Starting phenix.real_space_refine on Sun Jul 27 20:47:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0k_18795/07_2025/8r0k_18795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0k_18795/07_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_18795/07_2025/8r0k_18795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0k_18795/07_2025/8r0k_18795.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0k_18795/07_2025/8r0k_18795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0k_18795/07_2025/8r0k_18795.cif" } resolution = 2.94 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= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 8, 'ASP: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: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 8, 'ASP: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: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 8, 'ASP: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: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 8, 'ASP: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: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 8, 'ASP: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: 6.94, per 1000 atoms: 0.70 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: 3.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.84 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: 2.89 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: 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: 0.840 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.950 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.550 ------------------------------------------------------------------------------- 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 (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: -2.38 (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 TRP 0.032 0.008 TRP A 103 HIS 0.015 0.006 HIS A 249 PHE 0.048 0.010 PHE D 220 TYR 0.063 0.011 TYR D 214 ARG 0.018 0.003 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.18710 ( 871) hydrogen bonds : angle 7.84050 ( 2556) covalent geometry : bond 0.01064 (10078) covalent geometry : angle 1.38398 (13743) 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 : 0.961 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: 1.0041 time to fit residues: 127.4164 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 : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 chunk 118 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.122467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.100204 restraints weight = 11060.199| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.66 r_work: 0.3032 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10083 Z= 0.120 Angle : 0.533 6.796 13743 Z= 0.267 Chirality : 0.038 0.118 1710 Planarity : 0.005 0.037 1615 Dihedral : 6.913 98.731 1523 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.83 % Allowed : 6.46 % 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 (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: 2.51 (0.22), residues: 1290 helix: 2.37 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -1.18 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 225 HIS 0.008 0.002 HIS D 18 PHE 0.007 0.001 PHE D 75 TYR 0.011 0.001 TYR D 68 ARG 0.007 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 871) hydrogen bonds : angle 3.88126 ( 2556) covalent geometry : bond 0.00254 (10078) covalent geometry : angle 0.53261 (13743) Misc. bond : bond 0.00055 ( 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 106 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.010 Fit side-chains REVERT: A 82 VAL cc_start: 0.8241 (t) cc_final: 0.7994 (m) REVERT: A 204 MET cc_start: 0.8021 (mmp) cc_final: 0.7719 (mmt) REVERT: B 82 VAL cc_start: 0.8154 (t) cc_final: 0.7905 (m) REVERT: B 158 SER cc_start: 0.8101 (t) cc_final: 0.7709 (p) REVERT: C 82 VAL cc_start: 0.8142 (t) cc_final: 0.7839 (m) REVERT: C 158 SER cc_start: 0.8042 (t) cc_final: 0.7725 (p) REVERT: D 5 ILE cc_start: 0.8130 (tp) cc_final: 0.7890 (tt) REVERT: D 158 SER cc_start: 0.8081 (t) cc_final: 0.7714 (p) REVERT: E 43 ARG cc_start: 0.8133 (ptm-80) cc_final: 0.7875 (ptt90) REVERT: E 82 VAL cc_start: 0.8155 (t) cc_final: 0.7895 (m) REVERT: E 158 SER cc_start: 0.8107 (t) cc_final: 0.7721 (p) outliers start: 8 outliers final: 1 residues processed: 100 average time/residue: 0.9622 time to fit residues: 105.7344 Evaluate side-chains 91 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 61 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 HIS D 187 GLN E 81 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.094810 restraints weight = 11675.084| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.66 r_work: 0.2956 rms_B_bonded: 2.29 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: 0.8099 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10083 Z= 0.167 Angle : 0.530 5.644 13743 Z= 0.269 Chirality : 0.040 0.120 1710 Planarity : 0.004 0.038 1615 Dihedral : 5.691 55.256 1523 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.77 % Allowed : 7.40 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.28 (0.23), residues: 1290 helix: 2.93 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -1.02 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 225 HIS 0.005 0.001 HIS B 18 PHE 0.010 0.001 PHE E 137 TYR 0.013 0.002 TYR D 68 ARG 0.006 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 871) hydrogen bonds : angle 3.64395 ( 2556) covalent geometry : bond 0.00406 (10078) covalent geometry : angle 0.53010 (13743) Misc. bond : bond 0.00010 ( 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 126 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.014 Fit side-chains REVERT: B 68 TYR cc_start: 0.8572 (m-80) cc_final: 0.8352 (m-80) REVERT: C 158 SER cc_start: 0.8132 (t) cc_final: 0.7847 (p) REVERT: D 158 SER cc_start: 0.8139 (t) cc_final: 0.7831 (p) REVERT: E 43 ARG cc_start: 0.8111 (ptm-80) cc_final: 0.7879 (ptt90) REVERT: E 90 SER cc_start: 0.8644 (p) cc_final: 0.8425 (m) REVERT: E 158 SER cc_start: 0.8024 (t) cc_final: 0.7725 (p) outliers start: 17 outliers final: 7 residues processed: 116 average time/residue: 0.8055 time to fit residues: 104.0343 Evaluate side-chains 111 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 130 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 D residue 130 LEU 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 99 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.116317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.093882 restraints weight = 11629.186| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.65 r_work: 0.2946 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2427 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= 0.175 Angle : 0.528 9.418 13743 Z= 0.267 Chirality : 0.040 0.120 1710 Planarity : 0.004 0.040 1615 Dihedral : 5.615 54.447 1523 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.60 % Allowed : 7.71 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.33 (0.23), residues: 1290 helix: 2.95 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.97 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 225 HIS 0.004 0.001 HIS B 18 PHE 0.010 0.001 PHE B 24 TYR 0.012 0.002 TYR E 68 ARG 0.003 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 871) hydrogen bonds : angle 3.55495 ( 2556) covalent geometry : bond 0.00428 (10078) covalent geometry : angle 0.52840 (13743) Misc. bond : bond 0.00019 ( 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 135 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.997 Fit side-chains REVERT: B 68 TYR cc_start: 0.8500 (m-80) cc_final: 0.8265 (m-80) REVERT: C 158 SER cc_start: 0.8033 (t) cc_final: 0.7762 (p) REVERT: D 158 SER cc_start: 0.8042 (t) cc_final: 0.7770 (p) REVERT: E 43 ARG cc_start: 0.8039 (ptm-80) cc_final: 0.7839 (ptt90) REVERT: E 90 SER cc_start: 0.8667 (p) cc_final: 0.8405 (m) REVERT: E 158 SER cc_start: 0.7987 (t) cc_final: 0.7712 (p) outliers start: 25 outliers final: 11 residues processed: 122 average time/residue: 0.7553 time to fit residues: 103.6593 Evaluate side-chains 119 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 6 SER 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 6 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 130 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 67 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.119650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097256 restraints weight = 11504.828| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.65 r_work: 0.2991 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2632 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= 0.111 Angle : 0.465 8.963 13743 Z= 0.235 Chirality : 0.038 0.117 1710 Planarity : 0.004 0.038 1615 Dihedral : 5.226 54.254 1523 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.50 % Allowed : 8.12 % 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 (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: 3.78 (0.23), residues: 1290 helix: 3.28 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.82 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 225 HIS 0.004 0.001 HIS D 18 PHE 0.007 0.001 PHE B 24 TYR 0.009 0.001 TYR B 68 ARG 0.002 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 871) hydrogen bonds : angle 3.40663 ( 2556) covalent geometry : bond 0.00247 (10078) covalent geometry : angle 0.46501 (13743) Misc. bond : bond 0.00005 ( 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 131 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.056 Fit side-chains REVERT: C 204 MET cc_start: 0.7868 (mmt) cc_final: 0.7531 (mmp) REVERT: D 68 TYR cc_start: 0.8551 (m-80) cc_final: 0.8294 (m-80) REVERT: D 80 ASP cc_start: 0.8201 (m-30) cc_final: 0.7862 (m-30) REVERT: E 68 TYR cc_start: 0.8609 (m-80) cc_final: 0.8380 (m-80) REVERT: E 90 SER cc_start: 0.8635 (p) cc_final: 0.8378 (m) outliers start: 24 outliers final: 8 residues processed: 119 average time/residue: 0.7828 time to fit residues: 104.4721 Evaluate side-chains 108 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain E residue 94 MET 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 91 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.116567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.093916 restraints weight = 11707.399| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.66 r_work: 0.2948 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10083 Z= 0.177 Angle : 0.516 5.555 13743 Z= 0.264 Chirality : 0.040 0.122 1710 Planarity : 0.004 0.039 1615 Dihedral : 5.520 59.868 1523 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.12 % Allowed : 7.92 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.48 (0.23), residues: 1290 helix: 3.05 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.85 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 225 HIS 0.004 0.001 HIS D 18 PHE 0.011 0.001 PHE B 24 TYR 0.014 0.002 TYR B 68 ARG 0.002 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 871) hydrogen bonds : angle 3.49616 ( 2556) covalent geometry : bond 0.00436 (10078) covalent geometry : angle 0.51627 (13743) Misc. bond : bond 0.00024 ( 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 137 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.011 Fit side-chains REVERT: B 68 TYR cc_start: 0.8604 (m-80) cc_final: 0.8338 (m-80) REVERT: D 68 TYR cc_start: 0.8591 (m-80) cc_final: 0.8325 (m-80) REVERT: D 80 ASP cc_start: 0.8201 (m-30) cc_final: 0.7918 (m-30) REVERT: D 158 SER cc_start: 0.8101 (t) cc_final: 0.7857 (p) REVERT: E 68 TYR cc_start: 0.8633 (m-80) cc_final: 0.8417 (m-80) REVERT: E 90 SER cc_start: 0.8709 (p) cc_final: 0.8454 (m) REVERT: E 158 SER cc_start: 0.7896 (t) cc_final: 0.7680 (p) outliers start: 30 outliers final: 12 residues processed: 120 average time/residue: 0.7653 time to fit residues: 103.3096 Evaluate side-chains 119 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 6 SER 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 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 96 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 184 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 67 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.119196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.096013 restraints weight = 11589.636| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.71 r_work: 0.2983 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10083 Z= 0.116 Angle : 0.464 5.439 13743 Z= 0.237 Chirality : 0.038 0.113 1710 Planarity : 0.004 0.038 1615 Dihedral : 5.230 58.386 1523 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.29 % Allowed : 8.85 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.79 (0.23), residues: 1290 helix: 3.27 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.75 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 225 HIS 0.004 0.001 HIS D 18 PHE 0.008 0.001 PHE B 24 TYR 0.014 0.001 TYR C 68 ARG 0.002 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 871) hydrogen bonds : angle 3.38603 ( 2556) covalent geometry : bond 0.00264 (10078) covalent geometry : angle 0.46425 (13743) Misc. bond : bond 0.00002 ( 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 128 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.033 Fit side-chains REVERT: B 68 TYR cc_start: 0.8476 (m-80) cc_final: 0.8236 (m-80) REVERT: D 68 TYR cc_start: 0.8478 (m-80) cc_final: 0.8259 (m-80) REVERT: D 80 ASP cc_start: 0.8152 (m-30) cc_final: 0.7856 (m-30) REVERT: E 90 SER cc_start: 0.8709 (p) cc_final: 0.8406 (m) outliers start: 22 outliers final: 12 residues processed: 115 average time/residue: 0.7561 time to fit residues: 97.4762 Evaluate side-chains 116 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 C residue 130 LEU 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 Chi-restraints excluded: chain E residue 184 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.119842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.097343 restraints weight = 11687.247| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.67 r_work: 0.2994 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 0.021 10083 Z= 0.115 Angle : 0.464 5.439 13743 Z= 0.237 Chirality : 0.038 0.121 1710 Planarity : 0.004 0.038 1615 Dihedral : 5.083 54.786 1523 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.60 % Allowed : 9.06 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.85 (0.23), residues: 1290 helix: 3.31 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.71 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 225 HIS 0.004 0.001 HIS D 18 PHE 0.009 0.001 PHE B 24 TYR 0.013 0.001 TYR C 68 ARG 0.002 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 871) hydrogen bonds : angle 3.34894 ( 2556) covalent geometry : bond 0.00261 (10078) covalent geometry : angle 0.46415 (13743) Misc. bond : bond 0.00002 ( 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 130 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.006 Fit side-chains REVERT: B 167 THR cc_start: 0.8309 (m) cc_final: 0.8084 (m) REVERT: D 68 TYR cc_start: 0.8489 (m-80) cc_final: 0.8226 (m-80) REVERT: D 71 MET cc_start: 0.8608 (mtp) cc_final: 0.8345 (mtm) REVERT: D 80 ASP cc_start: 0.8192 (m-30) cc_final: 0.7914 (m-30) REVERT: E 68 TYR cc_start: 0.8554 (m-80) cc_final: 0.8341 (m-80) REVERT: E 90 SER cc_start: 0.8681 (p) cc_final: 0.8383 (m) outliers start: 25 outliers final: 10 residues processed: 117 average time/residue: 0.7611 time to fit residues: 99.7510 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 : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 96 ILE 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 73 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.117029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.093653 restraints weight = 11662.451| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.71 r_work: 0.2949 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2738 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= 0.166 Angle : 0.516 5.532 13743 Z= 0.264 Chirality : 0.041 0.139 1710 Planarity : 0.004 0.039 1615 Dihedral : 5.336 52.301 1523 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.88 % Allowed : 9.90 % 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 (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: 3.56 (0.23), residues: 1290 helix: 3.08 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.72 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 225 HIS 0.004 0.001 HIS D 18 PHE 0.012 0.001 PHE B 24 TYR 0.014 0.002 TYR B 68 ARG 0.005 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 871) hydrogen bonds : angle 3.44208 ( 2556) covalent geometry : bond 0.00408 (10078) covalent geometry : angle 0.51589 (13743) Misc. bond : bond 0.00024 ( 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 123 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.969 Fit side-chains REVERT: B 167 THR cc_start: 0.8219 (m) cc_final: 0.7986 (m) REVERT: D 68 TYR cc_start: 0.8536 (m-80) cc_final: 0.8283 (m-80) REVERT: D 80 ASP cc_start: 0.8169 (m-30) cc_final: 0.7905 (m-30) REVERT: E 90 SER cc_start: 0.8687 (p) cc_final: 0.8389 (m) REVERT: E 158 SER cc_start: 0.7843 (t) cc_final: 0.7632 (p) outliers start: 18 outliers final: 12 residues processed: 114 average time/residue: 0.8287 time to fit residues: 105.2558 Evaluate side-chains 117 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 6 SER 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 C residue 6 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain E residue 96 ILE 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 115 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.117626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.094387 restraints weight = 11524.062| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.70 r_work: 0.2962 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10083 Z= 0.147 Angle : 0.502 6.168 13743 Z= 0.257 Chirality : 0.040 0.218 1710 Planarity : 0.004 0.038 1615 Dihedral : 5.303 51.779 1523 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.46 % Allowed : 10.31 % 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 (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: 3.60 (0.23), residues: 1290 helix: 3.11 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.72 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 225 HIS 0.004 0.001 HIS D 18 PHE 0.010 0.001 PHE A 22 TYR 0.015 0.002 TYR C 68 ARG 0.005 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 871) hydrogen bonds : angle 3.42166 ( 2556) covalent geometry : bond 0.00354 (10078) covalent geometry : angle 0.50223 (13743) Misc. bond : bond 0.00014 ( 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 116 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.966 Fit side-chains REVERT: A 89 ASN cc_start: 0.8081 (m-40) cc_final: 0.7863 (m-40) REVERT: B 167 THR cc_start: 0.8200 (m) cc_final: 0.7968 (m) REVERT: D 68 TYR cc_start: 0.8502 (m-80) cc_final: 0.8252 (m-80) REVERT: D 80 ASP cc_start: 0.8164 (m-30) cc_final: 0.7898 (m-30) REVERT: E 90 SER cc_start: 0.8691 (p) cc_final: 0.8394 (m) outliers start: 14 outliers final: 12 residues processed: 111 average time/residue: 0.8000 time to fit residues: 99.2805 Evaluate side-chains 113 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 185 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 93 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.120427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.098182 restraints weight = 11615.870| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.62 r_work: 0.3012 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2896 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= 0.110 Angle : 0.467 5.648 13743 Z= 0.239 Chirality : 0.039 0.189 1710 Planarity : 0.004 0.038 1615 Dihedral : 5.021 47.179 1523 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.56 % Allowed : 10.42 % 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 (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: 3.88 (0.23), residues: 1290 helix: 3.31 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -0.63 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 225 HIS 0.004 0.001 HIS D 18 PHE 0.009 0.001 PHE B 24 TYR 0.012 0.001 TYR C 68 ARG 0.004 0.000 ARG E 43 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 871) hydrogen bonds : angle 3.33651 ( 2556) covalent geometry : bond 0.00246 (10078) covalent geometry : angle 0.46714 (13743) Misc. bond : bond 0.00003 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5229.50 seconds wall clock time: 90 minutes 12.75 seconds (5412.75 seconds total)