Starting phenix.real_space_refine on Sat Aug 23 04:25:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0k_18795/08_2025/8r0k_18795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0k_18795/08_2025/8r0k_18795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r0k_18795/08_2025/8r0k_18795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0k_18795/08_2025/8r0k_18795.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0k_18795/08_2025/8r0k_18795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0k_18795/08_2025/8r0k_18795.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.051 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 40 5.16 5 C 6653 2.51 5 N 1515 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9885 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1923 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 252} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 8, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1923 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 252} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 8, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1923 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 252} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 8, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1923 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 252} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 8, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1923 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 252} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 8, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'LFA': 3, 'RET': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'LFA': 3, 'RET': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'LFA': 3, 'RET': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'LFA': 3, 'RET': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'LFA': 3, 'RET': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.98, per 1000 atoms: 0.30 Number of scatterers: 9885 At special positions: 0 Unit cell: (92.796, 91.124, 80.256, 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 40 16.00 O 1677 8.00 N 1515 7.00 C 6653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 410.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 5 sheets defined 86.5% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 15 through 42 Processing helix chain 'A' and resid 43 through 46 removed outlier: 3.762A pdb=" N VAL A 46 " --> pdb=" O ARG A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 50 through 77 removed outlier: 3.914A pdb=" N VAL A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 96 removed outlier: 4.009A pdb=" N ILE A 93 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 118 removed outlier: 3.912A pdb=" N VAL A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.879A pdb=" N VAL A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 148 Processing helix chain 'A' and resid 155 through 185 Processing helix chain 'A' and resid 189 through 220 removed outlier: 3.660A pdb=" N VAL A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Proline residue: A 211 - end of helix removed outlier: 3.625A pdb=" N TYR A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 262 removed outlier: 3.558A pdb=" N CYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 42 Processing helix chain 'B' and resid 43 through 46 removed outlier: 3.810A pdb=" N VAL B 46 " --> pdb=" O ARG B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.918A pdb=" N VAL B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 96 removed outlier: 4.014A pdb=" N ILE B 93 " --> pdb=" O SER B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 118 removed outlier: 3.910A pdb=" N VAL B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Proline residue: B 108 - end of helix removed outlier: 3.883A pdb=" N VAL B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 148 Processing helix chain 'B' and resid 155 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 189 through 220 removed outlier: 3.662A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Proline residue: B 211 - end of helix removed outlier: 3.596A pdb=" N TYR B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 262 removed outlier: 3.573A pdb=" N CYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 42 Processing helix chain 'C' and resid 43 through 46 removed outlier: 3.779A pdb=" N VAL C 46 " --> pdb=" O ARG C 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 43 through 46' Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 50 through 77 removed outlier: 3.921A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 96 removed outlier: 3.999A pdb=" N ILE C 93 " --> pdb=" O SER C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 118 removed outlier: 3.908A pdb=" N VAL C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) Proline residue: C 108 - end of helix removed outlier: 3.864A pdb=" N VAL C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 148 Processing helix chain 'C' and resid 155 through 185 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 189 through 220 removed outlier: 3.694A pdb=" N VAL C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Proline residue: C 211 - end of helix removed outlier: 3.587A pdb=" N TYR C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 261 removed outlier: 3.560A pdb=" N CYS C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 42 Processing helix chain 'D' and resid 43 through 46 removed outlier: 3.771A pdb=" N VAL D 46 " --> pdb=" O ARG D 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 43 through 46' Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 50 through 77 removed outlier: 3.935A pdb=" N VAL D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 96 removed outlier: 4.017A pdb=" N ILE D 93 " --> pdb=" O SER D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 118 removed outlier: 3.908A pdb=" N VAL D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 105 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Proline residue: D 108 - end of helix removed outlier: 3.862A pdb=" N VAL D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 148 Processing helix chain 'D' and resid 155 through 185 Processing helix chain 'D' and resid 189 through 220 removed outlier: 3.653A pdb=" N VAL D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) Proline residue: D 211 - end of helix removed outlier: 3.633A pdb=" N TYR D 214 " --> pdb=" O TYR D 210 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 261 removed outlier: 3.558A pdb=" N CYS D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 42 Processing helix chain 'E' and resid 43 through 46 removed outlier: 3.810A pdb=" N VAL E 46 " --> pdb=" O ARG E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 43 through 46' Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 50 through 77 removed outlier: 3.916A pdb=" N VAL E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 97 through 118 removed outlier: 3.906A pdb=" N VAL E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Proline residue: E 108 - end of helix removed outlier: 3.887A pdb=" N VAL E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 148 Processing helix chain 'E' and resid 155 through 185 Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 189 through 220 removed outlier: 3.660A pdb=" N VAL E 209 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) Proline residue: E 211 - end of helix removed outlier: 3.632A pdb=" N TYR E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN E 217 " --> pdb=" O ALA E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 261 removed outlier: 3.556A pdb=" N CYS E 245 " --> pdb=" O LYS E 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.945A pdb=" N LEU A 85 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.942A pdb=" N LEU B 85 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.932A pdb=" N LEU C 85 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.946A pdb=" N LEU D 85 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.939A pdb=" N LEU E 85 " --> pdb=" O VAL E 82 " (cutoff:3.500A) 871 hydrogen bonds defined for protein. 2556 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: 1.63 Time building geometry restraints manager: 1.38 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: 2202 1.33 - 1.46: 3162 1.46 - 1.58: 4644 1.58 - 1.71: 0 1.71 - 1.84: 70 Bond restraints: 10078 Sorted by residual: bond pdb=" CA SER D 228 " pdb=" CB SER D 228 " ideal model delta sigma weight residual 1.528 1.464 0.064 1.66e-02 3.63e+03 1.48e+01 bond pdb=" CA SER E 228 " pdb=" CB SER E 228 " ideal model delta sigma weight residual 1.529 1.466 0.062 1.64e-02 3.72e+03 1.45e+01 bond pdb=" CA SER A 228 " pdb=" CB SER A 228 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.64e-02 3.72e+03 1.43e+01 bond pdb=" CA SER C 228 " pdb=" CB SER C 228 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.64e-02 3.72e+03 1.43e+01 bond pdb=" CA SER B 228 " pdb=" CB SER B 228 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.64e-02 3.72e+03 1.41e+01 ... (remaining 10073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 12414 2.25 - 4.51: 1245 4.51 - 6.76: 73 6.76 - 9.01: 10 9.01 - 11.27: 1 Bond angle restraints: 13743 Sorted by residual: angle pdb=" CA THR C 226 " pdb=" CB THR C 226 " pdb=" OG1 THR C 226 " ideal model delta sigma weight residual 109.60 101.40 8.20 1.50e+00 4.44e-01 2.99e+01 angle pdb=" CA THR B 226 " pdb=" CB THR B 226 " pdb=" OG1 THR B 226 " ideal model delta sigma weight residual 109.60 101.43 8.17 1.50e+00 4.44e-01 2.96e+01 angle pdb=" CA THR E 226 " pdb=" CB THR E 226 " pdb=" OG1 THR E 226 " ideal model delta sigma weight residual 109.60 101.48 8.12 1.50e+00 4.44e-01 2.93e+01 angle pdb=" CA THR D 226 " pdb=" CB THR D 226 " pdb=" OG1 THR D 226 " ideal model delta sigma weight residual 109.60 101.49 8.11 1.50e+00 4.44e-01 2.92e+01 angle pdb=" CA THR A 226 " pdb=" CB THR A 226 " pdb=" OG1 THR A 226 " ideal model delta sigma weight residual 109.60 101.61 7.99 1.50e+00 4.44e-01 2.84e+01 ... (remaining 13738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 5679 23.67 - 47.33: 66 47.33 - 71.00: 11 71.00 - 94.67: 4 94.67 - 118.33: 3 Dihedral angle restraints: 5763 sinusoidal: 2033 harmonic: 3730 Sorted by residual: dihedral pdb=" CG ARG E 154 " pdb=" CD ARG E 154 " pdb=" NE ARG E 154 " pdb=" CZ ARG E 154 " ideal model delta sinusoidal sigma weight residual 90.00 5.80 84.20 2 1.50e+01 4.44e-03 2.11e+01 dihedral pdb=" C1 RET E 404 " pdb=" C2 RET E 404 " pdb=" C3 RET E 404 " pdb=" C4 RET E 404 " ideal model delta sinusoidal sigma weight residual -62.54 55.79 -118.33 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C1 RET A 404 " pdb=" C2 RET A 404 " pdb=" C3 RET A 404 " pdb=" C4 RET A 404 " ideal model delta sinusoidal sigma weight residual -62.54 47.79 -110.33 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 5760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 984 0.052 - 0.104: 585 0.104 - 0.156: 105 0.156 - 0.208: 34 0.208 - 0.260: 2 Chirality restraints: 1710 Sorted by residual: chirality pdb=" CA ASN E 89 " pdb=" N ASN E 89 " pdb=" C ASN E 89 " pdb=" CB ASN E 89 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE A 5 " pdb=" CA ILE A 5 " pdb=" CG1 ILE A 5 " pdb=" CG2 ILE A 5 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA THR B 76 " pdb=" N THR B 76 " pdb=" C THR B 76 " pdb=" CB THR B 76 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 1707 not shown) Planarity restraints: 1615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 RET E 404 " 0.047 2.00e-02 2.50e+03 5.55e-02 3.85e+01 pdb=" C13 RET E 404 " -0.005 2.00e-02 2.50e+03 pdb=" C14 RET E 404 " -0.094 2.00e-02 2.50e+03 pdb=" C15 RET E 404 " 0.065 2.00e-02 2.50e+03 pdb=" C20 RET E 404 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET D 404 " -0.046 2.00e-02 2.50e+03 5.49e-02 3.77e+01 pdb=" C13 RET D 404 " 0.004 2.00e-02 2.50e+03 pdb=" C14 RET D 404 " 0.093 2.00e-02 2.50e+03 pdb=" C15 RET D 404 " -0.064 2.00e-02 2.50e+03 pdb=" C20 RET D 404 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET A 404 " 0.046 2.00e-02 2.50e+03 5.46e-02 3.73e+01 pdb=" C13 RET A 404 " -0.004 2.00e-02 2.50e+03 pdb=" C14 RET A 404 " -0.093 2.00e-02 2.50e+03 pdb=" C15 RET A 404 " 0.064 2.00e-02 2.50e+03 pdb=" C20 RET A 404 " -0.013 2.00e-02 2.50e+03 ... (remaining 1612 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3970 2.89 - 3.40: 10878 3.40 - 3.90: 17971 3.90 - 4.40: 21034 4.40 - 4.90: 34412 Nonbonded interactions: 88265 Sorted by model distance: nonbonded pdb=" OH TYR A 210 " pdb=" OD1 ASP A 237 " model vdw 2.394 3.040 nonbonded pdb=" OH TYR C 210 " pdb=" OD1 ASP C 237 " model vdw 2.394 3.040 nonbonded pdb=" OH TYR B 210 " pdb=" OD1 ASP B 237 " model vdw 2.395 3.040 nonbonded pdb=" OH TYR D 210 " pdb=" OD1 ASP D 237 " model vdw 2.395 3.040 nonbonded pdb=" OH TYR E 210 " pdb=" OD1 ASP E 237 " model vdw 2.396 3.040 ... (remaining 88260 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' and (resid 3 through 262 or (resid 401 and (name C8 or name C9 )) or \ resid 404)) selection = (chain 'B' and (resid 3 through 262 or (resid 401 and (name C8 or name C9 )) or \ resid 404)) selection = (chain 'C' and (resid 3 through 262 or (resid 401 and (name C8 or name C9 )) or \ resid 404)) selection = (chain 'D' and (resid 3 through 262 or (resid 401 and (name C8 or name C9 )) or \ resid 404)) selection = (chain 'E' and (resid 3 through 262 or (resid 401 and (name C8 or name C9 )) or \ resid 404)) } 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: 1.580 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.840 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:8.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 : 0.011 0.064 10083 Z= 0.701 Angle : 1.384 11.266 13743 Z= 0.949 Chirality : 0.063 0.260 1710 Planarity : 0.011 0.104 1615 Dihedral : 9.916 118.332 3363 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.35 % Allowed : 3.12 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.19), residues: 1290 helix: -1.34 (0.13), residues: 1005 sheet: None (None), residues: 0 loop : -1.70 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.003 ARG A 99 TYR 0.063 0.011 TYR D 214 PHE 0.048 0.010 PHE D 220 TRP 0.032 0.008 TRP A 103 HIS 0.015 0.006 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.01064 (10078) covalent geometry : angle 1.38398 (13743) hydrogen bonds : bond 0.18710 ( 871) hydrogen bonds : angle 7.84050 ( 2556) Misc. bond : bond 0.02847 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.343 Fit side-chains REVERT: C 204 MET cc_start: 0.8418 (mmt) cc_final: 0.8063 (mmt) REVERT: D 204 MET cc_start: 0.8315 (mmp) cc_final: 0.8073 (mmt) outliers start: 13 outliers final: 0 residues processed: 116 average time/residue: 0.5091 time to fit residues: 64.1438 Evaluate side-chains 94 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.0270 chunk 129 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 187 GLN B 15 GLN D 81 HIS D 187 GLN E 81 HIS E 187 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.100228 restraints weight = 11179.559| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.68 r_work: 0.3030 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10083 Z= 0.117 Angle : 0.530 6.412 13743 Z= 0.266 Chirality : 0.038 0.117 1710 Planarity : 0.005 0.037 1615 Dihedral : 6.935 100.993 1523 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.73 % Allowed : 6.56 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.22), residues: 1290 helix: 2.41 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -1.17 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 154 TYR 0.011 0.001 TYR E 214 PHE 0.006 0.001 PHE B 75 TRP 0.012 0.001 TRP D 225 HIS 0.008 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00244 (10078) covalent geometry : angle 0.53035 (13743) hydrogen bonds : bond 0.03878 ( 871) hydrogen bonds : angle 3.89529 ( 2556) Misc. bond : bond 0.00030 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.439 Fit side-chains REVERT: A 204 MET cc_start: 0.8006 (mmp) cc_final: 0.7691 (mmt) REVERT: A 224 LEU cc_start: 0.8212 (tp) cc_final: 0.8007 (tp) REVERT: B 158 SER cc_start: 0.8101 (t) cc_final: 0.7680 (p) REVERT: C 82 VAL cc_start: 0.8121 (t) cc_final: 0.7800 (m) REVERT: C 158 SER cc_start: 0.8059 (t) cc_final: 0.7719 (p) REVERT: D 5 ILE cc_start: 0.8087 (tp) cc_final: 0.7841 (tt) REVERT: D 158 SER cc_start: 0.8123 (t) cc_final: 0.7730 (p) REVERT: E 43 ARG cc_start: 0.8119 (ptm-80) cc_final: 0.7864 (ptt90) REVERT: E 82 VAL cc_start: 0.8125 (t) cc_final: 0.7842 (m) REVERT: E 158 SER cc_start: 0.8143 (t) cc_final: 0.7740 (p) outliers start: 7 outliers final: 1 residues processed: 100 average time/residue: 0.4723 time to fit residues: 51.7001 Evaluate side-chains 90 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 GLN D 81 HIS D 187 GLN E 81 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.093733 restraints weight = 11641.248| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.65 r_work: 0.2941 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10083 Z= 0.193 Angle : 0.554 5.707 13743 Z= 0.281 Chirality : 0.041 0.129 1710 Planarity : 0.004 0.039 1615 Dihedral : 5.817 55.493 1523 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.88 % Allowed : 6.98 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.13 (0.23), residues: 1290 helix: 2.82 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -1.06 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 154 TYR 0.017 0.002 TYR B 68 PHE 0.011 0.002 PHE B 24 TRP 0.010 0.001 TRP B 40 HIS 0.005 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00477 (10078) covalent geometry : angle 0.55420 (13743) hydrogen bonds : bond 0.04259 ( 871) hydrogen bonds : angle 3.70786 ( 2556) Misc. bond : bond 0.00017 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.331 Fit side-chains REVERT: A 204 MET cc_start: 0.7921 (mmp) cc_final: 0.7665 (mmt) REVERT: B 158 SER cc_start: 0.8119 (t) cc_final: 0.7824 (p) REVERT: C 158 SER cc_start: 0.8205 (t) cc_final: 0.7893 (p) REVERT: D 158 SER cc_start: 0.8185 (t) cc_final: 0.7854 (p) REVERT: E 43 ARG cc_start: 0.8123 (ptm-80) cc_final: 0.7873 (ptt90) REVERT: E 68 TYR cc_start: 0.8651 (m-80) cc_final: 0.8449 (m-80) REVERT: E 158 SER cc_start: 0.8167 (t) cc_final: 0.7840 (p) outliers start: 18 outliers final: 6 residues processed: 117 average time/residue: 0.3793 time to fit residues: 49.2745 Evaluate side-chains 112 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain E residue 130 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.094964 restraints weight = 11670.500| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.66 r_work: 0.2956 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10083 Z= 0.147 Angle : 0.504 8.605 13743 Z= 0.255 Chirality : 0.039 0.119 1710 Planarity : 0.004 0.039 1615 Dihedral : 5.513 53.218 1523 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.50 % Allowed : 7.71 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.45 (0.23), residues: 1290 helix: 3.04 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.93 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 154 TYR 0.013 0.001 TYR B 68 PHE 0.009 0.001 PHE B 24 TRP 0.008 0.001 TRP B 225 HIS 0.004 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00352 (10078) covalent geometry : angle 0.50374 (13743) hydrogen bonds : bond 0.03793 ( 871) hydrogen bonds : angle 3.52114 ( 2556) Misc. bond : bond 0.00008 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.230 Fit side-chains REVERT: B 68 TYR cc_start: 0.8581 (m-80) cc_final: 0.8352 (m-80) REVERT: C 4 MET cc_start: 0.8553 (tpt) cc_final: 0.8286 (tpt) REVERT: C 158 SER cc_start: 0.8076 (t) cc_final: 0.7823 (p) REVERT: D 71 MET cc_start: 0.8585 (mtp) cc_final: 0.8371 (mtm) REVERT: E 90 SER cc_start: 0.8623 (p) cc_final: 0.8400 (m) REVERT: E 158 SER cc_start: 0.7998 (t) cc_final: 0.7760 (p) outliers start: 24 outliers final: 9 residues processed: 118 average time/residue: 0.3250 time to fit residues: 43.1001 Evaluate side-chains 113 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 94 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 126 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.094809 restraints weight = 11763.919| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.67 r_work: 0.2956 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10083 Z= 0.146 Angle : 0.494 9.129 13743 Z= 0.251 Chirality : 0.039 0.119 1710 Planarity : 0.004 0.039 1615 Dihedral : 5.430 56.800 1523 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.23 % Allowed : 7.29 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.55 (0.23), residues: 1290 helix: 3.11 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.89 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 154 TYR 0.012 0.001 TYR B 68 PHE 0.009 0.001 PHE B 24 TRP 0.008 0.001 TRP B 225 HIS 0.004 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00349 (10078) covalent geometry : angle 0.49423 (13743) hydrogen bonds : bond 0.03744 ( 871) hydrogen bonds : angle 3.47106 ( 2556) Misc. bond : bond 0.00016 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.359 Fit side-chains REVERT: B 68 TYR cc_start: 0.8553 (m-80) cc_final: 0.8311 (m-80) REVERT: B 167 THR cc_start: 0.8228 (m) cc_final: 0.8000 (m) REVERT: C 4 MET cc_start: 0.8578 (tpt) cc_final: 0.8323 (tpt) REVERT: C 158 SER cc_start: 0.8004 (t) cc_final: 0.7772 (p) REVERT: D 80 ASP cc_start: 0.8207 (m-30) cc_final: 0.7860 (m-30) REVERT: E 68 TYR cc_start: 0.8594 (m-80) cc_final: 0.8362 (m-80) REVERT: E 90 SER cc_start: 0.8645 (p) cc_final: 0.8393 (m) REVERT: E 158 SER cc_start: 0.7877 (t) cc_final: 0.7670 (p) outliers start: 31 outliers final: 17 residues processed: 125 average time/residue: 0.3354 time to fit residues: 47.0785 Evaluate side-chains 123 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 58 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.097486 restraints weight = 11589.895| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.66 r_work: 0.2997 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10083 Z= 0.111 Angle : 0.462 9.214 13743 Z= 0.234 Chirality : 0.038 0.118 1710 Planarity : 0.004 0.038 1615 Dihedral : 5.134 57.974 1523 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.12 % Allowed : 7.50 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.87 (0.24), residues: 1290 helix: 3.34 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.78 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 154 TYR 0.010 0.001 TYR B 68 PHE 0.008 0.001 PHE B 24 TRP 0.008 0.001 TRP B 225 HIS 0.004 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00249 (10078) covalent geometry : angle 0.46210 (13743) hydrogen bonds : bond 0.03365 ( 871) hydrogen bonds : angle 3.37254 ( 2556) Misc. bond : bond 0.00002 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.341 Fit side-chains REVERT: B 68 TYR cc_start: 0.8527 (m-80) cc_final: 0.8289 (m-80) REVERT: D 80 ASP cc_start: 0.8224 (m-30) cc_final: 0.7964 (m-30) REVERT: E 90 SER cc_start: 0.8662 (p) cc_final: 0.8402 (m) outliers start: 30 outliers final: 10 residues processed: 121 average time/residue: 0.3521 time to fit residues: 47.6892 Evaluate side-chains 112 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.093121 restraints weight = 11602.500| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.70 r_work: 0.2942 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10083 Z= 0.178 Angle : 0.519 5.547 13743 Z= 0.265 Chirality : 0.041 0.131 1710 Planarity : 0.004 0.039 1615 Dihedral : 5.459 57.327 1523 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.60 % Allowed : 9.17 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.51 (0.23), residues: 1290 helix: 3.07 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.84 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 255 TYR 0.012 0.002 TYR B 68 PHE 0.011 0.001 PHE B 24 TRP 0.008 0.001 TRP A 225 HIS 0.004 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00440 (10078) covalent geometry : angle 0.51887 (13743) hydrogen bonds : bond 0.03968 ( 871) hydrogen bonds : angle 3.47645 ( 2556) Misc. bond : bond 0.00026 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.222 Fit side-chains REVERT: B 68 TYR cc_start: 0.8519 (m-80) cc_final: 0.8267 (m-80) REVERT: D 80 ASP cc_start: 0.8202 (m-30) cc_final: 0.7947 (m-30) REVERT: D 158 SER cc_start: 0.8131 (t) cc_final: 0.7870 (p) REVERT: E 68 TYR cc_start: 0.8596 (m-80) cc_final: 0.8363 (m-80) REVERT: E 90 SER cc_start: 0.8723 (p) cc_final: 0.8460 (m) REVERT: E 158 SER cc_start: 0.7851 (t) cc_final: 0.7630 (p) outliers start: 25 outliers final: 11 residues processed: 120 average time/residue: 0.3401 time to fit residues: 45.5563 Evaluate side-chains 118 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain E residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 40 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.091741 restraints weight = 11642.641| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.70 r_work: 0.2923 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10083 Z= 0.213 Angle : 0.554 5.633 13743 Z= 0.284 Chirality : 0.042 0.148 1710 Planarity : 0.004 0.040 1615 Dihedral : 5.706 55.866 1523 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.40 % Allowed : 9.48 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.33 (0.23), residues: 1290 helix: 2.97 (0.15), residues: 1010 sheet: None (None), residues: 0 loop : -0.85 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 43 TYR 0.013 0.002 TYR B 214 PHE 0.012 0.002 PHE B 24 TRP 0.008 0.001 TRP B 225 HIS 0.004 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00531 (10078) covalent geometry : angle 0.55359 (13743) hydrogen bonds : bond 0.04251 ( 871) hydrogen bonds : angle 3.55531 ( 2556) Misc. bond : bond 0.00039 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.342 Fit side-chains REVERT: B 68 TYR cc_start: 0.8553 (m-80) cc_final: 0.8317 (m-80) REVERT: B 158 SER cc_start: 0.8096 (t) cc_final: 0.7842 (p) REVERT: C 5 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8108 (tt) REVERT: D 71 MET cc_start: 0.8602 (mtp) cc_final: 0.8371 (mtm) REVERT: D 80 ASP cc_start: 0.8217 (m-30) cc_final: 0.7944 (m-30) REVERT: D 158 SER cc_start: 0.8167 (t) cc_final: 0.7859 (p) REVERT: E 68 TYR cc_start: 0.8612 (m-80) cc_final: 0.8349 (m-80) REVERT: E 90 SER cc_start: 0.8688 (p) cc_final: 0.8450 (m) REVERT: E 158 SER cc_start: 0.8072 (t) cc_final: 0.7782 (p) outliers start: 23 outliers final: 12 residues processed: 118 average time/residue: 0.3516 time to fit residues: 46.4504 Evaluate side-chains 122 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 184 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 0.0060 chunk 99 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 GLN E 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.098132 restraints weight = 11550.140| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.66 r_work: 0.3009 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10083 Z= 0.103 Angle : 0.459 5.408 13743 Z= 0.235 Chirality : 0.038 0.140 1710 Planarity : 0.004 0.040 1615 Dihedral : 5.195 53.236 1523 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.98 % Allowed : 10.00 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.84 (0.23), residues: 1290 helix: 3.30 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.71 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 43 TYR 0.008 0.001 TYR B 68 PHE 0.011 0.001 PHE B 24 TRP 0.008 0.001 TRP E 225 HIS 0.004 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00221 (10078) covalent geometry : angle 0.45867 (13743) hydrogen bonds : bond 0.03306 ( 871) hydrogen bonds : angle 3.36331 ( 2556) Misc. bond : bond 0.00014 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.355 Fit side-chains REVERT: B 68 TYR cc_start: 0.8486 (m-80) cc_final: 0.8253 (m-80) REVERT: B 167 THR cc_start: 0.8281 (m) cc_final: 0.8046 (m) REVERT: B 247 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7077 (tp) REVERT: C 5 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8232 (tt) REVERT: D 71 MET cc_start: 0.8617 (mtp) cc_final: 0.8406 (mtm) REVERT: D 80 ASP cc_start: 0.8166 (m-30) cc_final: 0.7906 (m-30) REVERT: E 68 TYR cc_start: 0.8551 (m-80) cc_final: 0.8347 (m-80) REVERT: E 90 SER cc_start: 0.8700 (p) cc_final: 0.8389 (m) outliers start: 19 outliers final: 7 residues processed: 111 average time/residue: 0.3835 time to fit residues: 47.2556 Evaluate side-chains 111 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain E residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.094251 restraints weight = 11489.917| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.70 r_work: 0.2959 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10083 Z= 0.157 Angle : 0.513 6.004 13743 Z= 0.263 Chirality : 0.041 0.198 1710 Planarity : 0.004 0.039 1615 Dihedral : 5.356 53.289 1523 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.56 % Allowed : 10.83 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.61 (0.23), residues: 1290 helix: 3.11 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.68 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 43 TYR 0.011 0.002 TYR B 68 PHE 0.010 0.001 PHE A 22 TRP 0.008 0.001 TRP C 225 HIS 0.004 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00382 (10078) covalent geometry : angle 0.51345 (13743) hydrogen bonds : bond 0.03810 ( 871) hydrogen bonds : angle 3.42884 ( 2556) Misc. bond : bond 0.00018 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.298 Fit side-chains REVERT: B 68 TYR cc_start: 0.8509 (m-80) cc_final: 0.8255 (m-80) REVERT: C 5 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8172 (tt) REVERT: D 80 ASP cc_start: 0.8219 (m-30) cc_final: 0.7955 (m-30) REVERT: E 68 TYR cc_start: 0.8580 (m-80) cc_final: 0.8344 (m-80) REVERT: E 90 SER cc_start: 0.8681 (p) cc_final: 0.8393 (m) outliers start: 15 outliers final: 7 residues processed: 108 average time/residue: 0.3844 time to fit residues: 46.0102 Evaluate side-chains 109 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain E residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 GLN E 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.096355 restraints weight = 11657.967| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.66 r_work: 0.2978 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10083 Z= 0.132 Angle : 0.492 5.865 13743 Z= 0.252 Chirality : 0.040 0.179 1710 Planarity : 0.004 0.039 1615 Dihedral : 5.303 58.641 1523 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.15 % Allowed : 11.46 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.71 (0.23), residues: 1290 helix: 3.18 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.63 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 43 TYR 0.011 0.001 TYR D 50 PHE 0.011 0.001 PHE B 24 TRP 0.008 0.001 TRP B 225 HIS 0.004 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00311 (10078) covalent geometry : angle 0.49238 (13743) hydrogen bonds : bond 0.03603 ( 871) hydrogen bonds : angle 3.39643 ( 2556) Misc. bond : bond 0.00006 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2517.70 seconds wall clock time: 43 minutes 53.09 seconds (2633.09 seconds total)