Starting phenix.real_space_refine on Sun Aug 24 17:09:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zgx_14714/08_2025/7zgx_14714.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zgx_14714/08_2025/7zgx_14714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zgx_14714/08_2025/7zgx_14714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zgx_14714/08_2025/7zgx_14714.map" model { file = "/net/cci-nas-00/data/ceres_data/7zgx_14714/08_2025/7zgx_14714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zgx_14714/08_2025/7zgx_14714.cif" } resolution = 2.88 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= 0.002 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 13245 2.51 5 N 3795 2.21 5 O 4293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 21351 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 7117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7117 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 918} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.25, per 1000 atoms: 0.25 Number of scatterers: 21351 At special positions: 0 Unit cell: (164.418, 155.42, 129.244, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 4293 8.00 N 3795 7.00 C 13245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 7.0% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 221 through 252 removed outlier: 3.575A pdb=" N THR A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.888A pdb=" N PHE A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.731A pdb=" N THR A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 removed outlier: 4.161A pdb=" N ALA A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 875 removed outlier: 4.242A pdb=" N GLY A 875 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 924 Processing helix chain 'B' and resid 221 through 252 removed outlier: 3.650A pdb=" N THR B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.852A pdb=" N PHE B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 451 through 456 removed outlier: 3.613A pdb=" N THR B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 594 removed outlier: 4.223A pdb=" N ALA B 594 " --> pdb=" O MET B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 787 Processing helix chain 'B' and resid 870 through 875 removed outlier: 4.283A pdb=" N GLY B 875 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 924 Processing helix chain 'C' and resid 221 through 252 removed outlier: 3.540A pdb=" N GLU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 removed outlier: 3.982A pdb=" N PHE C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.550A pdb=" N THR C 455 " --> pdb=" O THR C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 4.132A pdb=" N ALA C 594 " --> pdb=" O MET C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 870 through 875 removed outlier: 3.620A pdb=" N GLY C 873 " --> pdb=" O GLY C 870 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY C 875 " --> pdb=" O LEU C 872 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 269 removed outlier: 3.743A pdb=" N SER A 383 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER A 267 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLU A 381 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR A 269 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR A 379 " --> pdb=" O THR A 269 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 379 through 393 current: chain 'A' and resid 418 through 420 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 418 through 420 current: chain 'A' and resid 473 through 483 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 473 through 483 current: chain 'A' and resid 756 through 765 removed outlier: 3.799A pdb=" N PHE A 758 " --> pdb=" O THR A 777 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 789 through 792 current: chain 'A' and resid 803 through 814 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 932 through 936 current: chain 'A' and resid 977 through 984 removed outlier: 3.500A pdb=" N ALA A1016 " --> pdb=" O SER A 998 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1057 through 1061 current: chain 'A' and resid 1075 through 1085 removed outlier: 3.831A pdb=" N GLY A1115 " --> pdb=" O ASP A1081 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A1133 " --> pdb=" O ASN A1114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1125 through 1134 current: chain 'B' and resid 379 through 393 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 379 through 393 current: chain 'B' and resid 418 through 420 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 418 through 420 current: chain 'B' and resid 473 through 483 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 473 through 483 current: chain 'B' and resid 982 through 984 removed outlier: 3.558A pdb=" N ALA B1016 " --> pdb=" O SER B 998 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1014 through 1022 current: chain 'B' and resid 1054 through 1061 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1054 through 1061 current: chain 'B' and resid 1076 through 1085 removed outlier: 3.584A pdb=" N GLY B1115 " --> pdb=" O ASP B1081 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B1133 " --> pdb=" O ASN B1114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1126 through 1134 current: chain 'C' and resid 379 through 394 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 379 through 394 current: chain 'C' and resid 418 through 420 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 418 through 420 current: chain 'C' and resid 982 through 984 removed outlier: 3.725A pdb=" N ALA C1016 " --> pdb=" O SER C 998 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY C1063 " --> pdb=" O ASN C1036 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C1080 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY C1115 " --> pdb=" O ASP C1081 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C1133 " --> pdb=" O ASN C1114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 334 through 337 Processing sheet with id=AA3, first strand: chain 'A' and resid 436 through 438 Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AA5, first strand: chain 'A' and resid 487 through 490 removed outlier: 5.817A pdb=" N VAL A 562 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 611 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER A 622 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 650 through 651 removed outlier: 3.858A pdb=" N THR A 650 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 724 through 729 removed outlier: 6.165A pdb=" N LEU A 724 " --> pdb=" O ILE A 753 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 821 Processing sheet with id=AA9, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.564A pdb=" N ASP A 972 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1088 through 1091 Processing sheet with id=AB2, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AB3, first strand: chain 'B' and resid 465 through 467 Processing sheet with id=AB4, first strand: chain 'B' and resid 487 through 490 removed outlier: 5.848A pdb=" N VAL B 562 " --> pdb=" O ARG B 549 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 609 " --> pdb=" O TYR B 624 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 622 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.981A pdb=" N THR B 650 " --> pdb=" O ASP B 658 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 672 through 683 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 672 through 683 current: chain 'B' and resid 748 through 765 removed outlier: 3.557A pdb=" N PHE B 758 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 774 " --> pdb=" O GLY B 793 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 793 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 792 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 819 through 821 Processing sheet with id=AB8, first strand: chain 'B' and resid 962 through 963 Processing sheet with id=AB9, first strand: chain 'B' and resid 1088 through 1091 Processing sheet with id=AC1, first strand: chain 'C' and resid 334 through 337 Processing sheet with id=AC2, first strand: chain 'C' and resid 487 through 490 removed outlier: 5.734A pdb=" N VAL C 562 " --> pdb=" O ARG C 549 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 611 " --> pdb=" O SER C 622 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER C 622 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 650 through 651 removed outlier: 3.837A pdb=" N THR C 650 " --> pdb=" O ASP C 658 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 674 through 681 removed outlier: 6.373A pdb=" N LYS C 761 " --> pdb=" O TYR C 676 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU C 678 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY C 759 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR C 680 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY C 757 " --> pdb=" O TYR C 680 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 758 " --> pdb=" O THR C 777 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET C 789 " --> pdb=" O SER C 778 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 789 through 792 current: chain 'C' and resid 803 through 814 removed outlier: 6.449A pdb=" N VAL C 962 " --> pdb=" O PHE C 973 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N PHE C 973 " --> pdb=" O VAL C 962 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 724 through 726 removed outlier: 6.069A pdb=" N LEU C 724 " --> pdb=" O ILE C 753 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 819 through 821 Processing sheet with id=AC7, first strand: chain 'C' and resid 880 through 881 removed outlier: 3.687A pdb=" N ARG C 891 " --> pdb=" O SER C 880 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1088 through 1091 596 hydrogen bonds defined for protein. 1575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7370 1.34 - 1.46: 4133 1.46 - 1.57: 10241 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 21774 Sorted by residual: bond pdb=" C PHE B 881 " pdb=" N GLU B 882 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.46e-02 4.69e+03 4.16e+00 bond pdb=" C TYR C1090 " pdb=" N THR C1091 " ideal model delta sigma weight residual 1.332 1.309 0.023 1.44e-02 4.82e+03 2.65e+00 bond pdb=" C TYR A1090 " pdb=" N THR A1091 " ideal model delta sigma weight residual 1.333 1.310 0.024 1.61e-02 3.86e+03 2.18e+00 bond pdb=" C THR B 439 " pdb=" N ASN B 440 " ideal model delta sigma weight residual 1.334 1.313 0.022 1.52e-02 4.33e+03 2.04e+00 bond pdb=" CA GLY B 387 " pdb=" C GLY B 387 " ideal model delta sigma weight residual 1.520 1.510 0.010 7.30e-03 1.88e+04 2.03e+00 ... (remaining 21769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 28771 2.07 - 4.13: 751 4.13 - 6.20: 61 6.20 - 8.26: 11 8.26 - 10.33: 1 Bond angle restraints: 29595 Sorted by residual: angle pdb=" C ASN C 632 " pdb=" CA ASN C 632 " pdb=" CB ASN C 632 " ideal model delta sigma weight residual 116.54 109.34 7.20 1.15e+00 7.56e-01 3.92e+01 angle pdb=" C THR B 597 " pdb=" CA THR B 597 " pdb=" CB THR B 597 " ideal model delta sigma weight residual 116.54 110.29 6.25 1.15e+00 7.56e-01 2.95e+01 angle pdb=" C THR C 597 " pdb=" CA THR C 597 " pdb=" CB THR C 597 " ideal model delta sigma weight residual 116.54 110.39 6.15 1.15e+00 7.56e-01 2.86e+01 angle pdb=" C THR A 597 " pdb=" CA THR A 597 " pdb=" CB THR A 597 " ideal model delta sigma weight residual 116.54 110.41 6.13 1.15e+00 7.56e-01 2.85e+01 angle pdb=" N VAL C 990 " pdb=" CA VAL C 990 " pdb=" C VAL C 990 " ideal model delta sigma weight residual 113.22 106.77 6.45 1.23e+00 6.61e-01 2.75e+01 ... (remaining 29590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11623 17.76 - 35.52: 781 35.52 - 53.28: 109 53.28 - 71.05: 20 71.05 - 88.81: 13 Dihedral angle restraints: 12546 sinusoidal: 4599 harmonic: 7947 Sorted by residual: dihedral pdb=" CA TYR C 696 " pdb=" C TYR C 696 " pdb=" N GLY C 697 " pdb=" CA GLY C 697 " ideal model delta harmonic sigma weight residual 180.00 149.82 30.18 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA TYR A 696 " pdb=" C TYR A 696 " pdb=" N GLY A 697 " pdb=" CA GLY A 697 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA GLN B1086 " pdb=" C GLN B1086 " pdb=" N ASN B1087 " pdb=" CA ASN B1087 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 12543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2094 0.041 - 0.083: 813 0.083 - 0.124: 258 0.124 - 0.165: 33 0.165 - 0.206: 6 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CB ILE B 535 " pdb=" CA ILE B 535 " pdb=" CG1 ILE B 535 " pdb=" CG2 ILE B 535 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE A 262 " pdb=" CA ILE A 262 " pdb=" CG1 ILE A 262 " pdb=" CG2 ILE A 262 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CB ILE C 262 " pdb=" CA ILE C 262 " pdb=" CG1 ILE C 262 " pdb=" CG2 ILE C 262 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 3201 not shown) Planarity restraints: 4017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 512 " -0.028 2.00e-02 2.50e+03 2.05e-02 7.37e+00 pdb=" CG PHE A 512 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 512 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 512 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 512 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 512 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 512 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 512 " 0.026 2.00e-02 2.50e+03 1.94e-02 6.60e+00 pdb=" CG PHE B 512 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 512 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 512 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 512 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 512 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 512 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 468 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO C 469 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 469 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 469 " -0.035 5.00e-02 4.00e+02 ... (remaining 4014 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 982 2.71 - 3.26: 21430 3.26 - 3.80: 33614 3.80 - 4.35: 43816 4.35 - 4.90: 76532 Nonbonded interactions: 176374 Sorted by model distance: nonbonded pdb=" OH TYR B1117 " pdb=" OE1 GLU B1119 " model vdw 2.159 3.040 nonbonded pdb=" OD1 ASP B 307 " pdb=" OH TYR B1090 " model vdw 2.172 3.040 nonbonded pdb=" OD1 ASN A 733 " pdb=" N ASN A 734 " model vdw 2.179 3.120 nonbonded pdb=" OD1 ASP C 307 " pdb=" OH TYR C1090 " model vdw 2.208 3.040 nonbonded pdb=" O ARG B 251 " pdb=" OG SER B 395 " model vdw 2.212 3.040 ... (remaining 176369 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.120 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21774 Z= 0.258 Angle : 0.767 10.330 29595 Z= 0.466 Chirality : 0.048 0.206 3204 Planarity : 0.005 0.062 4017 Dihedral : 12.229 88.806 7614 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.30 % Favored : 88.28 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.11 (0.15), residues: 2841 helix: -1.25 (0.37), residues: 147 sheet: -1.69 (0.15), residues: 1212 loop : -2.48 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 816 TYR 0.020 0.002 TYR C 890 PHE 0.045 0.002 PHE A 512 TRP 0.004 0.001 TRP C 538 HIS 0.004 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00538 (21774) covalent geometry : angle 0.76672 (29595) hydrogen bonds : bond 0.15843 ( 596) hydrogen bonds : angle 7.48313 ( 1575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8328 (t70) cc_final: 0.7994 (t0) REVERT: A 831 ASP cc_start: 0.8144 (p0) cc_final: 0.7907 (p0) REVERT: B 250 GLU cc_start: 0.8218 (pt0) cc_final: 0.7840 (tm-30) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.5362 time to fit residues: 46.7303 Evaluate side-chains 44 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.0670 overall best weight: 1.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 503 GLN A 707 GLN A 818 GLN B 493 ASN ** B 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.071852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.059811 restraints weight = 54584.743| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.86 r_work: 0.3002 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21774 Z= 0.193 Angle : 0.619 7.597 29595 Z= 0.336 Chirality : 0.047 0.171 3204 Planarity : 0.004 0.055 4017 Dihedral : 5.124 27.750 3189 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.95 % Favored : 88.74 % Rotamer: Outliers : 0.51 % Allowed : 5.65 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.94 (0.15), residues: 2841 helix: -0.78 (0.38), residues: 147 sheet: -1.63 (0.15), residues: 1173 loop : -2.34 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1022 TYR 0.015 0.001 TYR A 837 PHE 0.020 0.002 PHE A 512 TRP 0.003 0.001 TRP C 538 HIS 0.004 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00430 (21774) covalent geometry : angle 0.61856 (29595) hydrogen bonds : bond 0.03504 ( 596) hydrogen bonds : angle 5.71786 ( 1575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8947 (t70) cc_final: 0.8451 (t0) REVERT: A 831 ASP cc_start: 0.8282 (p0) cc_final: 0.7911 (p0) REVERT: B 250 GLU cc_start: 0.8477 (pt0) cc_final: 0.8038 (tm-30) REVERT: C 789 MET cc_start: 0.8637 (ttp) cc_final: 0.8420 (ttm) outliers start: 11 outliers final: 5 residues processed: 63 average time/residue: 0.5146 time to fit residues: 39.1813 Evaluate side-chains 51 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 590 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 161 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 250 optimal weight: 4.9990 chunk 239 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 257 optimal weight: 0.0030 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 166 optimal weight: 0.0570 chunk 272 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 overall best weight: 1.8112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN A 818 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.059864 restraints weight = 55049.319| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.86 r_work: 0.3004 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21774 Z= 0.179 Angle : 0.588 6.851 29595 Z= 0.319 Chirality : 0.046 0.187 3204 Planarity : 0.004 0.055 4017 Dihedral : 4.954 26.075 3189 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.42 % Favored : 89.30 % Rotamer: Outliers : 1.15 % Allowed : 7.99 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.78 (0.15), residues: 2841 helix: -0.53 (0.39), residues: 147 sheet: -1.51 (0.15), residues: 1173 loop : -2.27 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1022 TYR 0.014 0.001 TYR A 837 PHE 0.022 0.001 PHE A 512 TRP 0.003 0.001 TRP C 538 HIS 0.003 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00403 (21774) covalent geometry : angle 0.58761 (29595) hydrogen bonds : bond 0.03139 ( 596) hydrogen bonds : angle 5.39881 ( 1575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8987 (t70) cc_final: 0.8487 (t0) REVERT: A 831 ASP cc_start: 0.8248 (p0) cc_final: 0.7859 (p0) REVERT: C 422 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8478 (t70) REVERT: C 789 MET cc_start: 0.8537 (ttp) cc_final: 0.7772 (ttm) REVERT: C 1022 ARG cc_start: 0.7269 (mtp-110) cc_final: 0.6405 (mtm180) outliers start: 25 outliers final: 14 residues processed: 72 average time/residue: 0.4137 time to fit residues: 37.3009 Evaluate side-chains 58 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 866 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 64 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 235 optimal weight: 0.3980 chunk 170 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 158 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 overall best weight: 0.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN A 707 GLN A 818 GLN B 493 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.073303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.061210 restraints weight = 54374.525| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.87 r_work: 0.3035 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21774 Z= 0.117 Angle : 0.548 7.070 29595 Z= 0.296 Chirality : 0.045 0.171 3204 Planarity : 0.004 0.051 4017 Dihedral : 4.698 22.880 3189 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.47 % Favored : 90.25 % Rotamer: Outliers : 1.29 % Allowed : 9.69 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.15), residues: 2841 helix: -0.34 (0.40), residues: 147 sheet: -1.30 (0.15), residues: 1155 loop : -2.19 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1088 TYR 0.012 0.001 TYR A 837 PHE 0.020 0.001 PHE A 512 TRP 0.002 0.000 TRP C 538 HIS 0.002 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00248 (21774) covalent geometry : angle 0.54833 (29595) hydrogen bonds : bond 0.02745 ( 596) hydrogen bonds : angle 5.16747 ( 1575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8988 (t70) cc_final: 0.8457 (t0) REVERT: A 586 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: A 590 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8035 (ppp) REVERT: A 831 ASP cc_start: 0.8233 (p0) cc_final: 0.7840 (p0) REVERT: A 1139 LEU cc_start: 0.8264 (mt) cc_final: 0.8010 (mp) REVERT: B 565 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.4627 (mtm180) REVERT: B 779 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8108 (m) REVERT: C 422 ASP cc_start: 0.9155 (OUTLIER) cc_final: 0.8459 (t70) REVERT: C 1022 ARG cc_start: 0.7246 (mtp-110) cc_final: 0.7018 (ttp-110) outliers start: 28 outliers final: 15 residues processed: 78 average time/residue: 0.4467 time to fit residues: 42.7763 Evaluate side-chains 66 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 866 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 119 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 187 optimal weight: 0.0050 chunk 8 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.075303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063136 restraints weight = 53197.761| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.83 r_work: 0.3082 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21774 Z= 0.102 Angle : 0.529 7.796 29595 Z= 0.284 Chirality : 0.044 0.148 3204 Planarity : 0.003 0.053 4017 Dihedral : 4.470 22.163 3189 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.05 % Favored : 90.71 % Rotamer: Outliers : 1.70 % Allowed : 10.38 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.15), residues: 2841 helix: -0.13 (0.41), residues: 147 sheet: -1.24 (0.15), residues: 1173 loop : -2.07 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 227 TYR 0.011 0.001 TYR A 837 PHE 0.019 0.001 PHE A 512 TRP 0.002 0.000 TRP C 538 HIS 0.002 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00218 (21774) covalent geometry : angle 0.52870 (29595) hydrogen bonds : bond 0.02527 ( 596) hydrogen bonds : angle 4.96210 ( 1575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 55 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.8968 (t70) cc_final: 0.8418 (t0) REVERT: A 586 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: A 590 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8025 (ppp) REVERT: A 611 LEU cc_start: 0.8938 (tp) cc_final: 0.8693 (tm) REVERT: A 800 TYR cc_start: 0.7285 (t80) cc_final: 0.7080 (t80) REVERT: A 831 ASP cc_start: 0.8260 (p0) cc_final: 0.7874 (p0) REVERT: A 1002 THR cc_start: 0.9204 (m) cc_final: 0.8828 (t) REVERT: A 1139 LEU cc_start: 0.8239 (mt) cc_final: 0.7967 (mp) REVERT: B 565 ARG cc_start: 0.6192 (mtt180) cc_final: 0.4640 (mtm180) REVERT: B 779 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8088 (t) REVERT: C 422 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8432 (t70) REVERT: C 624 TYR cc_start: 0.8505 (t80) cc_final: 0.7959 (t80) REVERT: C 865 SER cc_start: 0.8324 (m) cc_final: 0.7975 (t) outliers start: 37 outliers final: 17 residues processed: 87 average time/residue: 0.3835 time to fit residues: 42.4730 Evaluate side-chains 69 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 866 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 8 optimal weight: 0.0020 chunk 105 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN A 818 GLN B 570 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.070990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.058920 restraints weight = 54607.839| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.81 r_work: 0.2986 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 21774 Z= 0.300 Angle : 0.651 8.257 29595 Z= 0.352 Chirality : 0.049 0.184 3204 Planarity : 0.004 0.059 4017 Dihedral : 4.948 27.003 3189 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.90 % Favored : 87.89 % Rotamer: Outliers : 1.93 % Allowed : 11.07 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.15), residues: 2841 helix: -1.28 (0.34), residues: 186 sheet: -1.32 (0.15), residues: 1179 loop : -2.15 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1022 TYR 0.017 0.002 TYR A 837 PHE 0.022 0.002 PHE B 279 TRP 0.004 0.001 TRP A 538 HIS 0.005 0.002 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00689 (21774) covalent geometry : angle 0.65120 (29595) hydrogen bonds : bond 0.03248 ( 596) hydrogen bonds : angle 5.19200 ( 1575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 44 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.9067 (t70) cc_final: 0.8447 (OUTLIER) REVERT: A 423 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9011 (tt) REVERT: A 586 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: A 590 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8011 (ppp) REVERT: A 611 LEU cc_start: 0.8956 (tp) cc_final: 0.8647 (tm) REVERT: A 831 ASP cc_start: 0.8255 (p0) cc_final: 0.7913 (p0) REVERT: B 565 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5505 (mtt180) REVERT: C 356 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.8075 (p) REVERT: C 422 ASP cc_start: 0.9172 (OUTLIER) cc_final: 0.8503 (t70) REVERT: C 865 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.8004 (t) outliers start: 42 outliers final: 23 residues processed: 80 average time/residue: 0.3582 time to fit residues: 36.7324 Evaluate side-chains 73 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 44 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1007 ASP Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 866 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 82 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 ASN ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.060933 restraints weight = 53639.634| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.82 r_work: 0.3033 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21774 Z= 0.144 Angle : 0.559 6.828 29595 Z= 0.302 Chirality : 0.045 0.156 3204 Planarity : 0.004 0.054 4017 Dihedral : 4.727 25.033 3189 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.57 % Favored : 90.14 % Rotamer: Outliers : 1.61 % Allowed : 11.89 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.15), residues: 2841 helix: -1.04 (0.36), residues: 183 sheet: -1.22 (0.15), residues: 1173 loop : -2.10 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1022 TYR 0.013 0.001 TYR C1060 PHE 0.017 0.001 PHE C 512 TRP 0.004 0.001 TRP C 538 HIS 0.002 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00318 (21774) covalent geometry : angle 0.55888 (29595) hydrogen bonds : bond 0.02702 ( 596) hydrogen bonds : angle 5.04182 ( 1575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 47 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.9002 (t70) cc_final: 0.8418 (OUTLIER) REVERT: A 586 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: A 590 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7999 (ppp) REVERT: A 611 LEU cc_start: 0.8950 (tp) cc_final: 0.8676 (tm) REVERT: A 831 ASP cc_start: 0.8226 (p0) cc_final: 0.7867 (p0) REVERT: B 565 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.5440 (mtt180) REVERT: C 422 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8488 (t70) REVERT: C 789 MET cc_start: 0.8937 (tpp) cc_final: 0.7998 (ttm) REVERT: C 865 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.7917 (t) outliers start: 35 outliers final: 23 residues processed: 78 average time/residue: 0.3707 time to fit residues: 37.0900 Evaluate side-chains 71 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 44 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1029 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 244 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 240 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.073173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061065 restraints weight = 53645.188| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.81 r_work: 0.3037 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21774 Z= 0.145 Angle : 0.551 6.759 29595 Z= 0.297 Chirality : 0.045 0.153 3204 Planarity : 0.004 0.055 4017 Dihedral : 4.608 24.718 3189 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.74 % Favored : 89.12 % Rotamer: Outliers : 1.88 % Allowed : 11.89 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.15), residues: 2841 helix: -0.58 (0.39), residues: 165 sheet: -1.14 (0.16), residues: 1161 loop : -2.03 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1022 TYR 0.012 0.001 TYR A 837 PHE 0.021 0.001 PHE A 666 TRP 0.003 0.000 TRP C 538 HIS 0.002 0.001 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00324 (21774) covalent geometry : angle 0.55140 (29595) hydrogen bonds : bond 0.02644 ( 596) hydrogen bonds : angle 4.96201 ( 1575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 46 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.9015 (t70) cc_final: 0.8444 (OUTLIER) REVERT: A 423 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8903 (tt) REVERT: A 586 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: A 590 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8009 (ppp) REVERT: A 800 TYR cc_start: 0.7004 (t80) cc_final: 0.6548 (t80) REVERT: A 831 ASP cc_start: 0.8230 (p0) cc_final: 0.7870 (p0) REVERT: A 1139 LEU cc_start: 0.8172 (mt) cc_final: 0.7920 (mp) REVERT: B 565 ARG cc_start: 0.6306 (OUTLIER) cc_final: 0.4719 (mtm180) REVERT: C 422 ASP cc_start: 0.9166 (OUTLIER) cc_final: 0.8490 (t70) REVERT: C 789 MET cc_start: 0.8908 (tpp) cc_final: 0.7834 (ttm) REVERT: C 865 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.7866 (t) outliers start: 41 outliers final: 29 residues processed: 81 average time/residue: 0.4006 time to fit residues: 40.8699 Evaluate side-chains 79 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 45 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 493 ASN Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1029 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 151 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 79 optimal weight: 0.1980 chunk 189 optimal weight: 8.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.069222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.057295 restraints weight = 55457.708| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.83 r_work: 0.2946 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 21774 Z= 0.338 Angle : 0.686 9.798 29595 Z= 0.371 Chirality : 0.050 0.238 3204 Planarity : 0.005 0.060 4017 Dihedral : 5.112 28.394 3189 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.50 % Favored : 87.26 % Rotamer: Outliers : 1.74 % Allowed : 11.98 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.15), residues: 2841 helix: -1.31 (0.34), residues: 186 sheet: -1.34 (0.15), residues: 1179 loop : -2.14 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 378 TYR 0.019 0.002 TYR A 837 PHE 0.025 0.002 PHE B 279 TRP 0.005 0.001 TRP A 538 HIS 0.005 0.002 HIS B 621 Details of bonding type rmsd covalent geometry : bond 0.00775 (21774) covalent geometry : angle 0.68613 (29595) hydrogen bonds : bond 0.03387 ( 596) hydrogen bonds : angle 5.28351 ( 1575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 45 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.9120 (t70) cc_final: 0.8441 (OUTLIER) REVERT: A 586 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: A 590 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8054 (ppp) REVERT: A 611 LEU cc_start: 0.8983 (tp) cc_final: 0.8765 (tm) REVERT: A 800 TYR cc_start: 0.7140 (t80) cc_final: 0.6698 (t80) REVERT: A 831 ASP cc_start: 0.8243 (p0) cc_final: 0.7899 (p0) REVERT: C 422 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8529 (t70) REVERT: C 865 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.7995 (t) outliers start: 38 outliers final: 28 residues processed: 79 average time/residue: 0.3698 time to fit residues: 37.4497 Evaluate side-chains 74 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 43 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 865 SER Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1029 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 222 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 0.0970 chunk 129 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 260 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 GLN ** B 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.060652 restraints weight = 53739.075| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.81 r_work: 0.3027 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21774 Z= 0.136 Angle : 0.567 9.450 29595 Z= 0.305 Chirality : 0.045 0.175 3204 Planarity : 0.004 0.058 4017 Dihedral : 4.793 26.013 3189 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.96 % Favored : 89.86 % Rotamer: Outliers : 1.42 % Allowed : 12.35 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.15), residues: 2841 helix: -1.03 (0.36), residues: 183 sheet: -1.20 (0.16), residues: 1170 loop : -2.07 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1022 TYR 0.012 0.001 TYR A 837 PHE 0.028 0.001 PHE A 666 TRP 0.005 0.001 TRP C 538 HIS 0.002 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00295 (21774) covalent geometry : angle 0.56712 (29595) hydrogen bonds : bond 0.02723 ( 596) hydrogen bonds : angle 5.05027 ( 1575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 47 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 422 ASP cc_start: 0.9042 (t70) cc_final: 0.8415 (OUTLIER) REVERT: A 586 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: A 800 TYR cc_start: 0.7105 (t80) cc_final: 0.6674 (t80) REVERT: C 422 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8508 (t70) REVERT: C 789 MET cc_start: 0.8778 (ttt) cc_final: 0.7893 (ttm) outliers start: 31 outliers final: 25 residues processed: 74 average time/residue: 0.4578 time to fit residues: 41.5359 Evaluate side-chains 67 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 41 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1029 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.7011 > 50: distance: 30 - 31: 4.851 distance: 31 - 32: 11.911 distance: 31 - 34: 9.721 distance: 32 - 33: 5.782 distance: 32 - 37: 5.211 distance: 34 - 35: 14.692 distance: 34 - 36: 23.602 distance: 37 - 38: 12.401 distance: 38 - 39: 12.323 distance: 38 - 41: 19.297 distance: 39 - 40: 17.261 distance: 39 - 42: 22.929 distance: 42 - 43: 8.022 distance: 43 - 44: 5.374 distance: 43 - 46: 16.876 distance: 44 - 45: 8.061 distance: 44 - 54: 7.081 distance: 46 - 47: 16.594 distance: 47 - 48: 11.574 distance: 47 - 49: 6.435 distance: 48 - 50: 11.882 distance: 49 - 51: 7.956 distance: 50 - 52: 4.421 distance: 51 - 52: 9.573 distance: 52 - 53: 17.131 distance: 54 - 55: 18.254 distance: 55 - 56: 10.544 distance: 55 - 58: 18.718 distance: 56 - 57: 11.908 distance: 56 - 60: 9.468 distance: 58 - 59: 9.007 distance: 60 - 61: 12.858 distance: 61 - 62: 12.040 distance: 61 - 64: 10.018 distance: 62 - 63: 25.767 distance: 62 - 68: 13.319 distance: 64 - 65: 15.817 distance: 64 - 66: 20.969 distance: 65 - 67: 23.608 distance: 68 - 69: 5.019 distance: 69 - 70: 18.079 distance: 69 - 72: 18.882 distance: 70 - 71: 12.809 distance: 70 - 79: 26.533 distance: 72 - 73: 18.888 distance: 73 - 74: 3.631 distance: 73 - 75: 31.788 distance: 74 - 76: 8.644 distance: 75 - 77: 20.437 distance: 76 - 78: 15.997 distance: 77 - 78: 21.367 distance: 79 - 80: 20.867 distance: 79 - 141: 9.396 distance: 80 - 81: 15.379 distance: 80 - 83: 15.336 distance: 81 - 82: 8.556 distance: 81 - 85: 12.965 distance: 82 - 138: 14.121 distance: 83 - 84: 24.620 distance: 85 - 86: 12.222 distance: 86 - 87: 18.125 distance: 86 - 89: 18.590 distance: 87 - 88: 11.624 distance: 87 - 93: 15.596 distance: 89 - 90: 17.079 distance: 90 - 91: 7.132 distance: 90 - 92: 24.448 distance: 93 - 94: 17.225 distance: 93 - 127: 22.162 distance: 95 - 104: 8.560 distance: 96 - 124: 35.735 distance: 99 - 100: 7.974 distance: 100 - 101: 18.931 distance: 101 - 102: 16.250 distance: 101 - 103: 16.785 distance: 104 - 105: 52.729 distance: 105 - 106: 42.446 distance: 106 - 107: 8.958 distance: 106 - 108: 27.143