Starting phenix.real_space_refine on Sun May 18 11:14:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3p_38894/05_2025/8y3p_38894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3p_38894/05_2025/8y3p_38894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3p_38894/05_2025/8y3p_38894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3p_38894/05_2025/8y3p_38894.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3p_38894/05_2025/8y3p_38894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3p_38894/05_2025/8y3p_38894.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 72 5.16 5 C 10860 2.51 5 N 2946 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17028 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "G" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 952 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "D" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 952 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "F" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "E" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 952 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "H" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 8.98, per 1000 atoms: 0.53 Number of scatterers: 17028 At special positions: 0 Unit cell: (107, 109, 142, 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 72 16.00 O 3150 8.00 N 2946 7.00 C 10860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 89 " 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: 3.61 Conformation dependent library (CDL) restraints added in 2.0 seconds 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3960 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 40 sheets defined 9.1% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.839A pdb=" N THR G 91 " --> pdb=" O THR G 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 33 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.656A pdb=" N ASP L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 80 through 84' Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 220 through 228 Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.511A pdb=" N ALA A 344 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'A' and resid 567 through 571 removed outlier: 4.037A pdb=" N ALA A 570 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 571 " --> pdb=" O GLY A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 571' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.590A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.853A pdb=" N THR D 91 " --> pdb=" O THR D 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 33 Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.619A pdb=" N ASP F 83 " --> pdb=" O GLN F 80 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU F 84 " --> pdb=" O ALA F 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 80 through 84' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 220 through 228 Processing helix chain 'C' and resid 474 through 476 No H-bonds generated for 'chain 'C' and resid 474 through 476' Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 560 through 566 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.880A pdb=" N THR E 91 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 33 removed outlier: 3.501A pdb=" N TYR H 33 " --> pdb=" O THR H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.617A pdb=" N ASP H 83 " --> pdb=" O GLN H 80 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU H 84 " --> pdb=" O ALA H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 80 through 84' Processing sheet with id=AA1, first strand: chain 'B' and resid 74 through 77 removed outlier: 5.430A pdb=" N ASN B 409 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE B 109 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP B 103 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU B 417 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N PHE B 101 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N MET B 104 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 89 through 93 removed outlier: 3.687A pdb=" N ASN B 190 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP B 201 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 128 Processing sheet with id=AA5, first strand: chain 'B' and resid 153 through 158 removed outlier: 7.207A pdb=" N ARG B 389 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 522 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 176 through 177 Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 241 removed outlier: 6.474A pdb=" N ASN B 309 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 307 " --> pdb=" O PRO B 240 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 307 through 314 current: chain 'A' and resid 308 through 314 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 308 through 314 current: chain 'C' and resid 307 through 314 Processing sheet with id=AA8, first strand: chain 'B' and resid 443 through 446 Processing sheet with id=AA9, first strand: chain 'B' and resid 454 through 455 removed outlier: 5.418A pdb=" N ILE B 540 " --> pdb=" O LYS B 552 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 498 Processing sheet with id=AB2, first strand: chain 'G' and resid 6 through 7 Processing sheet with id=AB3, first strand: chain 'G' and resid 34 through 39 removed outlier: 7.265A pdb=" N ILE G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 50 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR G 59 " --> pdb=" O VAL G 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 59 through 60 current: chain 'G' and resid 110 through 114 Processing sheet with id=AB4, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 11 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 8 through 11 current: chain 'L' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 46 through 49 current: chain 'L' and resid 97 through 100 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 74 through 77 removed outlier: 5.311A pdb=" N ASN A 409 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE A 109 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASP A 103 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU A 417 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE A 101 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N MET A 104 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 89 through 93 removed outlier: 3.669A pdb=" N ASN A 190 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP A 201 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.637A pdb=" N TYR A 173 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AC1, first strand: chain 'A' and resid 153 through 158 removed outlier: 7.259A pdb=" N ARG A 389 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 522 " --> pdb=" O HIS A 502 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AC3, first strand: chain 'A' and resid 443 through 446 Processing sheet with id=AC4, first strand: chain 'A' and resid 454 through 455 removed outlier: 5.318A pdb=" N ILE A 540 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 528 through 534 removed outlier: 4.028A pdb=" N ASN A 495 " --> pdb=" O HIS C 246 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS C 246 " --> pdb=" O ASN A 495 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AC7, first strand: chain 'D' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 11 through 12 current: chain 'D' and resid 45 through 51 removed outlier: 3.656A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 60 current: chain 'D' and resid 110 through 114 Processing sheet with id=AC8, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AC9, first strand: chain 'F' and resid 8 through 11 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 8 through 11 current: chain 'F' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 46 through 49 current: chain 'F' and resid 97 through 100 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 74 through 77 removed outlier: 5.329A pdb=" N ASN C 409 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE C 109 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP C 103 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU C 417 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N PHE C 101 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N MET C 104 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 89 through 93 removed outlier: 3.660A pdb=" N ASN C 190 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP C 201 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.573A pdb=" N TYR C 173 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 126 through 128 Processing sheet with id=AD5, first strand: chain 'C' and resid 153 through 158 removed outlier: 7.210A pdb=" N ARG C 389 " --> pdb=" O SER C 521 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 522 " --> pdb=" O HIS C 502 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 176 through 177 Processing sheet with id=AD7, first strand: chain 'C' and resid 443 through 446 Processing sheet with id=AD8, first strand: chain 'C' and resid 454 through 455 removed outlier: 5.303A pdb=" N ILE C 540 " --> pdb=" O LYS C 552 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 492 through 498 Processing sheet with id=AE1, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AE2, first strand: chain 'E' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 11 through 12 current: chain 'E' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 51 current: chain 'E' and resid 110 through 114 No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AE4, first strand: chain 'H' and resid 8 through 11 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 8 through 11 current: chain 'H' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 46 through 49 current: chain 'H' and resid 97 through 100 No H-bonds generated for sheet with id=AE4 396 hydrogen bonds defined for protein. 999 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: 5.41 Time building geometry restraints manager: 4.30 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: 5512 1.34 - 1.46: 4221 1.46 - 1.58: 7670 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 17508 Sorted by residual: bond pdb=" C LEU G 106 " pdb=" N PRO G 107 " ideal model delta sigma weight residual 1.337 1.370 -0.033 9.80e-03 1.04e+04 1.14e+01 bond pdb=" C LEU D 106 " pdb=" N PRO D 107 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.19e-02 7.06e+03 9.36e+00 bond pdb=" C LEU E 106 " pdb=" N PRO E 107 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.19e-02 7.06e+03 9.27e+00 bond pdb=" C ASP B 159 " pdb=" N PRO B 160 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.08e-02 8.57e+03 3.95e+00 bond pdb=" C ASP A 159 " pdb=" N PRO A 160 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.19e-02 7.06e+03 3.55e+00 ... (remaining 17503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 23212 2.06 - 4.12: 514 4.12 - 6.19: 95 6.19 - 8.25: 22 8.25 - 10.31: 4 Bond angle restraints: 23847 Sorted by residual: angle pdb=" C ASN H 51 " pdb=" N THR H 52 " pdb=" CA THR H 52 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CA THR E 28 " pdb=" CB THR E 28 " pdb=" CG2 THR E 28 " ideal model delta sigma weight residual 110.50 117.29 -6.79 1.70e+00 3.46e-01 1.60e+01 angle pdb=" CA THR G 28 " pdb=" CB THR G 28 " pdb=" CG2 THR G 28 " ideal model delta sigma weight residual 110.50 117.24 -6.74 1.70e+00 3.46e-01 1.57e+01 angle pdb=" CB LYS C 365 " pdb=" CG LYS C 365 " pdb=" CD LYS C 365 " ideal model delta sigma weight residual 111.30 120.37 -9.07 2.30e+00 1.89e-01 1.55e+01 angle pdb=" CA THR D 28 " pdb=" CB THR D 28 " pdb=" CG2 THR D 28 " ideal model delta sigma weight residual 110.50 117.19 -6.69 1.70e+00 3.46e-01 1.55e+01 ... (remaining 23842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 9263 17.12 - 34.24: 822 34.24 - 51.36: 139 51.36 - 68.48: 21 68.48 - 85.60: 21 Dihedral angle restraints: 10266 sinusoidal: 4065 harmonic: 6201 Sorted by residual: dihedral pdb=" CA TYR B 178 " pdb=" C TYR B 178 " pdb=" N TYR B 179 " pdb=" CA TYR B 179 " ideal model delta harmonic sigma weight residual 180.00 137.38 42.62 0 5.00e+00 4.00e-02 7.26e+01 dihedral pdb=" CA TYR A 178 " pdb=" C TYR A 178 " pdb=" N TYR A 179 " pdb=" CA TYR A 179 " ideal model delta harmonic sigma weight residual 180.00 140.79 39.21 0 5.00e+00 4.00e-02 6.15e+01 dihedral pdb=" CA TYR C 178 " pdb=" C TYR C 178 " pdb=" N TYR C 179 " pdb=" CA TYR C 179 " ideal model delta harmonic sigma weight residual 180.00 142.28 37.72 0 5.00e+00 4.00e-02 5.69e+01 ... (remaining 10263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1982 0.053 - 0.106: 448 0.106 - 0.159: 127 0.159 - 0.212: 15 0.212 - 0.265: 8 Chirality restraints: 2580 Sorted by residual: chirality pdb=" CB THR B 83 " pdb=" CA THR B 83 " pdb=" OG1 THR B 83 " pdb=" CG2 THR B 83 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR C 83 " pdb=" CA THR C 83 " pdb=" OG1 THR C 83 " pdb=" CG2 THR C 83 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB THR D 28 " pdb=" CA THR D 28 " pdb=" OG1 THR D 28 " pdb=" CG2 THR D 28 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2577 not shown) Planarity restraints: 3093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 159 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO C 160 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR L 33 " -0.048 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO L 34 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO L 34 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 34 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 33 " -0.046 5.00e-02 4.00e+02 6.99e-02 7.81e+00 pdb=" N PRO H 34 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO H 34 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO H 34 " -0.038 5.00e-02 4.00e+02 ... (remaining 3090 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4690 2.82 - 3.34: 14329 3.34 - 3.86: 28747 3.86 - 4.38: 33455 4.38 - 4.90: 58627 Nonbonded interactions: 139848 Sorted by model distance: nonbonded pdb=" O TYR F 50 " pdb=" OG SER F 54 " model vdw 2.296 3.040 nonbonded pdb=" O PHE G 29 " pdb=" NH2 ARG G 72 " model vdw 2.309 3.120 nonbonded pdb=" O TYR C 142 " pdb=" OH TYR C 155 " model vdw 2.321 3.040 nonbonded pdb=" O GLU A 181 " pdb=" NE1 TRP A 487 " model vdw 2.322 3.120 nonbonded pdb=" OE1 GLU L 6 " pdb=" OG1 THR L 20 " model vdw 2.325 3.040 ... (remaining 139843 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.910 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 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 0.052 17514 Z= 0.174 Angle : 0.765 10.312 23859 Z= 0.406 Chirality : 0.052 0.265 2580 Planarity : 0.006 0.076 3093 Dihedral : 13.546 85.597 6288 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.17), residues: 2127 helix: -2.63 (0.32), residues: 132 sheet: -1.06 (0.17), residues: 855 loop : -1.04 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 487 HIS 0.003 0.001 HIS C 488 PHE 0.017 0.001 PHE C 508 TYR 0.031 0.002 TYR A 182 ARG 0.010 0.001 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.14168 ( 396) hydrogen bonds : angle 7.72811 ( 999) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.93331 ( 12) covalent geometry : bond 0.00371 (17508) covalent geometry : angle 0.76479 (23847) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 ARG cc_start: 0.7517 (ptp90) cc_final: 0.7233 (ptp90) REVERT: L 6 GLU cc_start: 0.7807 (pm20) cc_final: 0.7574 (pm20) REVERT: A 192 ARG cc_start: 0.7416 (ptp90) cc_final: 0.7136 (ptp90) REVERT: A 313 SER cc_start: 0.9212 (p) cc_final: 0.8980 (p) REVERT: A 498 MET cc_start: 0.6359 (mmp) cc_final: 0.5805 (mmp) REVERT: A 581 MET cc_start: 0.8850 (ptm) cc_final: 0.8548 (ptp) REVERT: C 202 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7272 (tt0) REVERT: C 203 TYR cc_start: 0.7850 (p90) cc_final: 0.7497 (p90) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.2941 time to fit residues: 113.4050 Evaluate side-chains 212 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 107 optimal weight: 0.0270 chunk 85 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 190 optimal weight: 0.0970 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 HIS B 409 ASN L 51 ASN A 415 ASN C 415 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.166662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127787 restraints weight = 20501.179| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.50 r_work: 0.3161 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17514 Z= 0.102 Angle : 0.552 11.467 23859 Z= 0.281 Chirality : 0.044 0.192 2580 Planarity : 0.005 0.066 3093 Dihedral : 4.774 36.391 2343 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.96 % Allowed : 6.90 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2127 helix: -1.62 (0.37), residues: 135 sheet: -0.92 (0.17), residues: 870 loop : -0.72 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 487 HIS 0.002 0.000 HIS B 488 PHE 0.014 0.001 PHE A 467 TYR 0.021 0.001 TYR B 465 ARG 0.005 0.000 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 396) hydrogen bonds : angle 6.32768 ( 999) SS BOND : bond 0.00094 ( 6) SS BOND : angle 0.54603 ( 12) covalent geometry : bond 0.00232 (17508) covalent geometry : angle 0.55165 (23847) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8705 (m-40) cc_final: 0.8500 (m110) REVERT: G 90 ASP cc_start: 0.8771 (m-30) cc_final: 0.8287 (t0) REVERT: A 192 ARG cc_start: 0.7360 (ptp90) cc_final: 0.7059 (ptp90) REVERT: A 581 MET cc_start: 0.8951 (ptm) cc_final: 0.8646 (ptp) REVERT: D 87 ARG cc_start: 0.7517 (mmt-90) cc_final: 0.7051 (mmp80) REVERT: C 202 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7757 (tm-30) REVERT: E 57 ARG cc_start: 0.8278 (ttp80) cc_final: 0.8016 (ttt-90) outliers start: 18 outliers final: 14 residues processed: 238 average time/residue: 0.3062 time to fit residues: 108.5655 Evaluate side-chains 223 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 21 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 106 optimal weight: 0.2980 chunk 48 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS B 246 HIS L 39 GLN L 47 GLN A 102 HIS F 47 GLN E 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120776 restraints weight = 20331.294| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.55 r_work: 0.2995 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17514 Z= 0.242 Angle : 0.652 10.376 23859 Z= 0.335 Chirality : 0.047 0.170 2580 Planarity : 0.005 0.073 3093 Dihedral : 5.106 37.747 2343 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.03 % Allowed : 9.58 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.18), residues: 2127 helix: -1.84 (0.36), residues: 135 sheet: -1.14 (0.17), residues: 873 loop : -0.75 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 100 HIS 0.006 0.001 HIS A 488 PHE 0.015 0.001 PHE C 508 TYR 0.022 0.002 TYR B 614 ARG 0.006 0.001 ARG G 38 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 396) hydrogen bonds : angle 6.39330 ( 999) SS BOND : bond 0.00484 ( 6) SS BOND : angle 0.42240 ( 12) covalent geometry : bond 0.00572 (17508) covalent geometry : angle 0.65241 (23847) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 90 ASP cc_start: 0.8917 (m-30) cc_final: 0.8360 (t0) REVERT: A 192 ARG cc_start: 0.7390 (ptp90) cc_final: 0.7117 (ptp90) REVERT: D 87 ARG cc_start: 0.7357 (mmt-90) cc_final: 0.6934 (mmp80) REVERT: C 202 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7808 (tm-30) REVERT: E 90 ASP cc_start: 0.8636 (t0) cc_final: 0.8257 (t0) outliers start: 38 outliers final: 25 residues processed: 248 average time/residue: 0.3037 time to fit residues: 112.5276 Evaluate side-chains 221 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 58 optimal weight: 0.7980 chunk 170 optimal weight: 40.0000 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 194 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN C 364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.155321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116202 restraints weight = 20551.490| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.41 r_work: 0.3024 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17514 Z= 0.161 Angle : 0.583 11.522 23859 Z= 0.297 Chirality : 0.045 0.144 2580 Planarity : 0.005 0.072 3093 Dihedral : 4.911 35.344 2343 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.77 % Allowed : 12.63 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.18), residues: 2127 helix: -1.45 (0.40), residues: 117 sheet: -1.14 (0.17), residues: 870 loop : -0.63 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 100 HIS 0.004 0.001 HIS A 488 PHE 0.014 0.001 PHE D 29 TYR 0.025 0.001 TYR B 465 ARG 0.006 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 396) hydrogen bonds : angle 6.14496 ( 999) SS BOND : bond 0.00323 ( 6) SS BOND : angle 0.29234 ( 12) covalent geometry : bond 0.00379 (17508) covalent geometry : angle 0.58272 (23847) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 TYR cc_start: 0.8939 (m-80) cc_final: 0.8668 (m-10) REVERT: G 90 ASP cc_start: 0.8872 (m-30) cc_final: 0.8305 (t0) REVERT: L 6 GLU cc_start: 0.8660 (pm20) cc_final: 0.8398 (pt0) REVERT: A 192 ARG cc_start: 0.7351 (ptp90) cc_final: 0.7049 (ptp90) REVERT: A 614 TYR cc_start: 0.7113 (t80) cc_final: 0.6860 (t80) REVERT: D 87 ARG cc_start: 0.7325 (mmt-90) cc_final: 0.6973 (mmp80) REVERT: C 202 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7724 (tm-30) REVERT: E 90 ASP cc_start: 0.8724 (t0) cc_final: 0.8233 (t0) outliers start: 33 outliers final: 25 residues processed: 239 average time/residue: 0.3007 time to fit residues: 108.7761 Evaluate side-chains 225 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 29 optimal weight: 40.0000 chunk 45 optimal weight: 0.0170 chunk 177 optimal weight: 5.9990 chunk 157 optimal weight: 0.5980 overall best weight: 2.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN A 364 GLN D 39 GLN F 39 GLN C 102 HIS C 135 GLN C 509 GLN H 47 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113053 restraints weight = 20983.568| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.58 r_work: 0.2965 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17514 Z= 0.223 Angle : 0.626 11.129 23859 Z= 0.320 Chirality : 0.046 0.158 2580 Planarity : 0.005 0.073 3093 Dihedral : 5.032 35.013 2343 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.57 % Allowed : 13.48 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.18), residues: 2127 helix: -1.37 (0.42), residues: 114 sheet: -1.27 (0.17), residues: 873 loop : -0.67 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 100 HIS 0.005 0.001 HIS A 488 PHE 0.015 0.001 PHE D 29 TYR 0.026 0.002 TYR B 465 ARG 0.007 0.001 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 396) hydrogen bonds : angle 6.20845 ( 999) SS BOND : bond 0.00473 ( 6) SS BOND : angle 0.42538 ( 12) covalent geometry : bond 0.00530 (17508) covalent geometry : angle 0.62658 (23847) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 TYR cc_start: 0.8984 (m-80) cc_final: 0.8740 (m-10) REVERT: B 614 TYR cc_start: 0.7403 (t80) cc_final: 0.6973 (t80) REVERT: G 90 ASP cc_start: 0.8846 (m-30) cc_final: 0.8366 (t0) REVERT: G 106 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8070 (tt) REVERT: A 614 TYR cc_start: 0.7246 (t80) cc_final: 0.6904 (t80) REVERT: D 38 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8263 (ttm170) REVERT: D 87 ARG cc_start: 0.7409 (mmt-90) cc_final: 0.7050 (mmp80) REVERT: D 106 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7956 (tt) REVERT: C 202 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7744 (tm-30) REVERT: E 90 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8097 (t0) outliers start: 48 outliers final: 35 residues processed: 245 average time/residue: 0.3011 time to fit residues: 110.2042 Evaluate side-chains 242 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 43 optimal weight: 0.9980 chunk 181 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 GLN A 439 HIS C 135 GLN C 409 ASN H 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111133 restraints weight = 20964.999| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.49 r_work: 0.2941 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17514 Z= 0.241 Angle : 0.643 10.878 23859 Z= 0.329 Chirality : 0.046 0.164 2580 Planarity : 0.005 0.071 3093 Dihedral : 5.159 34.958 2343 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.05 % Allowed : 14.45 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.18), residues: 2127 helix: -1.32 (0.43), residues: 114 sheet: -1.41 (0.17), residues: 858 loop : -0.76 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 100 HIS 0.005 0.001 HIS A 488 PHE 0.018 0.001 PHE D 29 TYR 0.027 0.002 TYR B 465 ARG 0.008 0.001 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 396) hydrogen bonds : angle 6.25248 ( 999) SS BOND : bond 0.00518 ( 6) SS BOND : angle 0.42555 ( 12) covalent geometry : bond 0.00568 (17508) covalent geometry : angle 0.64276 (23847) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 212 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.8975 (tpt) cc_final: 0.8770 (tpt) REVERT: B 614 TYR cc_start: 0.7313 (t80) cc_final: 0.6993 (t80) REVERT: G 90 ASP cc_start: 0.8880 (m-30) cc_final: 0.8452 (t0) REVERT: G 106 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8037 (tt) REVERT: L 104 THR cc_start: 0.8904 (m) cc_final: 0.8701 (m) REVERT: A 614 TYR cc_start: 0.7152 (t80) cc_final: 0.6786 (t80) REVERT: D 38 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8275 (ttm170) REVERT: D 87 ARG cc_start: 0.7445 (mmt-90) cc_final: 0.7063 (mmp80) REVERT: C 202 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7731 (tm-30) REVERT: C 307 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8893 (ptm160) REVERT: C 614 TYR cc_start: 0.7263 (t80) cc_final: 0.6867 (t80) REVERT: E 90 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8263 (t0) outliers start: 57 outliers final: 42 residues processed: 249 average time/residue: 0.2985 time to fit residues: 111.8792 Evaluate side-chains 251 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.376 > 50: distance: 106 - 112: 6.238 distance: 112 - 113: 4.556 distance: 113 - 114: 9.652 distance: 113 - 116: 5.427 distance: 114 - 115: 31.044 distance: 114 - 123: 26.410 distance: 117 - 118: 9.880 distance: 117 - 119: 10.091 distance: 118 - 120: 4.088 distance: 120 - 122: 11.504 distance: 121 - 122: 8.658 distance: 123 - 124: 13.573 distance: 124 - 125: 8.978 distance: 125 - 126: 5.109 distance: 125 - 127: 7.538 distance: 127 - 128: 4.026 distance: 127 - 263: 8.438 distance: 128 - 131: 5.418 distance: 129 - 130: 5.160 distance: 129 - 137: 3.425 distance: 130 - 260: 5.122 distance: 132 - 133: 5.059 distance: 133 - 135: 4.538 distance: 134 - 136: 3.729 distance: 135 - 136: 3.362 distance: 137 - 138: 4.870 distance: 138 - 139: 7.097 distance: 138 - 141: 5.050 distance: 139 - 140: 10.496 distance: 139 - 144: 5.453 distance: 141 - 142: 4.101 distance: 141 - 143: 3.824 distance: 144 - 249: 6.743 distance: 145 - 146: 3.815 distance: 145 - 148: 3.009 distance: 147 - 246: 5.328 distance: 148 - 149: 4.230 distance: 148 - 150: 7.480 distance: 151 - 152: 3.717 distance: 159 - 234: 3.670 distance: 160 - 161: 11.387 distance: 160 - 163: 3.079 distance: 161 - 162: 8.582 distance: 161 - 164: 9.328 distance: 162 - 231: 4.719 distance: 164 - 165: 3.894 distance: 165 - 166: 3.737 distance: 166 - 167: 3.645 distance: 172 - 221: 4.903 distance: 174 - 175: 3.930 distance: 175 - 218: 7.725 distance: 176 - 177: 3.821 distance: 177 - 178: 4.799 distance: 178 - 179: 4.388 distance: 180 - 181: 3.018 distance: 185 - 186: 4.426 distance: 186 - 187: 6.626 distance: 186 - 188: 7.534