Starting phenix.real_space_refine on Sat Aug 23 10:32:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qr0_18610/08_2025/8qr0_18610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qr0_18610/08_2025/8qr0_18610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qr0_18610/08_2025/8qr0_18610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qr0_18610/08_2025/8qr0_18610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qr0_18610/08_2025/8qr0_18610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qr0_18610/08_2025/8qr0_18610.map" } resolution = 2.5 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= 0.001 sd= 0.066 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 50 5.16 5 C 7798 2.51 5 N 1725 2.21 5 O 2025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 11598 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2167 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2167 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2167 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2167 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2167 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 259} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'LYR:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 123 Unusual residues: {'LFA': 7, 'LMT': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 89 Unusual residues: {'LFA': 5, 'LMT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {'LFA': 7, 'LMT': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 55 Chain: "D" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 152 Unusual residues: {'LFA': 9, 'LMT': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 63 Chain: "E" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 134 Unusual residues: {'LFA': 8, 'LMT': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" O BHOH A 428 " occ=0.50 residue: pdb=" O BHOH C 428 " occ=0.50 residue: pdb=" O BHOH C 429 " occ=0.50 residue: pdb=" O BHOH D 428 " occ=0.50 residue: pdb=" O BHOH E 428 " occ=0.50 Time building chain proxies: 2.94, per 1000 atoms: 0.25 Number of scatterers: 11598 At special positions: 0 Unit cell: (91.124, 94.468, 82.764, 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 50 16.00 O 2025 8.00 N 1725 7.00 C 7798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 412.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 5 sheets defined 85.3% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 removed outlier: 3.566A pdb=" N LEU A 8 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 40 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 75 removed outlier: 3.854A pdb=" N ALA A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 118 removed outlier: 4.019A pdb=" N MET A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 101 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) Proline residue: A 107 - end of helix Processing helix chain 'A' and resid 121 through 147 removed outlier: 3.669A pdb=" N TYR A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 160 through 188 removed outlier: 3.716A pdb=" N PHE A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 225 removed outlier: 3.735A pdb=" N ILE A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 227 through 264 removed outlier: 3.678A pdb=" N VAL A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'B' and resid 3 through 8 removed outlier: 3.566A pdb=" N LEU B 8 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 40 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 47 through 75 removed outlier: 3.854A pdb=" N ALA B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 118 removed outlier: 4.015A pdb=" N MET B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) Proline residue: B 107 - end of helix Processing helix chain 'B' and resid 121 through 147 removed outlier: 3.667A pdb=" N TYR B 147 " --> pdb=" O TYR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 160 through 188 removed outlier: 3.708A pdb=" N PHE B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 225 removed outlier: 3.736A pdb=" N ILE B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Proline residue: B 216 - end of helix Proline residue: B 222 - end of helix Processing helix chain 'B' and resid 227 through 264 removed outlier: 3.680A pdb=" N VAL B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 Processing helix chain 'C' and resid 3 through 8 removed outlier: 3.565A pdb=" N LEU C 8 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 40 Processing helix chain 'C' and resid 41 through 43 No H-bonds generated for 'chain 'C' and resid 41 through 43' Processing helix chain 'C' and resid 44 through 46 No H-bonds generated for 'chain 'C' and resid 44 through 46' Processing helix chain 'C' and resid 47 through 75 removed outlier: 3.852A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 118 removed outlier: 4.020A pdb=" N MET C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 103 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) Proline residue: C 107 - end of helix Processing helix chain 'C' and resid 121 through 147 removed outlier: 3.668A pdb=" N TYR C 147 " --> pdb=" O TYR C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 160 through 188 removed outlier: 3.715A pdb=" N PHE C 164 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 225 removed outlier: 3.735A pdb=" N ILE C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Proline residue: C 222 - end of helix Processing helix chain 'C' and resid 227 through 264 removed outlier: 3.678A pdb=" N VAL C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 Processing helix chain 'D' and resid 3 through 8 removed outlier: 3.565A pdb=" N LEU D 8 " --> pdb=" O GLU D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 40 Processing helix chain 'D' and resid 41 through 43 No H-bonds generated for 'chain 'D' and resid 41 through 43' Processing helix chain 'D' and resid 44 through 46 No H-bonds generated for 'chain 'D' and resid 44 through 46' Processing helix chain 'D' and resid 47 through 75 removed outlier: 3.855A pdb=" N ALA D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 118 removed outlier: 4.016A pdb=" N MET D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN D 101 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 103 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) Proline residue: D 107 - end of helix Processing helix chain 'D' and resid 121 through 147 removed outlier: 3.667A pdb=" N TYR D 147 " --> pdb=" O TYR D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 160 through 188 removed outlier: 3.710A pdb=" N PHE D 164 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 225 removed outlier: 3.737A pdb=" N ILE D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) Proline residue: D 216 - end of helix Proline residue: D 222 - end of helix Processing helix chain 'D' and resid 227 through 264 removed outlier: 3.674A pdb=" N VAL D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.564A pdb=" N LEU E 8 " --> pdb=" O GLU E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 40 Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 44 through 46 No H-bonds generated for 'chain 'E' and resid 44 through 46' Processing helix chain 'E' and resid 47 through 75 removed outlier: 3.855A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 118 removed outlier: 4.019A pdb=" N MET E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN E 101 " --> pdb=" O TYR E 97 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU E 103 " --> pdb=" O TYR E 99 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) Proline residue: E 107 - end of helix Processing helix chain 'E' and resid 121 through 147 removed outlier: 3.665A pdb=" N TYR E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 160 through 188 removed outlier: 3.710A pdb=" N PHE E 164 " --> pdb=" O GLY E 160 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 225 removed outlier: 3.734A pdb=" N ILE E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR E 215 " --> pdb=" O THR E 211 " (cutoff:3.500A) Proline residue: E 216 - end of helix Proline residue: E 222 - end of helix Processing helix chain 'E' and resid 227 through 264 removed outlier: 3.676A pdb=" N VAL E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 79 Processing sheet with id=AA4, first strand: chain 'D' and resid 76 through 79 Processing sheet with id=AA5, first strand: chain 'E' and resid 76 through 79 840 hydrogen bonds defined for protein. 2475 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: 2.32 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2419 1.33 - 1.45: 3506 1.45 - 1.57: 5747 1.57 - 1.69: 0 1.69 - 1.82: 90 Bond restraints: 11762 Sorted by residual: bond pdb=" C6 LMT C 303 " pdb=" C7 LMT C 303 " ideal model delta sigma weight residual 1.527 1.415 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C6 LYR C 246 " pdb=" C7 LYR C 246 " ideal model delta sigma weight residual 1.444 1.339 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C6 LYR E 246 " pdb=" C7 LYR E 246 " ideal model delta sigma weight residual 1.444 1.339 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C6 LYR D 246 " pdb=" C7 LYR D 246 " ideal model delta sigma weight residual 1.444 1.339 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C6 LYR A 246 " pdb=" C7 LYR A 246 " ideal model delta sigma weight residual 1.444 1.339 0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 11757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12534 1.89 - 3.77: 2773 3.77 - 5.66: 465 5.66 - 7.55: 98 7.55 - 9.43: 26 Bond angle restraints: 15896 Sorted by residual: angle pdb=" N PRO B 226 " pdb=" CA PRO B 226 " pdb=" CB PRO B 226 " ideal model delta sigma weight residual 102.36 97.44 4.92 7.80e-01 1.64e+00 3.98e+01 angle pdb=" N PRO E 226 " pdb=" CA PRO E 226 " pdb=" CB PRO E 226 " ideal model delta sigma weight residual 102.36 97.47 4.89 7.80e-01 1.64e+00 3.94e+01 angle pdb=" N PRO A 226 " pdb=" CA PRO A 226 " pdb=" CB PRO A 226 " ideal model delta sigma weight residual 102.36 97.66 4.70 7.80e-01 1.64e+00 3.63e+01 angle pdb=" N PRO D 226 " pdb=" CA PRO D 226 " pdb=" CB PRO D 226 " ideal model delta sigma weight residual 102.36 97.66 4.70 7.80e-01 1.64e+00 3.62e+01 angle pdb=" N PRO C 226 " pdb=" CA PRO C 226 " pdb=" CB PRO C 226 " ideal model delta sigma weight residual 102.36 97.67 4.69 7.80e-01 1.64e+00 3.62e+01 ... (remaining 15891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 6474 23.67 - 47.34: 389 47.34 - 71.00: 77 71.00 - 94.67: 15 94.67 - 118.34: 5 Dihedral angle restraints: 6960 sinusoidal: 3005 harmonic: 3955 Sorted by residual: dihedral pdb=" C GLU E 149 " pdb=" N GLU E 149 " pdb=" CA GLU E 149 " pdb=" CB GLU E 149 " ideal model delta harmonic sigma weight residual -122.60 -133.13 10.53 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" C GLU A 149 " pdb=" N GLU A 149 " pdb=" CA GLU A 149 " pdb=" CB GLU A 149 " ideal model delta harmonic sigma weight residual -122.60 -133.10 10.50 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" C GLU C 149 " pdb=" N GLU C 149 " pdb=" CA GLU C 149 " pdb=" CB GLU C 149 " ideal model delta harmonic sigma weight residual -122.60 -132.99 10.39 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 6957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1033 0.066 - 0.132: 437 0.132 - 0.198: 209 0.198 - 0.264: 41 0.264 - 0.330: 15 Chirality restraints: 1735 Sorted by residual: chirality pdb=" CA GLU A 149 " pdb=" N GLU A 149 " pdb=" C GLU A 149 " pdb=" CB GLU A 149 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA GLU E 149 " pdb=" N GLU E 149 " pdb=" C GLU E 149 " pdb=" CB GLU E 149 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA GLU D 149 " pdb=" N GLU D 149 " pdb=" C GLU D 149 " pdb=" CB GLU D 149 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1732 not shown) Planarity restraints: 1905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 128 " 0.055 2.00e-02 2.50e+03 3.47e-02 3.01e+01 pdb=" CG TRP C 128 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 128 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP C 128 " -0.037 2.00e-02 2.50e+03 pdb=" NE1 TRP C 128 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 128 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP C 128 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 128 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 128 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 128 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 128 " 0.050 2.00e-02 2.50e+03 3.28e-02 2.68e+01 pdb=" CG TRP B 128 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 128 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 128 " -0.036 2.00e-02 2.50e+03 pdb=" NE1 TRP B 128 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 128 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP B 128 " -0.047 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 128 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 128 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 128 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 72 " -0.008 2.00e-02 2.50e+03 3.09e-02 2.39e+01 pdb=" CG TRP B 72 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP B 72 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 TRP B 72 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 72 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP B 72 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP B 72 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 72 " -0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 72 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 72 " 0.047 2.00e-02 2.50e+03 ... (remaining 1902 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4516 2.87 - 3.38: 12014 3.38 - 3.88: 22018 3.88 - 4.39: 26863 4.39 - 4.90: 42560 Nonbonded interactions: 107971 Sorted by model distance: nonbonded pdb=" ND1 HIS B 20 " pdb=" OH TYR C 143 " model vdw 2.361 3.120 nonbonded pdb=" OH TYR A 143 " pdb=" ND1 HIS E 20 " model vdw 2.363 3.120 nonbonded pdb=" ND1 HIS C 20 " pdb=" OH TYR D 143 " model vdw 2.364 3.120 nonbonded pdb=" OG SER D 194 " pdb=" OE1 GLU D 263 " model vdw 2.367 3.040 nonbonded pdb=" ND1 HIS D 20 " pdb=" OH TYR E 143 " model vdw 2.367 3.120 ... (remaining 107966 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 1 through 272 or resid 304)) selection = (chain 'B' and (resid 1 through 272 or (resid 304 and (name C10 or name C11 or n \ ame C12 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 or name C9 )))) selection = (chain 'C' and (resid 1 through 272 or (resid 304 and (name C10 or name C11 or n \ ame C12 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 or name C9 )))) selection = (chain 'D' and (resid 1 through 272 or (resid 304 and (name C10 or name C11 or n \ ame C12 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 or name C9 )))) selection = (chain 'E' and (resid 1 through 272 or (resid 304 and (name C10 or name C11 or n \ ame C12 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 or name C9 )))) } 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=0.50 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: 2.770 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.770 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 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 : 0.014 0.112 11762 Z= 0.870 Angle : 1.669 9.435 15896 Z= 1.063 Chirality : 0.091 0.330 1735 Planarity : 0.018 0.190 1905 Dihedral : 16.281 118.337 4420 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.26 % Allowed : 6.02 % Favored : 89.72 % Cbeta Deviations : 0.79 % 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: -1.18 (0.21), residues: 1335 helix: -0.84 (0.14), residues: 1005 sheet: None (None), residues: 0 loop : 0.07 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.004 ARG D 200 TYR 0.037 0.015 TYR C 147 PHE 0.042 0.013 PHE C 203 TRP 0.066 0.017 TRP C 72 HIS 0.012 0.007 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.01429 (11762) covalent geometry : angle 1.66911 (15896) hydrogen bonds : bond 0.19476 ( 840) hydrogen bonds : angle 6.60613 ( 2475) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.258 Fit side-chains REVERT: A 67 GLN cc_start: 0.8742 (pt0) cc_final: 0.8186 (mt0) REVERT: A 162 GLU cc_start: 0.7722 (pm20) cc_final: 0.7510 (pm20) REVERT: A 194 SER cc_start: 0.8147 (OUTLIER) cc_final: 0.7850 (p) REVERT: A 259 ARG cc_start: 0.8658 (tpt-90) cc_final: 0.8311 (tpt-90) REVERT: B 38 MET cc_start: 0.9252 (mtp) cc_final: 0.8910 (mtp) REVERT: B 67 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8143 (mt0) REVERT: B 163 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8610 (mm-40) REVERT: B 184 ASN cc_start: 0.8274 (t0) cc_final: 0.7849 (m-40) REVERT: B 226 PRO cc_start: 0.8544 (OUTLIER) cc_final: 0.8293 (Cg_endo) REVERT: B 259 ARG cc_start: 0.8664 (tpt-90) cc_final: 0.8254 (tpt-90) REVERT: C 184 ASN cc_start: 0.8105 (t0) cc_final: 0.7727 (m-40) REVERT: C 229 ASP cc_start: 0.8516 (m-30) cc_final: 0.8166 (m-30) REVERT: C 259 ARG cc_start: 0.8635 (tpt-90) cc_final: 0.8160 (tpt-90) REVERT: D 67 GLN cc_start: 0.8620 (pt0) cc_final: 0.8197 (mt0) REVERT: D 184 ASN cc_start: 0.8088 (t0) cc_final: 0.7689 (m110) REVERT: D 194 SER cc_start: 0.7969 (OUTLIER) cc_final: 0.7697 (p) REVERT: D 221 MET cc_start: 0.8577 (tpp) cc_final: 0.8309 (tpt) REVERT: D 226 PRO cc_start: 0.8723 (OUTLIER) cc_final: 0.8483 (Cg_endo) REVERT: D 259 ARG cc_start: 0.8594 (tpt-90) cc_final: 0.8184 (tpt-90) REVERT: E 38 MET cc_start: 0.9223 (mtp) cc_final: 0.8894 (mtp) REVERT: E 67 GLN cc_start: 0.8766 (pt0) cc_final: 0.8233 (mt0) REVERT: E 184 ASN cc_start: 0.8056 (t0) cc_final: 0.7698 (m-40) REVERT: E 194 SER cc_start: 0.8083 (OUTLIER) cc_final: 0.7817 (p) REVERT: E 259 ARG cc_start: 0.8619 (tpt-90) cc_final: 0.8217 (tpt-90) outliers start: 46 outliers final: 18 residues processed: 210 average time/residue: 0.6547 time to fit residues: 146.5316 Evaluate side-chains 166 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 226 PRO Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 226 PRO Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 226 PRO Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 226 PRO Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 226 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 163 GLN A 184 ASN B 67 GLN B 112 GLN C 112 GLN C 163 GLN D 112 GLN D 163 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.095282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.083025 restraints weight = 12756.134| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 0.99 r_work: 0.2710 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11762 Z= 0.153 Angle : 0.666 11.567 15896 Z= 0.327 Chirality : 0.040 0.176 1735 Planarity : 0.004 0.030 1905 Dihedral : 13.785 102.891 2246 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 2.31 % Allowed : 7.22 % Favored : 90.46 % 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: 2.45 (0.22), residues: 1335 helix: 1.92 (0.15), residues: 1020 sheet: 0.36 (0.80), residues: 50 loop : 0.93 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 19 TYR 0.019 0.002 TYR D 238 PHE 0.017 0.002 PHE A 12 TRP 0.014 0.001 TRP E 128 HIS 0.002 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00309 (11762) covalent geometry : angle 0.66628 (15896) hydrogen bonds : bond 0.06038 ( 840) hydrogen bonds : angle 4.07038 ( 2475) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.478 Fit side-chains REVERT: A 67 GLN cc_start: 0.8517 (pt0) cc_final: 0.8017 (mt0) REVERT: A 162 GLU cc_start: 0.7447 (pm20) cc_final: 0.7122 (pm20) REVERT: A 259 ARG cc_start: 0.8234 (tpt-90) cc_final: 0.7652 (tpt-90) REVERT: B 67 GLN cc_start: 0.8400 (pt0) cc_final: 0.7909 (mt0) REVERT: C 184 ASN cc_start: 0.7629 (t0) cc_final: 0.7225 (m-40) REVERT: C 259 ARG cc_start: 0.8176 (tpt-90) cc_final: 0.7505 (tpt-90) REVERT: D 64 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: D 67 GLN cc_start: 0.8366 (pt0) cc_final: 0.7921 (mt0) REVERT: D 221 MET cc_start: 0.8622 (tpp) cc_final: 0.8416 (tpt) REVERT: D 259 ARG cc_start: 0.8210 (tpt-90) cc_final: 0.7655 (tpt-90) REVERT: D 263 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7487 (mt-10) REVERT: E 67 GLN cc_start: 0.8578 (pt0) cc_final: 0.7998 (mt0) REVERT: E 184 ASN cc_start: 0.7673 (t0) cc_final: 0.7357 (m-40) REVERT: E 259 ARG cc_start: 0.8117 (tpt-90) cc_final: 0.7591 (tpt-90) outliers start: 25 outliers final: 13 residues processed: 171 average time/residue: 0.7185 time to fit residues: 130.2953 Evaluate side-chains 158 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 80 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- 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 = 0.2933 r_free = 0.2933 target = 0.092159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.080240 restraints weight = 12997.957| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 0.94 r_work: 0.2666 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11762 Z= 0.201 Angle : 0.688 12.412 15896 Z= 0.332 Chirality : 0.043 0.229 1735 Planarity : 0.005 0.030 1905 Dihedral : 13.204 80.555 2217 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.33 % Allowed : 8.43 % Favored : 88.24 % 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: 2.88 (0.22), residues: 1335 helix: 2.20 (0.15), residues: 1035 sheet: 0.64 (0.78), residues: 50 loop : 1.09 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 259 TYR 0.017 0.002 TYR C 238 PHE 0.017 0.002 PHE B 7 TRP 0.013 0.002 TRP D 128 HIS 0.003 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00467 (11762) covalent geometry : angle 0.68825 (15896) hydrogen bonds : bond 0.06716 ( 840) hydrogen bonds : angle 3.98171 ( 2475) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.266 Fit side-chains REVERT: A 67 GLN cc_start: 0.8507 (pt0) cc_final: 0.7972 (mt0) REVERT: A 162 GLU cc_start: 0.7491 (pm20) cc_final: 0.7056 (pm20) REVERT: A 259 ARG cc_start: 0.8307 (tpt-90) cc_final: 0.7917 (tpt-90) REVERT: B 67 GLN cc_start: 0.8451 (pt0) cc_final: 0.7915 (mt0) REVERT: C 184 ASN cc_start: 0.7712 (t0) cc_final: 0.7309 (m-40) REVERT: C 259 ARG cc_start: 0.8212 (tpt-90) cc_final: 0.7510 (tpt-90) REVERT: D 67 GLN cc_start: 0.8438 (pt0) cc_final: 0.7937 (mt0) REVERT: D 259 ARG cc_start: 0.8277 (tpt-90) cc_final: 0.7814 (tpt-90) REVERT: E 67 GLN cc_start: 0.8622 (pt0) cc_final: 0.8006 (mt0) REVERT: E 184 ASN cc_start: 0.7674 (t0) cc_final: 0.7393 (m-40) REVERT: E 259 ARG cc_start: 0.8235 (tpt-90) cc_final: 0.7723 (tpt-90) outliers start: 36 outliers final: 22 residues processed: 171 average time/residue: 0.7048 time to fit residues: 128.1752 Evaluate side-chains 167 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 116 optimal weight: 0.0870 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.2990 r_free = 0.2990 target = 0.096046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.083883 restraints weight = 12944.308| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.00 r_work: 0.2724 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11762 Z= 0.131 Angle : 0.575 11.304 15896 Z= 0.281 Chirality : 0.038 0.179 1735 Planarity : 0.004 0.033 1905 Dihedral : 11.538 74.171 2217 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.96 % Allowed : 9.44 % Favored : 87.59 % 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: 3.50 (0.21), residues: 1335 helix: 2.63 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.35 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 270 TYR 0.010 0.001 TYR A 219 PHE 0.013 0.001 PHE C 12 TRP 0.011 0.001 TRP A 13 HIS 0.002 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00269 (11762) covalent geometry : angle 0.57500 (15896) hydrogen bonds : bond 0.05336 ( 840) hydrogen bonds : angle 3.84358 ( 2475) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.273 Fit side-chains REVERT: A 67 GLN cc_start: 0.8410 (pt0) cc_final: 0.7906 (mt0) REVERT: A 162 GLU cc_start: 0.7313 (pm20) cc_final: 0.7015 (pm20) REVERT: A 184 ASN cc_start: 0.7773 (t0) cc_final: 0.7276 (m-40) REVERT: A 259 ARG cc_start: 0.8209 (tpt-90) cc_final: 0.7665 (tpt-90) REVERT: B 67 GLN cc_start: 0.8435 (pt0) cc_final: 0.7823 (mt0) REVERT: B 259 ARG cc_start: 0.8242 (tpp80) cc_final: 0.7658 (tpt-90) REVERT: C 64 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: C 184 ASN cc_start: 0.7672 (t0) cc_final: 0.7187 (m-40) REVERT: C 259 ARG cc_start: 0.8167 (tpt-90) cc_final: 0.7495 (tpt-90) REVERT: D 67 GLN cc_start: 0.8375 (pt0) cc_final: 0.7781 (mt0) REVERT: D 70 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8645 (tp) REVERT: D 162 GLU cc_start: 0.7599 (pm20) cc_final: 0.7206 (pm20) REVERT: D 184 ASN cc_start: 0.7587 (t0) cc_final: 0.7143 (m-40) REVERT: D 259 ARG cc_start: 0.8206 (tpt-90) cc_final: 0.7756 (tpt-90) REVERT: D 263 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7431 (mt-10) REVERT: E 67 GLN cc_start: 0.8588 (pt0) cc_final: 0.7892 (mt0) REVERT: E 184 ASN cc_start: 0.7618 (t0) cc_final: 0.7241 (m-40) REVERT: E 259 ARG cc_start: 0.8151 (tpt-90) cc_final: 0.7671 (tpt-90) outliers start: 32 outliers final: 16 residues processed: 168 average time/residue: 0.6965 time to fit residues: 124.1102 Evaluate side-chains 165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 92 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 41 optimal weight: 0.0050 chunk 36 optimal weight: 2.9990 chunk 100 optimal weight: 0.0970 overall best weight: 1.1596 ------------------------------------------------------------------------------- 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 = 0.2975 r_free = 0.2975 target = 0.094935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.083002 restraints weight = 12934.843| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 0.96 r_work: 0.2710 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11762 Z= 0.150 Angle : 0.589 11.382 15896 Z= 0.288 Chirality : 0.040 0.199 1735 Planarity : 0.004 0.033 1905 Dihedral : 11.483 71.163 2213 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.87 % Allowed : 10.19 % Favored : 86.94 % 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: 3.49 (0.21), residues: 1335 helix: 2.63 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.35 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.011 0.002 TYR B 97 PHE 0.013 0.002 PHE C 12 TRP 0.010 0.001 TRP C 13 HIS 0.002 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00330 (11762) covalent geometry : angle 0.58860 (15896) hydrogen bonds : bond 0.05688 ( 840) hydrogen bonds : angle 3.81577 ( 2475) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.532 Fit side-chains REVERT: A 67 GLN cc_start: 0.8425 (pt0) cc_final: 0.7937 (mt0) REVERT: A 162 GLU cc_start: 0.7360 (pm20) cc_final: 0.7008 (pm20) REVERT: A 184 ASN cc_start: 0.7844 (t0) cc_final: 0.7378 (m-40) REVERT: A 259 ARG cc_start: 0.8243 (tpt-90) cc_final: 0.7739 (tpt-90) REVERT: B 67 GLN cc_start: 0.8469 (pt0) cc_final: 0.7886 (mt0) REVERT: B 259 ARG cc_start: 0.8286 (tpp80) cc_final: 0.7685 (tpt-90) REVERT: C 64 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: C 184 ASN cc_start: 0.7713 (t0) cc_final: 0.7285 (m-40) REVERT: C 259 ARG cc_start: 0.8233 (tpt-90) cc_final: 0.7648 (tpt-90) REVERT: D 67 GLN cc_start: 0.8409 (pt0) cc_final: 0.7842 (mt0) REVERT: D 162 GLU cc_start: 0.7669 (pm20) cc_final: 0.7279 (pm20) REVERT: D 184 ASN cc_start: 0.7677 (t0) cc_final: 0.7297 (m-40) REVERT: D 259 ARG cc_start: 0.8237 (tpt-90) cc_final: 0.7818 (tpt-90) REVERT: D 263 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7451 (mt-10) REVERT: E 67 GLN cc_start: 0.8620 (pt0) cc_final: 0.7966 (mt0) REVERT: E 184 ASN cc_start: 0.7677 (t0) cc_final: 0.7315 (m-40) REVERT: E 259 ARG cc_start: 0.8204 (tpt-90) cc_final: 0.7765 (tpt-90) outliers start: 31 outliers final: 22 residues processed: 172 average time/residue: 0.8303 time to fit residues: 151.3822 Evaluate side-chains 165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 134 optimal weight: 0.0980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.2957 r_free = 0.2957 target = 0.093766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.081599 restraints weight = 12916.274| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 0.99 r_work: 0.2687 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11762 Z= 0.169 Angle : 0.613 11.614 15896 Z= 0.300 Chirality : 0.041 0.209 1735 Planarity : 0.004 0.034 1905 Dihedral : 11.673 70.971 2211 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.06 % Allowed : 10.19 % Favored : 86.76 % 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: 3.42 (0.21), residues: 1335 helix: 2.58 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.32 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.013 0.002 TYR B 97 PHE 0.014 0.002 PHE B 7 TRP 0.010 0.002 TRP C 13 HIS 0.002 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00383 (11762) covalent geometry : angle 0.61263 (15896) hydrogen bonds : bond 0.06073 ( 840) hydrogen bonds : angle 3.83694 ( 2475) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.437 Fit side-chains REVERT: A 67 GLN cc_start: 0.8391 (pt0) cc_final: 0.7875 (mt0) REVERT: A 162 GLU cc_start: 0.7325 (pm20) cc_final: 0.7030 (pm20) REVERT: A 184 ASN cc_start: 0.7824 (t0) cc_final: 0.7328 (m-40) REVERT: A 200 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7790 (mtt180) REVERT: A 259 ARG cc_start: 0.8228 (tpt-90) cc_final: 0.7915 (tpt-90) REVERT: B 67 GLN cc_start: 0.8470 (pt0) cc_final: 0.7843 (mt0) REVERT: B 259 ARG cc_start: 0.8265 (tpp80) cc_final: 0.7612 (tpt-90) REVERT: B 263 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7702 (mt-10) REVERT: C 64 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: C 184 ASN cc_start: 0.7706 (t0) cc_final: 0.7247 (m-40) REVERT: C 259 ARG cc_start: 0.8204 (tpt-90) cc_final: 0.7594 (tpt-90) REVERT: D 67 GLN cc_start: 0.8422 (pt0) cc_final: 0.7821 (mt0) REVERT: D 184 ASN cc_start: 0.7627 (t0) cc_final: 0.7212 (m-40) REVERT: D 259 ARG cc_start: 0.8212 (tpt-90) cc_final: 0.7782 (tpt-90) REVERT: D 263 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7437 (mt-10) REVERT: E 67 GLN cc_start: 0.8637 (pt0) cc_final: 0.7951 (mt0) REVERT: E 184 ASN cc_start: 0.7695 (t0) cc_final: 0.7316 (m-40) REVERT: E 259 ARG cc_start: 0.8167 (tpt-90) cc_final: 0.7676 (tpt-90) outliers start: 33 outliers final: 21 residues processed: 171 average time/residue: 0.7622 time to fit residues: 138.2087 Evaluate side-chains 165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 258 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 10 optimal weight: 0.0770 chunk 85 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- 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 = 0.2989 r_free = 0.2989 target = 0.095924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.083734 restraints weight = 12926.438| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 0.99 r_work: 0.2721 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11762 Z= 0.138 Angle : 0.576 11.107 15896 Z= 0.281 Chirality : 0.039 0.182 1735 Planarity : 0.004 0.034 1905 Dihedral : 11.236 69.212 2209 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.41 % Allowed : 11.20 % Favored : 86.39 % 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: 3.58 (0.21), residues: 1335 helix: 2.71 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.34 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.012 0.001 TYR B 97 PHE 0.013 0.001 PHE C 12 TRP 0.011 0.001 TRP A 13 HIS 0.002 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00298 (11762) covalent geometry : angle 0.57579 (15896) hydrogen bonds : bond 0.05426 ( 840) hydrogen bonds : angle 3.77244 ( 2475) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.424 Fit side-chains REVERT: A 67 GLN cc_start: 0.8419 (pt0) cc_final: 0.7899 (mt0) REVERT: A 70 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8491 (tp) REVERT: A 162 GLU cc_start: 0.7293 (pm20) cc_final: 0.6918 (pm20) REVERT: A 184 ASN cc_start: 0.7837 (t0) cc_final: 0.7308 (m-40) REVERT: A 259 ARG cc_start: 0.8199 (tpt-90) cc_final: 0.7780 (tpt-90) REVERT: B 67 GLN cc_start: 0.8453 (pt0) cc_final: 0.7816 (mt0) REVERT: B 184 ASN cc_start: 0.7810 (t0) cc_final: 0.7379 (m-40) REVERT: B 259 ARG cc_start: 0.8252 (tpp80) cc_final: 0.7599 (tpt-90) REVERT: B 263 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7681 (mt-10) REVERT: C 64 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: C 184 ASN cc_start: 0.7692 (t0) cc_final: 0.7212 (m-40) REVERT: C 259 ARG cc_start: 0.8202 (tpt-90) cc_final: 0.7575 (tpt-90) REVERT: D 67 GLN cc_start: 0.8378 (pt0) cc_final: 0.7770 (mt0) REVERT: D 184 ASN cc_start: 0.7629 (t0) cc_final: 0.7201 (m-40) REVERT: D 259 ARG cc_start: 0.8185 (tpt-90) cc_final: 0.7755 (tpt-90) REVERT: D 263 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7452 (mt-10) REVERT: E 67 GLN cc_start: 0.8593 (pt0) cc_final: 0.7892 (mt0) REVERT: E 184 ASN cc_start: 0.7645 (t0) cc_final: 0.7226 (m-40) REVERT: E 259 ARG cc_start: 0.8113 (tpt-90) cc_final: 0.7688 (tpt-90) outliers start: 26 outliers final: 17 residues processed: 163 average time/residue: 0.8524 time to fit residues: 147.2250 Evaluate side-chains 157 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 258 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 130 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.2952 r_free = 0.2952 target = 0.093456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.081226 restraints weight = 12930.437| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 0.99 r_work: 0.2678 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11762 Z= 0.182 Angle : 0.627 11.689 15896 Z= 0.307 Chirality : 0.042 0.204 1735 Planarity : 0.004 0.034 1905 Dihedral : 11.713 71.512 2206 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 2.41 % Allowed : 11.57 % Favored : 86.02 % 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: 3.36 (0.21), residues: 1335 helix: 2.54 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.29 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.016 0.002 TYR B 97 PHE 0.015 0.002 PHE B 7 TRP 0.010 0.002 TRP C 13 HIS 0.002 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00419 (11762) covalent geometry : angle 0.62741 (15896) hydrogen bonds : bond 0.06267 ( 840) hydrogen bonds : angle 3.85178 ( 2475) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.284 Fit side-chains REVERT: A 67 GLN cc_start: 0.8490 (pt0) cc_final: 0.7885 (mt0) REVERT: A 162 GLU cc_start: 0.7303 (pm20) cc_final: 0.6964 (pm20) REVERT: A 184 ASN cc_start: 0.7827 (t0) cc_final: 0.7328 (m-40) REVERT: A 200 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7775 (mtt180) REVERT: A 259 ARG cc_start: 0.8211 (tpt-90) cc_final: 0.7900 (tpt-90) REVERT: B 67 GLN cc_start: 0.8470 (pt0) cc_final: 0.7845 (mt0) REVERT: B 259 ARG cc_start: 0.8247 (tpp80) cc_final: 0.7561 (tpt-90) REVERT: B 263 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7666 (mt-10) REVERT: C 64 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: C 184 ASN cc_start: 0.7711 (t0) cc_final: 0.7246 (m-40) REVERT: C 259 ARG cc_start: 0.8214 (tpt-90) cc_final: 0.7577 (tpt-90) REVERT: D 67 GLN cc_start: 0.8431 (pt0) cc_final: 0.7831 (mt0) REVERT: D 184 ASN cc_start: 0.7614 (t0) cc_final: 0.7213 (m-40) REVERT: D 259 ARG cc_start: 0.8209 (tpt-90) cc_final: 0.7782 (tpt-90) REVERT: D 263 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7473 (mt-10) REVERT: E 67 GLN cc_start: 0.8632 (pt0) cc_final: 0.7942 (mt0) REVERT: E 184 ASN cc_start: 0.7704 (t0) cc_final: 0.7318 (m-40) REVERT: E 259 ARG cc_start: 0.8136 (tpt-90) cc_final: 0.7665 (tpt-90) outliers start: 26 outliers final: 17 residues processed: 164 average time/residue: 0.7934 time to fit residues: 137.8549 Evaluate side-chains 162 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 258 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 79 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 100 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3005 r_free = 0.3005 target = 0.097040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.084971 restraints weight = 12817.738| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 0.98 r_work: 0.2742 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11762 Z= 0.129 Angle : 0.570 10.917 15896 Z= 0.277 Chirality : 0.038 0.174 1735 Planarity : 0.004 0.035 1905 Dihedral : 11.000 69.215 2206 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.04 % Allowed : 12.04 % Favored : 85.93 % 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: 3.66 (0.21), residues: 1335 helix: 2.78 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.33 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.012 0.001 TYR A 219 PHE 0.012 0.001 PHE C 12 TRP 0.012 0.001 TRP A 13 HIS 0.002 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00273 (11762) covalent geometry : angle 0.56997 (15896) hydrogen bonds : bond 0.05175 ( 840) hydrogen bonds : angle 3.74780 ( 2475) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.424 Fit side-chains REVERT: A 67 GLN cc_start: 0.8420 (pt0) cc_final: 0.7906 (mt0) REVERT: A 70 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8473 (tp) REVERT: A 162 GLU cc_start: 0.7268 (pm20) cc_final: 0.6987 (pm20) REVERT: A 184 ASN cc_start: 0.7849 (t0) cc_final: 0.7327 (m-40) REVERT: A 200 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7808 (mtt180) REVERT: A 259 ARG cc_start: 0.8217 (tpt-90) cc_final: 0.7753 (tpt-90) REVERT: B 67 GLN cc_start: 0.8464 (pt0) cc_final: 0.7833 (mt0) REVERT: B 184 ASN cc_start: 0.7815 (t0) cc_final: 0.7411 (m-40) REVERT: B 259 ARG cc_start: 0.8315 (tpp80) cc_final: 0.7622 (tpt-90) REVERT: B 263 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 64 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: C 184 ASN cc_start: 0.7698 (t0) cc_final: 0.7230 (m-40) REVERT: C 259 ARG cc_start: 0.8205 (tpt-90) cc_final: 0.7583 (tpt-90) REVERT: D 67 GLN cc_start: 0.8388 (pt0) cc_final: 0.7789 (mt0) REVERT: D 184 ASN cc_start: 0.7634 (t0) cc_final: 0.7204 (m-40) REVERT: D 259 ARG cc_start: 0.8202 (tpt-90) cc_final: 0.7788 (tpt-90) REVERT: D 263 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7487 (mt-10) REVERT: E 67 GLN cc_start: 0.8570 (pt0) cc_final: 0.7850 (mt0) REVERT: E 70 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8577 (tp) REVERT: E 184 ASN cc_start: 0.7627 (t0) cc_final: 0.7236 (m-40) REVERT: E 259 ARG cc_start: 0.8107 (tpt-90) cc_final: 0.7707 (tpt-90) outliers start: 22 outliers final: 13 residues processed: 161 average time/residue: 0.8845 time to fit residues: 150.6519 Evaluate side-chains 157 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 62 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.2990 r_free = 0.2990 target = 0.095940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.083923 restraints weight = 12951.905| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 0.96 r_work: 0.2725 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11762 Z= 0.144 Angle : 0.592 11.227 15896 Z= 0.287 Chirality : 0.039 0.180 1735 Planarity : 0.004 0.034 1905 Dihedral : 11.086 70.320 2206 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.85 % Allowed : 12.41 % Favored : 85.74 % 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: 3.63 (0.21), residues: 1335 helix: 2.75 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.33 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.012 0.001 TYR B 97 PHE 0.013 0.002 PHE B 164 TRP 0.010 0.001 TRP A 13 HIS 0.002 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00316 (11762) covalent geometry : angle 0.59181 (15896) hydrogen bonds : bond 0.05506 ( 840) hydrogen bonds : angle 3.75971 ( 2475) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.433 Fit side-chains REVERT: A 67 GLN cc_start: 0.8401 (pt0) cc_final: 0.7889 (mt0) REVERT: A 70 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8518 (tp) REVERT: A 162 GLU cc_start: 0.7305 (pm20) cc_final: 0.7019 (pm20) REVERT: A 184 ASN cc_start: 0.7882 (t0) cc_final: 0.7360 (m-40) REVERT: A 200 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7832 (mtt180) REVERT: A 259 ARG cc_start: 0.8246 (tpt-90) cc_final: 0.7798 (tpt-90) REVERT: B 67 GLN cc_start: 0.8483 (pt0) cc_final: 0.7872 (mt0) REVERT: B 184 ASN cc_start: 0.7828 (t0) cc_final: 0.7435 (m-40) REVERT: B 259 ARG cc_start: 0.8359 (tpp80) cc_final: 0.7686 (tpt-90) REVERT: B 263 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7668 (mt-10) REVERT: C 64 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: C 184 ASN cc_start: 0.7722 (t0) cc_final: 0.7277 (m-40) REVERT: C 259 ARG cc_start: 0.8268 (tpt-90) cc_final: 0.7669 (tpt-90) REVERT: D 67 GLN cc_start: 0.8413 (pt0) cc_final: 0.7832 (mt0) REVERT: D 184 ASN cc_start: 0.7669 (t0) cc_final: 0.7275 (m-40) REVERT: D 259 ARG cc_start: 0.8247 (tpt-90) cc_final: 0.7842 (tpt-90) REVERT: D 263 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7483 (mt-10) REVERT: E 67 GLN cc_start: 0.8597 (pt0) cc_final: 0.7906 (mt0) REVERT: E 70 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8637 (tp) REVERT: E 184 ASN cc_start: 0.7683 (t0) cc_final: 0.7304 (m-40) REVERT: E 259 ARG cc_start: 0.8179 (tpt-90) cc_final: 0.7741 (tpt-90) outliers start: 20 outliers final: 13 residues processed: 156 average time/residue: 0.9449 time to fit residues: 155.8180 Evaluate side-chains 156 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 11 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 110 optimal weight: 0.1980 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.2983 r_free = 0.2983 target = 0.095516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.083232 restraints weight = 12974.847| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.00 r_work: 0.2712 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11762 Z= 0.149 Angle : 0.596 11.268 15896 Z= 0.290 Chirality : 0.040 0.184 1735 Planarity : 0.004 0.034 1905 Dihedral : 11.139 70.472 2206 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.04 % Allowed : 12.13 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.58 (0.21), residues: 1335 helix: 2.72 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.29 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.012 0.001 TYR B 97 PHE 0.013 0.002 PHE B 164 TRP 0.010 0.001 TRP A 13 HIS 0.001 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00330 (11762) covalent geometry : angle 0.59605 (15896) hydrogen bonds : bond 0.05634 ( 840) hydrogen bonds : angle 3.77030 ( 2475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3787.66 seconds wall clock time: 65 minutes 29.82 seconds (3929.82 seconds total)