Starting phenix.real_space_refine on Thu Sep 26 09:41:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxf_16317/09_2024/8bxf_16317.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxf_16317/09_2024/8bxf_16317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxf_16317/09_2024/8bxf_16317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxf_16317/09_2024/8bxf_16317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxf_16317/09_2024/8bxf_16317.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxf_16317/09_2024/8bxf_16317.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.076 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 80 5.16 5 C 8385 2.51 5 N 2041 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12692 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2517 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 7 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E Time building chain proxies: 6.67, per 1000 atoms: 0.53 Number of scatterers: 12692 At special positions: 0 Unit cell: (90.944, 90.16, 121.52, 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 80 16.00 O 2186 8.00 N 2041 7.00 C 8385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.04 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 167 " " NAG B 501 " - " ASN B 167 " " NAG C 501 " - " ASN C 167 " " NAG D 501 " - " ASN D 167 " " NAG E 501 " - " ASN E 167 " Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.7 seconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3130 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 25 sheets defined 36.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.776A pdb=" N ARG A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.586A pdb=" N ASP A 81 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 239 removed outlier: 4.784A pdb=" N MET A 227 " --> pdb=" O TYR A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 417 through 443 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.736A pdb=" N LEU B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.586A pdb=" N ASP B 81 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 239 removed outlier: 4.784A pdb=" N MET B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) Proline residue: B 228 - end of helix Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 279 through 305 Processing helix chain 'B' and resid 417 through 443 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.737A pdb=" N LEU C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.587A pdb=" N ASP C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 239 removed outlier: 4.782A pdb=" N MET C 227 " --> pdb=" O TYR C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 417 through 443 Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.738A pdb=" N LEU D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.587A pdb=" N ASP D 81 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 239 removed outlier: 4.784A pdb=" N MET D 227 " --> pdb=" O TYR D 223 " (cutoff:3.500A) Proline residue: D 228 - end of helix Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 279 through 305 Processing helix chain 'D' and resid 417 through 443 Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.736A pdb=" N LEU E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.587A pdb=" N ASP E 81 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 239 removed outlier: 4.784A pdb=" N MET E 227 " --> pdb=" O TYR E 223 " (cutoff:3.500A) Proline residue: E 228 - end of helix Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 279 through 305 Processing helix chain 'E' and resid 417 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL A 59 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP A 52 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR A 61 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN A 63 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN A 71 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN A 40 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 39 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR A 169 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 41 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 199 Processing sheet with id=AA6, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL B 59 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP B 52 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR B 61 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN B 63 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN B 71 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASN B 40 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 39 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR B 169 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 41 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'B' and resid 197 through 199 Processing sheet with id=AB2, first strand: chain 'C' and resid 88 through 90 Processing sheet with id=AB3, first strand: chain 'C' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL C 59 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP C 52 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR C 61 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL C 50 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN C 63 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN C 71 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN C 40 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 39 " --> pdb=" O ASN C 167 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR C 169 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL C 41 " --> pdb=" O THR C 169 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB6, first strand: chain 'C' and resid 197 through 199 Processing sheet with id=AB7, first strand: chain 'D' and resid 88 through 90 Processing sheet with id=AB8, first strand: chain 'D' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL D 59 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP D 52 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR D 61 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN D 63 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN D 71 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN D 40 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL D 39 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR D 169 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL D 41 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AC1, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AC2, first strand: chain 'D' and resid 197 through 199 Processing sheet with id=AC3, first strand: chain 'E' and resid 88 through 90 Processing sheet with id=AC4, first strand: chain 'E' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL E 59 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP E 52 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR E 61 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL E 50 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN E 63 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN E 71 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN E 40 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL E 39 " --> pdb=" O ASN E 167 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR E 169 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL E 41 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AC6, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AC7, first strand: chain 'E' and resid 197 through 199 695 hydrogen bonds defined for protein. 1935 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: 4.21 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3172 1.33 - 1.45: 2598 1.45 - 1.57: 7091 1.57 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 13001 Sorted by residual: bond pdb=" N LEU E 140 " pdb=" CA LEU E 140 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.24e-02 6.50e+03 4.78e+00 bond pdb=" N LEU C 140 " pdb=" CA LEU C 140 " ideal model delta sigma weight residual 1.457 1.483 -0.027 1.24e-02 6.50e+03 4.59e+00 bond pdb=" CB PHE D 425 " pdb=" CG PHE D 425 " ideal model delta sigma weight residual 1.502 1.551 -0.049 2.30e-02 1.89e+03 4.59e+00 bond pdb=" N MET D 301 " pdb=" CA MET D 301 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.54e+00 bond pdb=" CB PHE C 425 " pdb=" CG PHE C 425 " ideal model delta sigma weight residual 1.502 1.551 -0.049 2.30e-02 1.89e+03 4.52e+00 ... (remaining 12996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16963 2.02 - 4.05: 678 4.05 - 6.07: 103 6.07 - 8.10: 45 8.10 - 10.12: 10 Bond angle restraints: 17799 Sorted by residual: angle pdb=" C TYR A 199 " pdb=" N ASN A 200 " pdb=" CA ASN A 200 " ideal model delta sigma weight residual 122.08 127.82 -5.74 1.47e+00 4.63e-01 1.53e+01 angle pdb=" C TYR E 199 " pdb=" N ASN E 200 " pdb=" CA ASN E 200 " ideal model delta sigma weight residual 122.08 127.81 -5.73 1.47e+00 4.63e-01 1.52e+01 angle pdb=" C TYR C 199 " pdb=" N ASN C 200 " pdb=" CA ASN C 200 " ideal model delta sigma weight residual 122.08 127.74 -5.66 1.47e+00 4.63e-01 1.48e+01 angle pdb=" C TYR D 199 " pdb=" N ASN D 200 " pdb=" CA ASN D 200 " ideal model delta sigma weight residual 122.08 127.72 -5.64 1.47e+00 4.63e-01 1.47e+01 angle pdb=" C TYR B 199 " pdb=" N ASN B 200 " pdb=" CA ASN B 200 " ideal model delta sigma weight residual 122.08 127.71 -5.63 1.47e+00 4.63e-01 1.47e+01 ... (remaining 17794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 6813 15.42 - 30.83: 603 30.83 - 46.25: 167 46.25 - 61.66: 20 61.66 - 77.08: 15 Dihedral angle restraints: 7618 sinusoidal: 2778 harmonic: 4840 Sorted by residual: dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 47.24 45.76 1 1.00e+01 1.00e-02 2.90e+01 dihedral pdb=" CA GLU B 274 " pdb=" C GLU B 274 " pdb=" N LEU B 275 " pdb=" CA LEU B 275 " ideal model delta harmonic sigma weight residual -180.00 -164.55 -15.45 0 5.00e+00 4.00e-02 9.55e+00 dihedral pdb=" CA GLU E 274 " pdb=" C GLU E 274 " pdb=" N LEU E 275 " pdb=" CA LEU E 275 " ideal model delta harmonic sigma weight residual -180.00 -164.59 -15.41 0 5.00e+00 4.00e-02 9.50e+00 ... (remaining 7615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1462 0.047 - 0.093: 498 0.093 - 0.140: 171 0.140 - 0.186: 34 0.186 - 0.233: 20 Chirality restraints: 2185 Sorted by residual: chirality pdb=" CA MET E 227 " pdb=" N MET E 227 " pdb=" C MET E 227 " pdb=" CB MET E 227 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA MET A 227 " pdb=" N MET A 227 " pdb=" C MET A 227 " pdb=" CB MET A 227 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA MET D 227 " pdb=" N MET D 227 " pdb=" C MET D 227 " pdb=" CB MET D 227 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2182 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 425 " 0.016 2.00e-02 2.50e+03 2.39e-02 9.96e+00 pdb=" CG PHE E 425 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE E 425 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE E 425 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE E 425 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 425 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 425 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 425 " 0.016 2.00e-02 2.50e+03 2.38e-02 9.94e+00 pdb=" CG PHE B 425 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 425 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 425 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B 425 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 425 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 425 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 425 " -0.016 2.00e-02 2.50e+03 2.37e-02 9.84e+00 pdb=" CG PHE D 425 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE D 425 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE D 425 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE D 425 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 425 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 425 " 0.001 2.00e-02 2.50e+03 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 15 2.19 - 2.86: 4284 2.86 - 3.54: 17185 3.54 - 4.22: 29094 4.22 - 4.90: 50019 Nonbonded interactions: 100597 Sorted by model distance: nonbonded pdb=" CB ASN E 200 " pdb=" CG ASN E 200 " model vdw 1.507 3.670 nonbonded pdb=" CB ASN C 172 " pdb=" CG ASN C 172 " model vdw 1.514 3.670 nonbonded pdb=" CB ASN B 172 " pdb=" CG ASN B 172 " model vdw 1.514 3.670 nonbonded pdb=" CB ASN E 172 " pdb=" CG ASN E 172 " model vdw 1.515 3.670 nonbonded pdb=" CB ASN D 172 " pdb=" CG ASN D 172 " model vdw 1.515 3.670 ... (remaining 100592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 443 or resid 501)) selection = (chain 'C' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 443 or resid 501)) selection = (chain 'D' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 443 or resid 501)) selection = (chain 'E' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 443 or resid 501)) } 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: 3.720 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.400 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 0.049 13001 Z= 0.293 Angle : 0.954 10.124 17799 Z= 0.501 Chirality : 0.056 0.233 2185 Planarity : 0.007 0.043 2139 Dihedral : 13.468 77.077 4485 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.38 % Allowed : 1.51 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.19), residues: 1610 helix: -0.93 (0.19), residues: 530 sheet: -1.31 (0.25), residues: 450 loop : -1.72 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 70 HIS 0.021 0.003 HIS C 58 PHE 0.054 0.004 PHE E 425 TYR 0.014 0.001 TYR B 178 ARG 0.002 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 306 time to evaluate : 1.481 Fit side-chains REVERT: A 219 ILE cc_start: 0.8458 (tt) cc_final: 0.8191 (tt) REVERT: A 222 GLN cc_start: 0.8353 (mt0) cc_final: 0.8075 (mt0) REVERT: A 301 MET cc_start: 0.7955 (tmm) cc_final: 0.7699 (tmm) REVERT: B 219 ILE cc_start: 0.8474 (tt) cc_final: 0.8209 (tt) REVERT: B 222 GLN cc_start: 0.8269 (mt0) cc_final: 0.7959 (mt0) REVERT: B 301 MET cc_start: 0.7904 (tmm) cc_final: 0.7624 (tmm) REVERT: C 219 ILE cc_start: 0.8332 (tt) cc_final: 0.7954 (tp) REVERT: C 301 MET cc_start: 0.7964 (tmm) cc_final: 0.7710 (tmm) REVERT: D 16 ARG cc_start: 0.8746 (ttp-110) cc_final: 0.8187 (ttp-110) REVERT: D 66 ILE cc_start: 0.8897 (pt) cc_final: 0.8654 (pt) REVERT: D 219 ILE cc_start: 0.8457 (tt) cc_final: 0.8161 (tt) REVERT: D 222 GLN cc_start: 0.8311 (mt0) cc_final: 0.7869 (mp10) REVERT: D 301 MET cc_start: 0.7960 (tmm) cc_final: 0.7637 (tmm) REVERT: E 219 ILE cc_start: 0.8358 (tt) cc_final: 0.8092 (tt) REVERT: E 222 GLN cc_start: 0.8354 (mt0) cc_final: 0.8079 (mt0) REVERT: E 301 MET cc_start: 0.7926 (tmm) cc_final: 0.7583 (tmm) outliers start: 5 outliers final: 0 residues processed: 311 average time/residue: 0.2783 time to fit residues: 120.7798 Evaluate side-chains 232 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 chunk 64 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13001 Z= 0.249 Angle : 0.598 7.978 17799 Z= 0.306 Chirality : 0.044 0.144 2185 Planarity : 0.004 0.033 2139 Dihedral : 4.486 16.746 1870 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.21 % Allowed : 10.52 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1610 helix: 0.59 (0.21), residues: 535 sheet: -1.43 (0.26), residues: 440 loop : -1.49 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 70 HIS 0.004 0.001 HIS B 58 PHE 0.013 0.001 PHE A 241 TYR 0.009 0.001 TYR B 199 ARG 0.004 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 245 time to evaluate : 1.393 Fit side-chains REVERT: A 127 MET cc_start: 0.7096 (mtt) cc_final: 0.6836 (mtp) REVERT: A 219 ILE cc_start: 0.8107 (tt) cc_final: 0.7767 (tt) REVERT: A 222 GLN cc_start: 0.8442 (mt0) cc_final: 0.8181 (mt0) REVERT: A 301 MET cc_start: 0.7938 (tmm) cc_final: 0.7614 (tmm) REVERT: B 127 MET cc_start: 0.7226 (mtt) cc_final: 0.6946 (mtp) REVERT: B 222 GLN cc_start: 0.8343 (mt0) cc_final: 0.8070 (mt0) REVERT: B 301 MET cc_start: 0.7989 (tmm) cc_final: 0.7736 (tmm) REVERT: C 219 ILE cc_start: 0.8141 (tt) cc_final: 0.7880 (tt) REVERT: C 301 MET cc_start: 0.8026 (tmm) cc_final: 0.7720 (tmm) REVERT: D 127 MET cc_start: 0.7172 (mtt) cc_final: 0.6903 (mtp) REVERT: D 219 ILE cc_start: 0.8124 (tt) cc_final: 0.7889 (tt) REVERT: D 222 GLN cc_start: 0.8343 (mt0) cc_final: 0.8061 (mt0) REVERT: D 265 MET cc_start: 0.7262 (ttt) cc_final: 0.6867 (ttm) REVERT: D 301 MET cc_start: 0.8069 (tmm) cc_final: 0.7744 (tmm) REVERT: E 222 GLN cc_start: 0.8338 (mt0) cc_final: 0.8088 (mt0) REVERT: E 265 MET cc_start: 0.7174 (ttt) cc_final: 0.6657 (ttm) REVERT: E 301 MET cc_start: 0.7951 (tmm) cc_final: 0.7640 (tmm) outliers start: 16 outliers final: 5 residues processed: 252 average time/residue: 0.2105 time to fit residues: 79.9308 Evaluate side-chains 225 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 220 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 170 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 13001 Z= 0.534 Angle : 0.742 9.501 17799 Z= 0.374 Chirality : 0.048 0.151 2185 Planarity : 0.004 0.032 2139 Dihedral : 4.589 16.581 1870 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.18 % Allowed : 16.58 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1610 helix: 1.02 (0.23), residues: 535 sheet: -1.68 (0.24), residues: 465 loop : -1.25 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 65 HIS 0.006 0.001 HIS A 58 PHE 0.015 0.002 PHE C 298 TYR 0.015 0.002 TYR E 121 ARG 0.002 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 228 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: A 127 MET cc_start: 0.7190 (mtt) cc_final: 0.6937 (mtp) REVERT: A 265 MET cc_start: 0.6979 (ttt) cc_final: 0.6633 (ttp) REVERT: A 269 ASP cc_start: 0.8776 (t0) cc_final: 0.8468 (t0) REVERT: A 301 MET cc_start: 0.7950 (tmm) cc_final: 0.7454 (tmm) REVERT: B 222 GLN cc_start: 0.8392 (mt0) cc_final: 0.8136 (mt0) REVERT: B 245 LEU cc_start: 0.8451 (mm) cc_final: 0.7598 (pp) REVERT: C 20 CYS cc_start: 0.8948 (t) cc_final: 0.8730 (t) REVERT: D 87 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8422 (ttmm) REVERT: D 127 MET cc_start: 0.7255 (mtt) cc_final: 0.6967 (mtp) REVERT: E 301 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7813 (tmm) outliers start: 42 outliers final: 25 residues processed: 255 average time/residue: 0.2135 time to fit residues: 82.0533 Evaluate side-chains 249 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 222 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 301 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 154 optimal weight: 0.0020 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13001 Z= 0.177 Angle : 0.559 7.700 17799 Z= 0.282 Chirality : 0.043 0.131 2185 Planarity : 0.004 0.031 2139 Dihedral : 4.092 15.855 1870 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.59 % Allowed : 18.77 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.21), residues: 1610 helix: 1.61 (0.22), residues: 535 sheet: -1.54 (0.25), residues: 440 loop : -1.04 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 70 HIS 0.004 0.001 HIS A 68 PHE 0.008 0.001 PHE D 145 TYR 0.008 0.001 TYR C 67 ARG 0.002 0.000 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 249 time to evaluate : 1.442 Fit side-chains REVERT: A 127 MET cc_start: 0.7015 (mtt) cc_final: 0.6799 (mtp) REVERT: A 269 ASP cc_start: 0.8714 (t0) cc_final: 0.8365 (t0) REVERT: A 301 MET cc_start: 0.7979 (tmm) cc_final: 0.7719 (tmm) REVERT: A 431 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7653 (tt) REVERT: B 66 ILE cc_start: 0.8749 (pt) cc_final: 0.8496 (pt) REVERT: B 127 MET cc_start: 0.7205 (mtt) cc_final: 0.6803 (mtp) REVERT: B 173 GLN cc_start: 0.7865 (mp10) cc_final: 0.6847 (pm20) REVERT: B 222 GLN cc_start: 0.8361 (mt0) cc_final: 0.8132 (mt0) REVERT: B 431 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7539 (tt) REVERT: C 66 ILE cc_start: 0.8784 (pt) cc_final: 0.8534 (pt) REVERT: C 173 GLN cc_start: 0.7987 (mp10) cc_final: 0.6962 (pt0) REVERT: D 87 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8350 (ttmm) REVERT: D 127 MET cc_start: 0.7035 (mtt) cc_final: 0.6796 (mtp) REVERT: D 173 GLN cc_start: 0.7956 (mp10) cc_final: 0.7080 (pt0) REVERT: E 66 ILE cc_start: 0.8792 (pt) cc_final: 0.8536 (pt) REVERT: E 173 GLN cc_start: 0.7934 (mp10) cc_final: 0.6886 (pm20) REVERT: E 301 MET cc_start: 0.7909 (tmm) cc_final: 0.7702 (tmm) outliers start: 21 outliers final: 7 residues processed: 262 average time/residue: 0.2143 time to fit residues: 85.7603 Evaluate side-chains 227 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 217 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 13001 Z= 0.304 Angle : 0.614 8.397 17799 Z= 0.304 Chirality : 0.044 0.137 2185 Planarity : 0.004 0.030 2139 Dihedral : 4.071 13.736 1870 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.18 % Allowed : 19.68 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1610 helix: 1.71 (0.22), residues: 535 sheet: -1.55 (0.25), residues: 455 loop : -0.95 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 65 HIS 0.005 0.001 HIS D 68 PHE 0.011 0.001 PHE E 145 TYR 0.013 0.001 TYR C 67 ARG 0.001 0.000 ARG E 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7799 (mm) REVERT: A 127 MET cc_start: 0.7125 (mtt) cc_final: 0.6857 (mtp) REVERT: A 265 MET cc_start: 0.7241 (ttp) cc_final: 0.6747 (mtp) REVERT: A 269 ASP cc_start: 0.8725 (t0) cc_final: 0.8361 (t0) REVERT: A 431 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7704 (tt) REVERT: B 127 MET cc_start: 0.7260 (mtt) cc_final: 0.6840 (mtp) REVERT: B 173 GLN cc_start: 0.8111 (mp10) cc_final: 0.7020 (pm20) REVERT: B 265 MET cc_start: 0.8286 (ttm) cc_final: 0.7836 (mtp) REVERT: B 305 MET cc_start: 0.7470 (ptp) cc_final: 0.7085 (ptp) REVERT: B 431 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7552 (tt) REVERT: C 66 ILE cc_start: 0.8777 (pt) cc_final: 0.8565 (pt) REVERT: C 173 GLN cc_start: 0.8175 (mp10) cc_final: 0.7064 (pt0) REVERT: C 231 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8437 (tt) REVERT: C 245 LEU cc_start: 0.8560 (mm) cc_final: 0.7835 (pt) REVERT: C 301 MET cc_start: 0.7932 (tmm) cc_final: 0.7664 (tmm) REVERT: D 87 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8405 (ttmm) REVERT: D 127 MET cc_start: 0.7112 (mtt) cc_final: 0.6822 (mtp) REVERT: D 173 GLN cc_start: 0.8215 (mp10) cc_final: 0.7177 (pt0) REVERT: D 231 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8469 (tt) REVERT: D 245 LEU cc_start: 0.8619 (mm) cc_final: 0.7875 (pt) REVERT: D 265 MET cc_start: 0.8317 (ttm) cc_final: 0.7637 (mtp) REVERT: E 173 GLN cc_start: 0.8150 (mp10) cc_final: 0.7067 (pm20) REVERT: E 248 GLU cc_start: 0.7016 (pm20) cc_final: 0.6718 (pm20) REVERT: E 301 MET cc_start: 0.7953 (tmm) cc_final: 0.7654 (tmm) REVERT: E 305 MET cc_start: 0.7387 (ptp) cc_final: 0.7143 (ptp) outliers start: 42 outliers final: 18 residues processed: 261 average time/residue: 0.2013 time to fit residues: 80.3673 Evaluate side-chains 249 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 225 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 238 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 0.0370 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13001 Z= 0.233 Angle : 0.585 8.330 17799 Z= 0.289 Chirality : 0.043 0.168 2185 Planarity : 0.003 0.027 2139 Dihedral : 3.935 14.023 1870 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.56 % Allowed : 20.06 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1610 helix: 1.97 (0.22), residues: 530 sheet: -1.52 (0.25), residues: 445 loop : -0.98 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 65 HIS 0.005 0.001 HIS A 68 PHE 0.009 0.001 PHE E 145 TYR 0.010 0.001 TYR C 67 ARG 0.001 0.000 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 240 time to evaluate : 1.637 Fit side-chains REVERT: A 117 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7776 (mm) REVERT: A 127 MET cc_start: 0.7071 (mtt) cc_final: 0.6840 (mtp) REVERT: A 265 MET cc_start: 0.7372 (ttp) cc_final: 0.6855 (mtp) REVERT: A 269 ASP cc_start: 0.8721 (t0) cc_final: 0.8334 (t0) REVERT: A 431 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7691 (tt) REVERT: B 127 MET cc_start: 0.7190 (mtt) cc_final: 0.6839 (mtp) REVERT: B 173 GLN cc_start: 0.8219 (mp10) cc_final: 0.7058 (pm20) REVERT: B 265 MET cc_start: 0.8335 (ttm) cc_final: 0.7803 (mtp) REVERT: B 305 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6885 (ptp) REVERT: B 431 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7516 (tt) REVERT: C 173 GLN cc_start: 0.8250 (mp10) cc_final: 0.7143 (pt0) REVERT: C 231 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8360 (tt) REVERT: D 87 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8399 (ttmm) REVERT: D 127 MET cc_start: 0.7082 (mtt) cc_final: 0.6848 (mtp) REVERT: D 173 GLN cc_start: 0.8281 (mp10) cc_final: 0.7241 (pt0) REVERT: D 231 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8412 (tt) REVERT: D 265 MET cc_start: 0.8256 (ttm) cc_final: 0.7593 (mtp) REVERT: E 173 GLN cc_start: 0.8246 (mp10) cc_final: 0.7174 (pm20) REVERT: E 301 MET cc_start: 0.7986 (tmm) cc_final: 0.7730 (tmm) outliers start: 47 outliers final: 27 residues processed: 269 average time/residue: 0.2035 time to fit residues: 83.8893 Evaluate side-chains 261 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 227 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 257 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13001 Z= 0.202 Angle : 0.578 8.549 17799 Z= 0.282 Chirality : 0.043 0.146 2185 Planarity : 0.003 0.026 2139 Dihedral : 3.833 12.613 1870 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.79 % Allowed : 20.89 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1610 helix: 2.04 (0.22), residues: 530 sheet: -1.51 (0.25), residues: 445 loop : -0.93 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 70 HIS 0.005 0.001 HIS A 68 PHE 0.008 0.001 PHE D 145 TYR 0.014 0.001 TYR D 223 ARG 0.001 0.000 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 248 time to evaluate : 1.530 Fit side-chains REVERT: A 117 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7766 (mm) REVERT: A 127 MET cc_start: 0.7052 (mtt) cc_final: 0.6840 (mtp) REVERT: A 183 LYS cc_start: 0.8574 (ptpt) cc_final: 0.8221 (ptmt) REVERT: A 265 MET cc_start: 0.7410 (ttp) cc_final: 0.6897 (mtp) REVERT: A 269 ASP cc_start: 0.8722 (t0) cc_final: 0.8303 (t0) REVERT: A 431 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7687 (tt) REVERT: B 127 MET cc_start: 0.7123 (mtt) cc_final: 0.6788 (mtp) REVERT: B 173 GLN cc_start: 0.8262 (mp10) cc_final: 0.7114 (pm20) REVERT: B 227 MET cc_start: 0.8514 (ppp) cc_final: 0.8265 (tmm) REVERT: B 265 MET cc_start: 0.8331 (ttm) cc_final: 0.7693 (mtp) REVERT: B 305 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6875 (ptp) REVERT: B 431 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7518 (tt) REVERT: C 44 GLU cc_start: 0.8082 (tt0) cc_final: 0.7773 (tt0) REVERT: C 173 GLN cc_start: 0.8281 (mp10) cc_final: 0.7152 (pt0) REVERT: C 231 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8355 (tt) REVERT: D 87 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8401 (ttmm) REVERT: D 127 MET cc_start: 0.7011 (mtt) cc_final: 0.6739 (mtp) REVERT: D 173 GLN cc_start: 0.8309 (mp10) cc_final: 0.7282 (pt0) REVERT: D 265 MET cc_start: 0.8226 (ttm) cc_final: 0.7577 (mtp) REVERT: E 173 GLN cc_start: 0.8372 (mp10) cc_final: 0.7192 (pm20) REVERT: E 301 MET cc_start: 0.7991 (tmm) cc_final: 0.7744 (tmm) outliers start: 50 outliers final: 33 residues processed: 280 average time/residue: 0.2035 time to fit residues: 88.6858 Evaluate side-chains 269 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.0170 chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13001 Z= 0.194 Angle : 0.584 8.822 17799 Z= 0.285 Chirality : 0.043 0.148 2185 Planarity : 0.003 0.024 2139 Dihedral : 3.767 11.471 1870 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.31 % Allowed : 20.89 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1610 helix: 2.10 (0.22), residues: 530 sheet: -1.41 (0.25), residues: 445 loop : -0.84 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 70 HIS 0.006 0.001 HIS A 68 PHE 0.009 0.001 PHE E 425 TYR 0.019 0.001 TYR D 223 ARG 0.001 0.000 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 243 time to evaluate : 1.340 Fit side-chains REVERT: A 117 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7765 (mm) REVERT: A 127 MET cc_start: 0.7008 (mtt) cc_final: 0.6807 (mtp) REVERT: A 183 LYS cc_start: 0.8598 (ptpt) cc_final: 0.8254 (ptmt) REVERT: A 265 MET cc_start: 0.7359 (ttp) cc_final: 0.6843 (mtp) REVERT: A 269 ASP cc_start: 0.8728 (t0) cc_final: 0.8328 (t0) REVERT: A 431 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 19 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8679 (mtpp) REVERT: B 55 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: B 127 MET cc_start: 0.7106 (mtt) cc_final: 0.6764 (mtp) REVERT: B 227 MET cc_start: 0.8494 (ppp) cc_final: 0.8168 (tmm) REVERT: B 265 MET cc_start: 0.8284 (ttm) cc_final: 0.7990 (mtp) REVERT: B 305 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6861 (ptp) REVERT: B 431 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7503 (tt) REVERT: C 44 GLU cc_start: 0.8017 (tt0) cc_final: 0.7758 (tt0) REVERT: C 173 GLN cc_start: 0.8319 (mp10) cc_final: 0.7176 (pt0) REVERT: D 19 LYS cc_start: 0.9104 (ttpt) cc_final: 0.8577 (mtpp) REVERT: D 55 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: D 87 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8402 (ttmm) REVERT: D 127 MET cc_start: 0.6989 (mtt) cc_final: 0.6731 (mtp) REVERT: D 173 GLN cc_start: 0.8332 (mp10) cc_final: 0.7314 (pt0) REVERT: D 265 MET cc_start: 0.8221 (ttm) cc_final: 0.7538 (mtp) REVERT: E 173 GLN cc_start: 0.8375 (mp10) cc_final: 0.7197 (pm20) REVERT: E 301 MET cc_start: 0.8017 (tmm) cc_final: 0.7778 (tmm) outliers start: 57 outliers final: 42 residues processed: 278 average time/residue: 0.1976 time to fit residues: 84.8791 Evaluate side-chains 283 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 257 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 0.0070 chunk 143 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 129 optimal weight: 0.0870 chunk 135 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13001 Z= 0.148 Angle : 0.574 8.923 17799 Z= 0.276 Chirality : 0.042 0.136 2185 Planarity : 0.003 0.024 2139 Dihedral : 3.677 17.667 1870 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.73 % Allowed : 22.48 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.22), residues: 1610 helix: 2.15 (0.22), residues: 530 sheet: -1.35 (0.25), residues: 445 loop : -0.73 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 70 HIS 0.005 0.001 HIS A 68 PHE 0.008 0.001 PHE E 289 TYR 0.018 0.001 TYR D 223 ARG 0.002 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 240 time to evaluate : 1.294 Fit side-chains REVERT: A 19 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8540 (mtpp) REVERT: A 117 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7711 (mm) REVERT: A 183 LYS cc_start: 0.8576 (ptpt) cc_final: 0.8241 (ptmt) REVERT: A 265 MET cc_start: 0.7395 (ttp) cc_final: 0.6870 (mtp) REVERT: A 269 ASP cc_start: 0.8729 (t0) cc_final: 0.8318 (t0) REVERT: A 431 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7684 (tt) REVERT: B 19 LYS cc_start: 0.9113 (ttpt) cc_final: 0.8683 (mtpp) REVERT: B 127 MET cc_start: 0.6957 (mtt) cc_final: 0.6649 (mtp) REVERT: B 208 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.8025 (tt) REVERT: B 266 MET cc_start: 0.8035 (mmm) cc_final: 0.7772 (mtt) REVERT: B 431 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7504 (tt) REVERT: C 265 MET cc_start: 0.7083 (ttt) cc_final: 0.6786 (mtp) REVERT: D 19 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8554 (mtpp) REVERT: D 265 MET cc_start: 0.8139 (ttm) cc_final: 0.7505 (mtp) REVERT: D 305 MET cc_start: 0.7281 (ptp) cc_final: 0.6870 (ptp) REVERT: E 19 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8665 (mtpp) REVERT: E 66 ILE cc_start: 0.8688 (pt) cc_final: 0.8485 (pt) REVERT: E 301 MET cc_start: 0.8022 (tmm) cc_final: 0.7764 (tmm) outliers start: 36 outliers final: 21 residues processed: 260 average time/residue: 0.1975 time to fit residues: 80.8689 Evaluate side-chains 255 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 230 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 248 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0517 > 50: distance: 10 - 16: 22.746 distance: 16 - 17: 39.337 distance: 17 - 18: 18.566 distance: 17 - 20: 16.844 distance: 18 - 19: 25.922 distance: 18 - 21: 16.172 distance: 21 - 22: 13.176 distance: 22 - 23: 13.074 distance: 22 - 25: 19.487 distance: 23 - 24: 14.064 distance: 23 - 29: 8.214 distance: 26 - 27: 21.310 distance: 26 - 28: 22.412 distance: 29 - 30: 12.850 distance: 30 - 31: 12.465 distance: 30 - 33: 13.995 distance: 31 - 32: 23.670 distance: 31 - 35: 20.904 distance: 33 - 34: 16.786 distance: 35 - 36: 21.427 distance: 36 - 37: 4.589 distance: 36 - 39: 9.817 distance: 37 - 38: 11.618 distance: 37 - 46: 16.917 distance: 39 - 40: 7.433 distance: 40 - 41: 14.938 distance: 41 - 42: 11.855 distance: 42 - 43: 7.844 distance: 46 - 47: 19.909 distance: 47 - 48: 10.401 distance: 47 - 50: 8.931 distance: 48 - 49: 16.270 distance: 48 - 57: 15.771 distance: 50 - 51: 12.781 distance: 51 - 52: 6.318 distance: 51 - 53: 5.882 distance: 52 - 54: 12.477 distance: 53 - 55: 6.289 distance: 54 - 56: 8.251 distance: 55 - 56: 5.541 distance: 57 - 58: 15.988 distance: 57 - 63: 22.048 distance: 58 - 59: 12.568 distance: 58 - 61: 23.145 distance: 59 - 64: 10.677 distance: 61 - 62: 31.670 distance: 62 - 63: 31.178 distance: 64 - 65: 31.029 distance: 65 - 66: 31.380 distance: 65 - 68: 24.054 distance: 66 - 67: 16.134 distance: 66 - 75: 9.255 distance: 68 - 69: 15.092 distance: 69 - 70: 15.807 distance: 69 - 71: 5.911 distance: 70 - 72: 10.326 distance: 71 - 73: 13.231 distance: 72 - 74: 6.845 distance: 73 - 74: 11.030 distance: 75 - 76: 24.442 distance: 76 - 77: 18.888 distance: 76 - 79: 23.800 distance: 77 - 78: 25.573 distance: 77 - 83: 12.779 distance: 79 - 80: 13.796 distance: 80 - 81: 19.407 distance: 80 - 82: 39.534 distance: 83 - 84: 9.297 distance: 84 - 85: 9.237 distance: 84 - 87: 31.118 distance: 85 - 86: 17.746 distance: 85 - 89: 25.984 distance: 87 - 88: 10.518 distance: 89 - 90: 14.470 distance: 90 - 91: 5.653 distance: 90 - 93: 5.493 distance: 91 - 92: 15.359 distance: 91 - 98: 4.714 distance: 93 - 94: 12.091 distance: 94 - 95: 12.348 distance: 95 - 97: 3.546