Starting phenix.real_space_refine on Mon Aug 25 10:24:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8avc_15678/08_2025/8avc_15678.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avc_15678/08_2025/8avc_15678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8avc_15678/08_2025/8avc_15678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avc_15678/08_2025/8avc_15678.map" model { file = "/net/cci-nas-00/data/ceres_data/8avc_15678/08_2025/8avc_15678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avc_15678/08_2025/8avc_15678.cif" } resolution = 4.6 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11844 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ni 3 6.56 5 S 81 5.16 5 C 11199 2.51 5 N 2940 2.21 5 O 3282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s 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: 17505 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Chain: "C" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "D" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Chain: "E" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1077 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "F" Number of atoms: 4757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4757 Classifications: {'peptide': 593} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 555} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.54, per 1000 atoms: 0.20 Number of scatterers: 17505 At special positions: 0 Unit cell: (137.614, 142.588, 169.116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ni 3 28.00 S 81 16.00 O 3282 8.00 N 2940 7.00 C 11199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 167 " distance=2.04 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 410 " distance=2.03 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 526 " distance=2.02 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 496 " distance=2.03 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 350 " - pdb=" SG CYS D 410 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 434 " - pdb=" SG CYS D 445 " distance=2.05 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS D 526 " distance=2.03 Simple disulfide: pdb=" SG CYS D 486 " - pdb=" SG CYS D 496 " distance=2.03 Simple disulfide: pdb=" SG CYS D 602 " - pdb=" SG CYS D 672 " distance=2.03 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS E 167 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 410 " distance=2.04 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 434 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 471 " - pdb=" SG CYS F 526 " distance=2.03 Simple disulfide: pdb=" SG CYS F 486 " - pdb=" SG CYS F 496 " distance=2.03 Simple disulfide: pdb=" SG CYS F 602 " - pdb=" SG CYS F 672 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 753.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4212 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 42 sheets defined 16.6% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 23 through 45 removed outlier: 3.823A pdb=" N ILE A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.655A pdb=" N GLN A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 71 through 89 removed outlier: 3.847A pdb=" N SER A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 116 Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.758A pdb=" N VAL A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.975A pdb=" N VAL B 533 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'C' and resid 23 through 45 removed outlier: 3.594A pdb=" N ILE C 45 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 50 removed outlier: 3.629A pdb=" N GLN C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 50' Processing helix chain 'C' and resid 71 through 89 removed outlier: 3.884A pdb=" N SER C 88 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 116 Processing helix chain 'C' and resid 130 through 138 removed outlier: 3.631A pdb=" N VAL C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 160 Processing helix chain 'D' and resid 528 through 533 removed outlier: 3.819A pdb=" N VAL D 533 " --> pdb=" O ASP D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 671 Processing helix chain 'D' and resid 732 through 736 Processing helix chain 'E' and resid 23 through 45 removed outlier: 3.527A pdb=" N ILE E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 50 removed outlier: 3.940A pdb=" N SER E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 removed outlier: 3.793A pdb=" N SER E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 89 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 116 Processing helix chain 'E' and resid 130 through 138 removed outlier: 3.801A pdb=" N VAL E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 160 Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 528 through 533 removed outlier: 3.868A pdb=" N VAL F 532 " --> pdb=" O LEU F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 736 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 246 removed outlier: 3.679A pdb=" N LEU B 240 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 242 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER B 255 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET B 244 " --> pdb=" O LYS B 253 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS B 253 " --> pdb=" O MET B 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 286 Processing sheet with id=AA4, first strand: chain 'B' and resid 332 through 334 Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 341 removed outlier: 3.571A pdb=" N GLU B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 341 removed outlier: 6.833A pdb=" N CYS B 410 " --> pdb=" O HIS B 417 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N HIS B 417 " --> pdb=" O CYS B 410 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N CYS B 416 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 433 through 436 Processing sheet with id=AA8, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.250A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.250A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 545 removed outlier: 3.672A pdb=" N VAL B 541 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N SER B 555 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA B 543 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS B 553 " --> pdb=" O ALA B 543 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 582 through 586 Processing sheet with id=AB3, first strand: chain 'B' and resid 643 through 648 Processing sheet with id=AB4, first strand: chain 'B' and resid 690 through 694 removed outlier: 5.842A pdb=" N TYR B 677 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 739 through 748 removed outlier: 5.459A pdb=" N LEU B 742 " --> pdb=" O THR B 757 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR B 757 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ALA B 744 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N SER B 755 " --> pdb=" O ALA B 744 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 753 " --> pdb=" O PRO B 746 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 782 through 787 removed outlier: 3.599A pdb=" N TYR B 767 " --> pdb=" O VAL B 812 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 240 through 246 removed outlier: 5.457A pdb=" N GLY D 241 " --> pdb=" O ASP D 257 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP D 257 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 279 through 286 Processing sheet with id=AB9, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AC1, first strand: chain 'D' and resid 337 through 340 removed outlier: 3.805A pdb=" N GLU D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 416 through 417 removed outlier: 7.468A pdb=" N CYS D 416 " --> pdb=" O THR E 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 433 through 436 Processing sheet with id=AC4, first strand: chain 'D' and resid 482 through 484 removed outlier: 4.177A pdb=" N LEU D 462 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 482 through 484 removed outlier: 4.177A pdb=" N LEU D 462 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 539 through 545 removed outlier: 4.102A pdb=" N VAL D 541 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER D 555 " --> pdb=" O VAL D 541 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 543 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS D 553 " --> pdb=" O ALA D 543 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 582 through 586 Processing sheet with id=AC8, first strand: chain 'D' and resid 643 through 648 Processing sheet with id=AC9, first strand: chain 'D' and resid 687 through 694 removed outlier: 5.788A pdb=" N TYR D 677 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 739 through 745 Processing sheet with id=AD2, first strand: chain 'D' and resid 782 through 787 removed outlier: 3.642A pdb=" N TYR D 767 " --> pdb=" O VAL D 812 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS D 773 " --> pdb=" O GLN D 806 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 240 through 246 removed outlier: 6.045A pdb=" N GLY F 241 " --> pdb=" O ASP F 257 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP F 257 " --> pdb=" O GLY F 241 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 279 through 286 Processing sheet with id=AD5, first strand: chain 'F' and resid 331 through 334 Processing sheet with id=AD6, first strand: chain 'F' and resid 337 through 341 Processing sheet with id=AD7, first strand: chain 'F' and resid 433 through 436 Processing sheet with id=AD8, first strand: chain 'F' and resid 482 through 484 removed outlier: 4.479A pdb=" N LEU F 462 " --> pdb=" O LYS F 484 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 482 through 484 removed outlier: 4.479A pdb=" N LEU F 462 " --> pdb=" O LYS F 484 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 539 through 545 removed outlier: 5.594A pdb=" N ASN F 540 " --> pdb=" O GLU F 557 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU F 557 " --> pdb=" O ASN F 540 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 582 through 586 Processing sheet with id=AE3, first strand: chain 'F' and resid 643 through 648 Processing sheet with id=AE4, first strand: chain 'F' and resid 687 through 694 removed outlier: 5.818A pdb=" N TYR F 677 " --> pdb=" O VAL F 693 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 739 through 745 Processing sheet with id=AE6, first strand: chain 'F' and resid 782 through 787 removed outlier: 3.544A pdb=" N TYR F 767 " --> pdb=" O VAL F 812 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2938 1.32 - 1.46: 6297 1.46 - 1.59: 8585 1.59 - 1.73: 0 1.73 - 1.87: 114 Bond restraints: 17934 Sorted by residual: bond pdb=" CB GLN C 96 " pdb=" CG GLN C 96 " ideal model delta sigma weight residual 1.520 1.424 0.096 3.00e-02 1.11e+03 1.02e+01 bond pdb=" CD GLN C 96 " pdb=" NE2 GLN C 96 " ideal model delta sigma weight residual 1.328 1.274 0.054 2.10e-02 2.27e+03 6.67e+00 bond pdb=" CB ASN C 99 " pdb=" CG ASN C 99 " ideal model delta sigma weight residual 1.516 1.455 0.061 2.50e-02 1.60e+03 5.93e+00 bond pdb=" CG ASN A 103 " pdb=" OD1 ASN A 103 " ideal model delta sigma weight residual 1.231 1.186 0.045 1.90e-02 2.77e+03 5.51e+00 bond pdb=" CG GLN C 96 " pdb=" CD GLN C 96 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.44e+00 ... (remaining 17929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 24265 3.53 - 7.06: 147 7.06 - 10.59: 25 10.59 - 14.12: 2 14.12 - 17.65: 2 Bond angle restraints: 24441 Sorted by residual: angle pdb=" CB GLN C 96 " pdb=" CG GLN C 96 " pdb=" CD GLN C 96 " ideal model delta sigma weight residual 112.60 94.95 17.65 1.70e+00 3.46e-01 1.08e+02 angle pdb=" N CYS D 434 " pdb=" CA CYS D 434 " pdb=" C CYS D 434 " ideal model delta sigma weight residual 108.38 116.42 -8.04 1.35e+00 5.49e-01 3.55e+01 angle pdb=" N GLN C 96 " pdb=" CA GLN C 96 " pdb=" C GLN C 96 " ideal model delta sigma weight residual 111.36 104.87 6.49 1.09e+00 8.42e-01 3.55e+01 angle pdb=" C ASN A 103 " pdb=" CA ASN A 103 " pdb=" CB ASN A 103 " ideal model delta sigma weight residual 110.63 120.80 -10.17 1.85e+00 2.92e-01 3.02e+01 angle pdb=" CA ASN A 103 " pdb=" CB ASN A 103 " pdb=" CG ASN A 103 " ideal model delta sigma weight residual 112.60 118.09 -5.49 1.00e+00 1.00e+00 3.02e+01 ... (remaining 24436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 10063 17.59 - 35.19: 653 35.19 - 52.78: 101 52.78 - 70.38: 27 70.38 - 87.97: 10 Dihedral angle restraints: 10854 sinusoidal: 4368 harmonic: 6486 Sorted by residual: dihedral pdb=" CA ILE D 501 " pdb=" C ILE D 501 " pdb=" N PHE D 502 " pdb=" CA PHE D 502 " ideal model delta harmonic sigma weight residual 180.00 137.16 42.84 0 5.00e+00 4.00e-02 7.34e+01 dihedral pdb=" CB CYS B 350 " pdb=" SG CYS B 350 " pdb=" SG CYS B 410 " pdb=" CB CYS B 410 " ideal model delta sinusoidal sigma weight residual -86.00 -22.47 -63.53 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 496 " pdb=" CB CYS B 496 " ideal model delta sinusoidal sigma weight residual 93.00 30.11 62.89 1 1.00e+01 1.00e-02 5.23e+01 ... (remaining 10851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2636 0.106 - 0.211: 154 0.211 - 0.317: 8 0.317 - 0.422: 0 0.422 - 0.528: 1 Chirality restraints: 2799 Sorted by residual: chirality pdb=" CA ASN A 103 " pdb=" N ASN A 103 " pdb=" C ASN A 103 " pdb=" CB ASN A 103 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.97e+00 chirality pdb=" CB ILE E 69 " pdb=" CA ILE E 69 " pdb=" CG1 ILE E 69 " pdb=" CG2 ILE E 69 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CG LEU A 60 " pdb=" CB LEU A 60 " pdb=" CD1 LEU A 60 " pdb=" CD2 LEU A 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 2796 not shown) Planarity restraints: 3078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 96 " 0.022 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" CD GLN C 96 " -0.080 2.00e-02 2.50e+03 pdb=" OE1 GLN C 96 " 0.029 2.00e-02 2.50e+03 pdb=" NE2 GLN C 96 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 103 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" CG ASN A 103 " -0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN A 103 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 103 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 759 " -0.061 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO B 760 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 760 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 760 " -0.050 5.00e-02 4.00e+02 ... (remaining 3075 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 191 2.52 - 3.12: 13291 3.12 - 3.71: 28949 3.71 - 4.31: 39823 4.31 - 4.90: 63889 Nonbonded interactions: 146143 Sorted by model distance: nonbonded pdb=" OE1 GLN C 96 " pdb=" O ILE D 501 " model vdw 1.931 3.040 nonbonded pdb=" ND2 ASN A 103 " pdb=" N LEU B 504 " model vdw 1.987 3.200 nonbonded pdb=" NH1 ARG B 467 " pdb="NI NI B 901 " model vdw 2.014 2.260 nonbonded pdb=" NE2 GLN C 83 " pdb=" O ALA C 98 " model vdw 2.110 3.120 nonbonded pdb=" OH TYR B 409 " pdb=" CB SER C 141 " model vdw 2.122 3.440 ... (remaining 146138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.390 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 17955 Z= 0.169 Angle : 0.802 17.651 24483 Z= 0.445 Chirality : 0.052 0.528 2799 Planarity : 0.005 0.089 3078 Dihedral : 12.050 87.969 6579 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.31 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.17 (0.18), residues: 2181 helix: -0.69 (0.26), residues: 327 sheet: 0.27 (0.17), residues: 847 loop : -0.08 (0.21), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 149 TYR 0.019 0.001 TYR D 268 PHE 0.052 0.001 PHE D 502 TRP 0.017 0.001 TRP B 447 HIS 0.006 0.001 HIS B 465 Details of bonding type rmsd covalent geometry : bond 0.00360 (17934) covalent geometry : angle 0.79906 (24441) SS BOND : bond 0.00494 ( 21) SS BOND : angle 1.90445 ( 42) hydrogen bonds : bond 0.11941 ( 743) hydrogen bonds : angle 6.70910 ( 2076) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9694 (mt) cc_final: 0.9448 (mt) REVERT: A 102 GLU cc_start: 0.8539 (mp0) cc_final: 0.8269 (pm20) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0297 time to fit residues: 1.3477 Evaluate side-chains 32 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.037 Evaluate side-chains 35 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5244 (ppp) cc_final: 0.4220 (pmm) REVERT: B 443 MET cc_start: 0.9131 (tpp) cc_final: 0.8734 (tpp) REVERT: B 548 ASN cc_start: 0.8571 (m-40) cc_final: 0.8305 (m-40) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0590 time to fit residues: 2.8118 Evaluate side-chains 31 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.0030 chunk 200 optimal weight: 0.0870 chunk 212 optimal weight: 9.9990 overall best weight: 1.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN B 412 ASN B 489 GLN B 567 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.037856 restraints weight = 6770.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.039521 restraints weight = 4772.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.040904 restraints weight = 3596.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.041972 restraints weight = 2825.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.042911 restraints weight = 2301.959| |-----------------------------------------------------------------------------| r_work (final): 0.2912 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.075748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.059556 restraints weight = 29831.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.060065 restraints weight = 22057.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.059833 restraints weight = 9819.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.059740 restraints weight = 9663.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.060043 restraints weight = 8208.700| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 1.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17955 Z= 0.170 Angle : 0.680 7.395 24483 Z= 0.368 Chirality : 0.047 0.179 2799 Planarity : 0.005 0.051 3078 Dihedral : 5.582 59.447 2367 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.10 (0.18), residues: 2181 helix: -0.09 (0.26), residues: 318 sheet: 0.18 (0.16), residues: 909 loop : 0.22 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 105 TYR 0.028 0.002 TYR E 140 PHE 0.010 0.001 PHE F 403 TRP 0.008 0.001 TRP D 447 HIS 0.005 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00356 (17934) covalent geometry : angle 0.67810 (24441) SS BOND : bond 0.00423 ( 21) SS BOND : angle 1.39216 ( 42) hydrogen bonds : bond 0.05090 ( 743) hydrogen bonds : angle 6.30246 ( 2076) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.045 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.9507 (m-30) cc_final: 0.9196 (p0) REVERT: A 139 LEU cc_start: 0.8981 (pt) cc_final: 0.8681 (mp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0395 time to fit residues: 1.7007 Evaluate side-chains 29 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.040 Evaluate side-chains 42 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5118 (ppp) cc_final: 0.4388 (pmm) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0541 time to fit residues: 3.0603 Evaluate side-chains 31 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 0.0270 chunk 203 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 148 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 0.0040 overall best weight: 0.3050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.036867 restraints weight = 6376.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.038345 restraints weight = 4624.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.039689 restraints weight = 3601.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.040678 restraints weight = 2884.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.041415 restraints weight = 2381.066| |-----------------------------------------------------------------------------| r_work (final): 0.2837 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.076325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.060299 restraints weight = 30191.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.060981 restraints weight = 23858.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.060572 restraints weight = 12155.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.060593 restraints weight = 10525.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.061202 restraints weight = 8614.468| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 1.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 17955 Z= 0.241 Angle : 0.933 14.166 24483 Z= 0.498 Chirality : 0.058 0.466 2799 Planarity : 0.008 0.058 3078 Dihedral : 5.639 33.908 2367 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.71 % Favored : 96.15 % Rotamer: Outliers : 0.89 % Allowed : 4.74 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.25 (0.18), residues: 2181 helix: -0.47 (0.28), residues: 321 sheet: 0.24 (0.16), residues: 885 loop : -0.28 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG E 56 TYR 0.085 0.007 TYR D 420 PHE 0.074 0.004 PHE D 403 TRP 0.056 0.004 TRP B 581 HIS 0.022 0.003 HIS D 478 Details of bonding type rmsd covalent geometry : bond 0.00547 (17934) covalent geometry : angle 0.93183 (24441) SS BOND : bond 0.00576 ( 21) SS BOND : angle 1.43017 ( 42) hydrogen bonds : bond 0.05343 ( 743) hydrogen bonds : angle 6.47185 ( 2076) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.9525 (m-30) cc_final: 0.9189 (p0) REVERT: A 101 LEU cc_start: 0.9304 (mt) cc_final: 0.9072 (mt) REVERT: A 102 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8363 (mm-30) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.0327 time to fit residues: 1.3736 Evaluate side-chains 27 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.043 Evaluate side-chains 43 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5305 (ppp) cc_final: 0.4394 (pmm) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 0.0434 time to fit residues: 2.6504 Evaluate side-chains 34 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 134 optimal weight: 0.5980 chunk 171 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 170 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.048596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.037113 restraints weight = 7003.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.038952 restraints weight = 4946.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.040309 restraints weight = 3673.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.041364 restraints weight = 2862.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.042176 restraints weight = 2313.701| |-----------------------------------------------------------------------------| r_work (final): 0.2875 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.076760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.061033 restraints weight = 30756.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.061088 restraints weight = 25975.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.061437 restraints weight = 13444.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.061581 restraints weight = 10559.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.061853 restraints weight = 9626.052| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 1.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 17955 Z= 0.283 Angle : 0.931 14.150 24483 Z= 0.497 Chirality : 0.058 0.466 2799 Planarity : 0.008 0.082 3078 Dihedral : 5.639 33.907 2367 Min Nonbonded Distance : 1.247 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.71 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.25 (0.18), residues: 2181 helix: -0.47 (0.28), residues: 321 sheet: 0.24 (0.16), residues: 885 loop : -0.28 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG C 56 TYR 0.085 0.007 TYR B 420 PHE 0.074 0.004 PHE F 403 TRP 0.056 0.004 TRP B 581 HIS 0.022 0.003 HIS F 478 Details of bonding type rmsd covalent geometry : bond 0.00585 (17934) covalent geometry : angle 0.92980 (24441) SS BOND : bond 0.00572 ( 21) SS BOND : angle 1.42934 ( 42) hydrogen bonds : bond 0.05343 ( 743) hydrogen bonds : angle 6.47215 ( 2076) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.043 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.9525 (m-30) cc_final: 0.9188 (p0) REVERT: A 101 LEU cc_start: 0.9286 (mt) cc_final: 0.9043 (mt) REVERT: A 102 GLU cc_start: 0.9049 (tp30) cc_final: 0.8811 (mm-30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0451 time to fit residues: 1.9971 Evaluate side-chains 31 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.026 Evaluate side-chains 39 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5294 (ppp) cc_final: 0.4378 (pmm) REVERT: B 273 LEU cc_start: 0.9571 (pp) cc_final: 0.9218 (tt) REVERT: B 443 MET cc_start: 0.9241 (tpt) cc_final: 0.8949 (tpp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0377 time to fit residues: 2.1386 Evaluate side-chains 30 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 146 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 176 optimal weight: 0.0050 chunk 164 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 57 optimal weight: 0.7980 chunk 13 optimal weight: 0.0470 chunk 4 optimal weight: 0.3980 chunk 92 optimal weight: 0.0770 overall best weight: 0.2650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.049175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.038459 restraints weight = 7097.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.040382 restraints weight = 4684.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.041782 restraints weight = 3301.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.042844 restraints weight = 2483.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.043633 restraints weight = 1940.370| |-----------------------------------------------------------------------------| r_work (final): 0.2920 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.076754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.061008 restraints weight = 31558.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.060958 restraints weight = 25207.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.061381 restraints weight = 13064.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.061413 restraints weight = 10328.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.061773 restraints weight = 9228.663| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 1.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 17955 Z= 0.277 Angle : 0.929 14.258 24483 Z= 0.496 Chirality : 0.058 0.467 2799 Planarity : 0.008 0.081 3078 Dihedral : 5.639 33.904 2367 Min Nonbonded Distance : 1.039 Molprobity Statistics. All-atom Clashscore : 28.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.71 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.25 (0.18), residues: 2181 helix: -0.48 (0.28), residues: 321 sheet: 0.24 (0.16), residues: 885 loop : -0.28 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG E 56 TYR 0.081 0.007 TYR B 420 PHE 0.075 0.004 PHE F 403 TRP 0.056 0.004 TRP B 581 HIS 0.022 0.003 HIS F 478 Details of bonding type rmsd covalent geometry : bond 0.00582 (17934) covalent geometry : angle 0.92749 (24441) SS BOND : bond 0.00564 ( 21) SS BOND : angle 1.42829 ( 42) hydrogen bonds : bond 0.05341 ( 743) hydrogen bonds : angle 6.47256 ( 2076) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.035 Fit side-chains revert: symmetry clash REVERT: A 30 ASP cc_start: 0.9520 (m-30) cc_final: 0.9183 (p0) REVERT: A 101 LEU cc_start: 0.9282 (mt) cc_final: 0.9035 (mt) REVERT: A 102 GLU cc_start: 0.9043 (tp30) cc_final: 0.8805 (mm-30) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0423 time to fit residues: 1.7902 Evaluate side-chains 30 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.026 Evaluate side-chains 39 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5318 (ppp) cc_final: 0.4408 (pmm) REVERT: B 273 LEU cc_start: 0.9574 (pp) cc_final: 0.9223 (tt) REVERT: B 443 MET cc_start: 0.9249 (tpt) cc_final: 0.8954 (tpp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0536 time to fit residues: 2.9627 Evaluate side-chains 30 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 52 optimal weight: 0.0030 chunk 37 optimal weight: 3.9990 chunk 115 optimal weight: 0.0020 chunk 212 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 135 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS B 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.048329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.037192 restraints weight = 6764.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.038866 restraints weight = 4500.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.040226 restraints weight = 3265.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.041257 restraints weight = 2499.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.042100 restraints weight = 1983.317| |-----------------------------------------------------------------------------| r_work (final): 0.2902 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.077278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.061361 restraints weight = 30288.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.061365 restraints weight = 24982.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.061879 restraints weight = 12716.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.061882 restraints weight = 10113.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.062231 restraints weight = 8842.031| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 1.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17955 Z= 0.195 Angle : 0.905 13.100 24483 Z= 0.471 Chirality : 0.061 0.497 2799 Planarity : 0.009 0.120 3078 Dihedral : 5.716 27.094 2367 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.48 (0.18), residues: 2181 helix: -0.76 (0.28), residues: 321 sheet: 0.12 (0.16), residues: 900 loop : -0.45 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.002 ARG E 41 TYR 0.058 0.006 TYR D 464 PHE 0.020 0.003 PHE A 62 TRP 0.060 0.005 TRP D 447 HIS 0.022 0.004 HIS D 478 Details of bonding type rmsd covalent geometry : bond 0.00423 (17934) covalent geometry : angle 0.90392 (24441) SS BOND : bond 0.00434 ( 21) SS BOND : angle 1.29333 ( 42) hydrogen bonds : bond 0.05406 ( 743) hydrogen bonds : angle 6.44075 ( 2076) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.026 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.3595 (p) cc_final: 0.3122 (p) REVERT: A 102 GLU cc_start: 0.8964 (tp30) cc_final: 0.8712 (tp30) REVERT: A 150 LEU cc_start: 0.9863 (tt) cc_final: 0.9652 (pp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0388 time to fit residues: 1.7011 Evaluate side-chains 26 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.043 Evaluate side-chains 42 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5283 (ppp) cc_final: 0.4352 (pmm) REVERT: B 273 LEU cc_start: 0.9578 (pp) cc_final: 0.9305 (tt) REVERT: B 443 MET cc_start: 0.9459 (tpt) cc_final: 0.8902 (tpp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0458 time to fit residues: 2.8237 Evaluate side-chains 29 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 125 optimal weight: 0.0870 chunk 161 optimal weight: 0.8980 chunk 173 optimal weight: 0.4980 chunk 70 optimal weight: 30.0000 chunk 126 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 180 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 175 optimal weight: 0.0570 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.049936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.039019 restraints weight = 6838.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.040775 restraints weight = 4674.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.042190 restraints weight = 3429.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.043253 restraints weight = 2645.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.044200 restraints weight = 2114.012| |-----------------------------------------------------------------------------| r_work (final): 0.2949 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.076993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.061164 restraints weight = 31275.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.061059 restraints weight = 25147.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.061615 restraints weight = 12434.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.061489 restraints weight = 10285.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.061871 restraints weight = 9016.646| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 1.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 17955 Z= 0.218 Angle : 0.930 11.559 24483 Z= 0.489 Chirality : 0.061 0.640 2799 Planarity : 0.008 0.076 3078 Dihedral : 5.783 26.407 2367 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.99 % Favored : 95.87 % Rotamer: Outliers : 0.15 % Allowed : 2.37 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.55 (0.18), residues: 2181 helix: -0.78 (0.28), residues: 318 sheet: 0.07 (0.16), residues: 900 loop : -0.50 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG F 466 TYR 0.060 0.007 TYR C 140 PHE 0.054 0.004 PHE D 498 TRP 0.056 0.005 TRP F 447 HIS 0.036 0.005 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00489 (17934) covalent geometry : angle 0.92848 (24441) SS BOND : bond 0.00737 ( 21) SS BOND : angle 1.67543 ( 42) hydrogen bonds : bond 0.05158 ( 743) hydrogen bonds : angle 6.48091 ( 2076) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.029 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8962 (tp30) cc_final: 0.8696 (tp30) REVERT: A 150 LEU cc_start: 0.9865 (tt) cc_final: 0.9662 (pp) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.0418 time to fit residues: 1.9273 Evaluate side-chains 27 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.046 Evaluate side-chains 36 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5323 (ppp) cc_final: 0.4415 (pmm) REVERT: B 370 LEU cc_start: 0.8821 (pp) cc_final: 0.8592 (mt) REVERT: B 443 MET cc_start: 0.9459 (tpt) cc_final: 0.8942 (tpp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0512 time to fit residues: 2.6616 Evaluate side-chains 32 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 106 optimal weight: 0.1980 chunk 180 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 182 optimal weight: 0.0370 chunk 123 optimal weight: 0.0070 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 20 optimal weight: 0.0050 chunk 6 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 overall best weight: 0.2290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.051846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.040620 restraints weight = 6535.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.042341 restraints weight = 4521.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.043680 restraints weight = 3359.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.044757 restraints weight = 2614.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045651 restraints weight = 2102.651| |-----------------------------------------------------------------------------| r_work (final): 0.3054 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.077052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.060961 restraints weight = 30899.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.061138 restraints weight = 25366.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.061547 restraints weight = 12797.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.061582 restraints weight = 10105.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.061895 restraints weight = 8903.227| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 1.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17955 Z= 0.202 Angle : 0.910 12.091 24483 Z= 0.475 Chirality : 0.059 0.473 2799 Planarity : 0.009 0.095 3078 Dihedral : 5.865 26.826 2367 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.13 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.64 (0.18), residues: 2181 helix: -0.78 (0.29), residues: 318 sheet: 0.09 (0.17), residues: 885 loop : -0.67 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.003 ARG C 56 TYR 0.058 0.006 TYR C 140 PHE 0.021 0.003 PHE B 348 TRP 0.056 0.005 TRP D 447 HIS 0.021 0.003 HIS F 478 Details of bonding type rmsd covalent geometry : bond 0.00457 (17934) covalent geometry : angle 0.90890 (24441) SS BOND : bond 0.00509 ( 21) SS BOND : angle 1.36217 ( 42) hydrogen bonds : bond 0.05139 ( 743) hydrogen bonds : angle 6.37840 ( 2076) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4358 Ramachandran restraints generated. 2179 Oldfield, 0 Emsley, 2179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9674 (pttm) cc_final: 0.9470 (pptt) REVERT: A 44 ASP cc_start: 0.8403 (p0) cc_final: 0.7998 (p0) REVERT: A 102 GLU cc_start: 0.8871 (tp30) cc_final: 0.8580 (tp30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0354 time to fit residues: 1.6074 Evaluate side-chains 30 residues out of total 129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.032 Evaluate side-chains 36 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 261 MET cc_start: 0.5228 (ppp) cc_final: 0.4309 (pmm) REVERT: B 273 LEU cc_start: 0.9563 (pp) cc_final: 0.9292 (tt) REVERT: B 443 MET cc_start: 0.9467 (tpt) cc_final: 0.8899 (tpp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0433 time to fit residues: 2.2856 Evaluate side-chains 31 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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 704, in refine_xyz self.minimization_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 794, in minimization_ncs weight = 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 394, 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 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ 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/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = 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: 64.6169 > 50: distance: 0 - 1: 8.492 distance: 0 - 9: 11.817 distance: 2 - 3: 13.087 distance: 3 - 4: 10.449 distance: 5 - 6: 7.377 distance: 6 - 7: 30.573 distance: 6 - 8: 34.142 distance: 9 - 10: 12.752 distance: 10 - 11: 3.793 distance: 10 - 13: 5.188 distance: 11 - 12: 4.637 distance: 11 - 15: 13.966 distance: 13 - 14: 14.123 distance: 15 - 16: 10.149 distance: 16 - 17: 7.817 distance: 16 - 19: 18.776 distance: 17 - 18: 16.915 distance: 17 - 23: 13.325 distance: 19 - 20: 34.333 distance: 20 - 21: 42.395 distance: 20 - 22: 33.713 distance: 23 - 24: 14.321 distance: 24 - 25: 16.477 distance: 24 - 27: 4.408 distance: 25 - 26: 12.840 distance: 25 - 35: 14.027 distance: 27 - 28: 13.178 distance: 28 - 29: 25.041 distance: 28 - 30: 31.439 distance: 29 - 31: 26.969 distance: 30 - 32: 25.686 distance: 31 - 33: 11.608 distance: 32 - 33: 4.834 distance: 33 - 34: 10.306 distance: 35 - 36: 11.106 distance: 36 - 37: 3.390 distance: 36 - 39: 7.114 distance: 37 - 41: 4.683 distance: 39 - 40: 10.644 distance: 41 - 42: 6.423 distance: 41 - 47: 8.978 distance: 42 - 43: 19.249 distance: 42 - 45: 12.037 distance: 43 - 44: 25.259 distance: 43 - 48: 39.239 distance: 45 - 46: 11.377 distance: 46 - 47: 8.694 distance: 48 - 49: 11.774 distance: 49 - 50: 31.468 distance: 49 - 52: 17.259 distance: 50 - 51: 20.863 distance: 50 - 56: 38.667 distance: 52 - 53: 14.636 distance: 53 - 54: 13.866 distance: 53 - 55: 11.365 distance: 56 - 57: 7.372 distance: 57 - 58: 14.426 distance: 57 - 60: 17.164 distance: 58 - 59: 7.650 distance: 58 - 62: 7.026 distance: 60 - 61: 25.952 distance: 62 - 63: 8.097 distance: 62 - 68: 13.945 distance: 63 - 64: 18.728 distance: 63 - 66: 24.684 distance: 64 - 65: 15.003 distance: 64 - 69: 10.113 distance: 66 - 67: 10.727 distance: 67 - 68: 17.905 distance: 69 - 70: 5.115 distance: 70 - 71: 3.693 distance: 77 - 83: 4.020 distance: 83 - 84: 3.194 distance: 84 - 85: 5.669 distance: 84 - 87: 3.366 distance: 85 - 86: 5.103