cc_final: 0.7284 (tt) REVERT: A 1084 LYS cc_start: 0.7983 (mtmt) cc_final: 0.7524 (tttt) REVERT: A 1091 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6670 (mt-10) REVERT: B 144 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7884 (tm-30) REVERT: B 194 GLU cc_start: 0.7047 (pt0) cc_final: 0.6136 (tp30) REVERT: B 196 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7870 (mt) REVERT: B 221 ILE cc_start: 0.7685 (tt) cc_final: 0.7410 (tt) REVERT: B 299 CYS cc_start: 0.7559 (m) cc_final: 0.7238 (m) REVERT: B 379 HIS cc_start: 0.7427 (t70) cc_final: 0.6699 (t-90) REVERT: B 483 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8339 (mtpp) REVERT: B 526 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6742 (mtt180) REVERT: B 561 ASP cc_start: 0.6268 (OUTLIER) cc_final: 0.5085 (t0) REVERT: C 882 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: C 930 ILE cc_start: 0.7503 (mm) cc_final: 0.7229 (tt) REVERT: C 1084 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7407 (tttt) REVERT: C 1091 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6572 (mt-10) REVERT: D 144 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8003 (tm-30) REVERT: D 194 GLU cc_start: 0.6863 (pt0) cc_final: 0.5938 (tp30) REVERT: D 196 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7753 (mt) REVERT: D 213 ARG cc_start: 0.1725 (OUTLIER) cc_final: 0.1389 (tpm170) REVERT: D 299 CYS cc_start: 0.7575 (m) cc_final: 0.7120 (m) REVERT: D 378 ARG cc_start: 0.7537 (mtp85) cc_final: 0.7181 (mtt-85) REVERT: D 526 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6540 (mtm180) REVERT: D 561 ASP cc_start: 0.5985 (OUTLIER) cc_final: 0.5112 (t0) REVERT: D 566 ASN cc_start: 0.1656 (OUTLIER) cc_final: 0.1320 (m-40) outliers start: 61 outliers final: 42 residues processed: 221 average time/residue: 0.2671 time to fit residues: 89.1754 Evaluate side-chains 213 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 161 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 526 ARG Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 882 GLU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 526 ARG Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 566 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.6278 > 50: distance: 42 - 70: 12.839 distance: 54 - 78: 21.440 distance: 66 - 70: 13.200 distance: 70 - 71: 6.849 distance: 71 - 72: 20.106 distance: 71 - 74: 7.577 distance: 72 - 73: 30.867 distance: 72 - 78: 34.062 distance: 74 - 75: 12.578 distance: 75 - 76: 17.465 distance: 76 - 77: 16.452 distance: 78 - 79: 27.506 distance: 79 - 80: 22.196 distance: 79 - 82: 15.481 distance: 80 - 81: 43.697 distance: 80 - 85: 22.256 distance: 82 - 83: 7.267 distance: 82 - 84: 8.975 distance: 85 - 86: 3.897 distance: 86 - 87: 21.751 distance: 86 - 89: 7.342 distance: 87 - 88: 34.274 distance: 87 - 94: 9.502 distance: 89 - 90: 19.399 distance: 90 - 91: 20.950 distance: 91 - 92: 28.539 distance: 91 - 93: 24.354 distance: 94 - 95: 32.923 distance: 95 - 96: 3.269 distance: 95 - 98: 10.167 distance: 96 - 97: 23.162 distance: 96 - 99: 19.535 distance: 99 - 100: 6.643 distance: 100 - 101: 8.532 distance: 100 - 103: 16.953 distance: 101 - 102: 33.307 distance: 101 - 108: 33.300 distance: 103 - 104: 19.213 distance: 104 - 105: 10.015 distance: 105 - 106: 11.321 distance: 105 - 107: 10.380 distance: 108 - 109: 7.980 distance: 108 - 114: 23.449 distance: 109 - 110: 7.589 distance: 109 - 112: 9.765 distance: 110 - 111: 14.836 distance: 110 - 115: 19.259 distance: 112 - 113: 18.922 distance: 113 - 114: 20.044 distance: 115 - 116: 19.202 distance: 116 - 117: 8.434 distance: 116 - 119: 16.919 distance: 117 - 118: 3.479 distance: 117 - 124: 7.441 distance: 119 - 120: 21.479 distance: 120 - 121: 15.525 distance: 121 - 122: 14.054 distance: 122 - 123: 4.207 distance: 124 - 125: 8.652 distance: 125 - 126: 24.342 distance: 125 - 128: 9.882 distance: 126 - 127: 11.173 distance: 126 - 135: 11.844 distance: 128 - 129: 9.207 distance: 129 - 130: 12.329 distance: 129 - 131: 3.409 distance: 130 - 132: 15.681 distance: 131 - 133: 7.473 distance: 133 - 134: 5.468 distance: 135 - 136: 8.505 distance: 136 - 137: 18.618 distance: 136 - 139: 17.872 distance: 137 - 138: 32.160 distance: 137 - 141: 16.199 distance: 139 - 140: 18.177 distance: 141 - 142: 15.199 distance: 142 - 143: 27.629 distance: 142 - 145: 25.567 distance: 143 - 144: 18.505 distance: 143 - 147: 13.758 distance: 145 - 146: 25.706