Starting phenix.real_space_refine on Tue Jul 29 16:16:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qr0_18610/07_2025/8qr0_18610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qr0_18610/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qr0_18610/07_2025/8qr0_18610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qr0_18610/07_2025/8qr0_18610.map" model { file = "/net/cci-nas-00/data/ceres_data/8qr0_18610/07_2025/8qr0_18610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qr0_18610/07_2025/8qr0_18610.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 2, 'ARG:plan': 1, '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: {'GLU:plan': 2, 'ARG:plan': 1, '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: {'GLU:plan': 2, 'ARG:plan': 1, '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: {'GLU:plan': 2, 'ARG:plan': 1, '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: {'GLU:plan': 2, 'ARG:plan': 1, '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: 8.03, per 1000 atoms: 0.69 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: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.98 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: 3.23 Time building geometry restraints manager: 3.47 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.430 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.460 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (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 TRP 0.066 0.017 TRP C 72 HIS 0.012 0.007 HIS B 20 PHE 0.042 0.013 PHE C 203 TYR 0.037 0.015 TYR C 147 ARG 0.022 0.004 ARG D 200 Details of bonding type rmsd hydrogen bonds : bond 0.19476 ( 840) hydrogen bonds : angle 6.60613 ( 2475) covalent geometry : bond 0.01429 (11762) covalent geometry : angle 1.66911 (15896) *********************** 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 : 1.280 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: 0.8183 (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: 1.6219 time to fit residues: 364.1420 Evaluate side-chains 167 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 113 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN C 112 GLN C 163 GLN D 112 GLN D 163 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.093632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.081623 restraints weight = 12612.568| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 0.95 r_work: 0.2688 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11762 Z= 0.162 Angle : 0.676 11.846 15896 Z= 0.333 Chirality : 0.040 0.189 1735 Planarity : 0.004 0.034 1905 Dihedral : 13.915 103.823 2246 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 2.59 % Allowed : 6.85 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.22), residues: 1335 helix: 1.84 (0.15), residues: 1035 sheet: 0.36 (0.80), residues: 50 loop : 0.94 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 128 HIS 0.002 0.001 HIS B 20 PHE 0.017 0.002 PHE A 12 TYR 0.021 0.002 TYR D 238 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd hydrogen bonds : bond 0.06524 ( 840) hydrogen bonds : angle 4.07834 ( 2475) covalent geometry : bond 0.00329 (11762) covalent geometry : angle 0.67585 (15896) *********************** 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 179 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.226 Fit side-chains REVERT: A 67 GLN cc_start: 0.8529 (pt0) cc_final: 0.8066 (mt0) REVERT: A 162 GLU cc_start: 0.7522 (pm20) cc_final: 0.7121 (pm20) REVERT: A 259 ARG cc_start: 0.8305 (tpt-90) cc_final: 0.7723 (tpt-90) REVERT: B 67 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: B 149 GLU cc_start: 0.8932 (pt0) cc_final: 0.8686 (pt0) REVERT: B 259 ARG cc_start: 0.8168 (tpt-90) cc_final: 0.7564 (tpt-90) REVERT: C 184 ASN cc_start: 0.7702 (t0) cc_final: 0.7330 (m-40) REVERT: C 259 ARG cc_start: 0.8224 (tpt-90) cc_final: 0.7560 (tpt-90) REVERT: D 64 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8698 (tt0) REVERT: D 67 GLN cc_start: 0.8392 (pt0) cc_final: 0.7971 (mt0) REVERT: D 263 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7477 (mt-10) REVERT: E 67 GLN cc_start: 0.8582 (pt0) cc_final: 0.8035 (mt0) REVERT: E 184 ASN cc_start: 0.7672 (t0) cc_final: 0.7414 (m-40) outliers start: 28 outliers final: 16 residues processed: 171 average time/residue: 1.5891 time to fit residues: 289.2699 Evaluate side-chains 163 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 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 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 258 LEU 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 39 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN C 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.092296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.080022 restraints weight = 12962.955| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 1.00 r_work: 0.2659 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 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 = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 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 : 0.004 0.069 11762 Z= 0.190 Angle : 0.682 12.058 15896 Z= 0.328 Chirality : 0.042 0.235 1735 Planarity : 0.005 0.030 1905 Dihedral : 13.182 74.047 2222 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.52 % Allowed : 8.43 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.22), residues: 1335 helix: 2.27 (0.15), residues: 1035 sheet: 0.71 (0.79), residues: 50 loop : 1.11 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 128 HIS 0.002 0.001 HIS B 20 PHE 0.016 0.002 PHE B 7 TYR 0.017 0.002 TYR E 238 ARG 0.002 0.000 ARG D 98 Details of bonding type rmsd hydrogen bonds : bond 0.06596 ( 840) hydrogen bonds : angle 3.94822 ( 2475) covalent geometry : bond 0.00436 (11762) covalent geometry : angle 0.68164 (15896) *********************** 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 186 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 1.544 Fit side-chains REVERT: A 67 GLN cc_start: 0.8507 (pt0) cc_final: 0.7936 (mt0) REVERT: A 162 GLU cc_start: 0.7439 (pm20) cc_final: 0.7018 (pm20) REVERT: A 184 ASN cc_start: 0.7809 (t0) cc_final: 0.7341 (m-40) REVERT: A 259 ARG cc_start: 0.8250 (tpt-90) cc_final: 0.7852 (tpt-90) REVERT: B 67 GLN cc_start: 0.8432 (pt0) cc_final: 0.7847 (mt0) REVERT: B 259 ARG cc_start: 0.8177 (tpt-90) cc_final: 0.7550 (tpt-90) REVERT: C 184 ASN cc_start: 0.7722 (t0) cc_final: 0.7277 (m-40) REVERT: C 259 ARG cc_start: 0.8195 (tpt-90) cc_final: 0.7538 (tpt-90) REVERT: D 67 GLN cc_start: 0.8442 (pt0) cc_final: 0.7893 (mt0) REVERT: D 184 ASN cc_start: 0.7601 (t0) cc_final: 0.7203 (m-40) REVERT: D 259 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7716 (tpt-90) REVERT: D 263 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7539 (mt-10) REVERT: E 67 GLN cc_start: 0.8626 (pt0) cc_final: 0.7966 (mt0) REVERT: E 184 ASN cc_start: 0.7678 (t0) cc_final: 0.7356 (m-40) REVERT: E 259 ARG cc_start: 0.8182 (tpt90) cc_final: 0.7642 (tpt-90) outliers start: 38 outliers final: 20 residues processed: 179 average time/residue: 1.8542 time to fit residues: 354.0855 Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 208 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 97 TYR 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 D residue 258 LEU 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 58 optimal weight: 0.9990 chunk 73 optimal weight: 0.0770 chunk 123 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.0020 chunk 19 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 42 optimal weight: 0.0980 overall best weight: 0.3948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.086362 restraints weight = 12887.181| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.00 r_work: 0.2764 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11762 Z= 0.121 Angle : 0.553 11.053 15896 Z= 0.270 Chirality : 0.038 0.168 1735 Planarity : 0.004 0.033 1905 Dihedral : 11.134 72.778 2217 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.87 % Allowed : 9.81 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.21), residues: 1335 helix: 2.76 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.41 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 13 HIS 0.003 0.001 HIS C 20 PHE 0.013 0.001 PHE C 12 TYR 0.013 0.001 TYR A 219 ARG 0.001 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 840) hydrogen bonds : angle 3.78762 ( 2475) covalent geometry : bond 0.00245 (11762) covalent geometry : angle 0.55301 (15896) *********************** 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 184 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.198 Fit side-chains REVERT: A 67 GLN cc_start: 0.8404 (pt0) cc_final: 0.7874 (mt0) REVERT: A 162 GLU cc_start: 0.7269 (pm20) cc_final: 0.6885 (pm20) REVERT: A 184 ASN cc_start: 0.7790 (t0) cc_final: 0.7270 (m-40) REVERT: A 259 ARG cc_start: 0.8206 (tpt-90) cc_final: 0.7680 (tpt-90) REVERT: B 67 GLN cc_start: 0.8428 (pt0) cc_final: 0.7791 (mt0) REVERT: B 184 ASN cc_start: 0.7764 (t0) cc_final: 0.7314 (m-40) REVERT: B 259 ARG cc_start: 0.8150 (tpt-90) cc_final: 0.7523 (tpt-90) REVERT: C 64 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: C 70 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8570 (tp) REVERT: C 184 ASN cc_start: 0.7653 (t0) cc_final: 0.7152 (m-40) REVERT: C 259 ARG cc_start: 0.8142 (tpt-90) cc_final: 0.7486 (tpt-90) REVERT: D 67 GLN cc_start: 0.8381 (pt0) cc_final: 0.7766 (mt0) REVERT: D 70 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8602 (tp) REVERT: D 162 GLU cc_start: 0.7518 (pm20) cc_final: 0.7088 (pm20) REVERT: D 184 ASN cc_start: 0.7572 (t0) cc_final: 0.7103 (m-40) REVERT: D 259 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7682 (tpt-90) REVERT: D 263 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7415 (mt-10) REVERT: E 64 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8387 (pt0) REVERT: E 67 GLN cc_start: 0.8541 (pt0) cc_final: 0.7794 (mt0) REVERT: E 184 ASN cc_start: 0.7579 (t0) cc_final: 0.7185 (m-40) REVERT: E 259 ARG cc_start: 0.8176 (tpt90) cc_final: 0.7671 (tpt-90) outliers start: 31 outliers final: 16 residues processed: 176 average time/residue: 1.6402 time to fit residues: 307.0165 Evaluate side-chains 166 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 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 70 LEU 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 64 GLU Chi-restraints excluded: chain E residue 70 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 127 optimal weight: 0.3980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.094002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.081825 restraints weight = 12905.638| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 0.99 r_work: 0.2689 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2010 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= 0.174 Angle : 0.613 11.657 15896 Z= 0.301 Chirality : 0.041 0.218 1735 Planarity : 0.004 0.034 1905 Dihedral : 11.668 71.592 2214 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 3.06 % Allowed : 10.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.21), residues: 1335 helix: 2.61 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.31 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 128 HIS 0.002 0.001 HIS B 20 PHE 0.014 0.002 PHE B 7 TYR 0.013 0.002 TYR B 97 ARG 0.002 0.000 ARG A 234 Details of bonding type rmsd hydrogen bonds : bond 0.06026 ( 840) hydrogen bonds : angle 3.83132 ( 2475) covalent geometry : bond 0.00399 (11762) covalent geometry : angle 0.61332 (15896) *********************** 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: 33 poor density : 145 time to evaluate : 1.215 Fit side-chains REVERT: A 67 GLN cc_start: 0.8389 (pt0) cc_final: 0.7863 (mt0) REVERT: A 162 GLU cc_start: 0.7348 (pm20) cc_final: 0.7056 (pm20) REVERT: A 184 ASN cc_start: 0.7860 (t0) cc_final: 0.7334 (m-40) REVERT: A 200 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7877 (mtt180) REVERT: A 259 ARG cc_start: 0.8208 (tpt-90) cc_final: 0.7880 (tpt-90) REVERT: B 67 GLN cc_start: 0.8459 (pt0) cc_final: 0.7843 (mt0) REVERT: B 259 ARG cc_start: 0.8164 (tpt-90) cc_final: 0.7551 (tpt-90) REVERT: C 64 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: C 184 ASN cc_start: 0.7716 (t0) cc_final: 0.7239 (m-40) REVERT: C 259 ARG cc_start: 0.8249 (tpt-90) cc_final: 0.7622 (tpt-90) REVERT: D 67 GLN cc_start: 0.8397 (pt0) cc_final: 0.7798 (mt0) REVERT: D 70 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8674 (tp) REVERT: D 162 GLU cc_start: 0.7634 (pm20) cc_final: 0.7220 (pm20) REVERT: D 184 ASN cc_start: 0.7640 (t0) cc_final: 0.7225 (m-40) REVERT: D 259 ARG cc_start: 0.8278 (tpp80) cc_final: 0.7885 (tpt90) REVERT: D 263 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7539 (mt-10) REVERT: E 67 GLN cc_start: 0.8641 (pt0) cc_final: 0.7948 (mt0) REVERT: E 184 ASN cc_start: 0.7689 (t0) cc_final: 0.7291 (m-40) REVERT: E 259 ARG cc_start: 0.8179 (tpt90) cc_final: 0.7641 (tpt-90) outliers start: 33 outliers final: 22 residues processed: 173 average time/residue: 1.8170 time to fit residues: 333.1189 Evaluate side-chains 171 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 A residue 247 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL 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 97 TYR 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 D residue 258 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 78 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.2945 r_free = 0.2945 target = 0.092964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.080961 restraints weight = 13051.194| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 0.96 r_work: 0.2675 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 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 = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11762 Z= 0.190 Angle : 0.636 11.831 15896 Z= 0.312 Chirality : 0.043 0.222 1735 Planarity : 0.005 0.035 1905 Dihedral : 11.982 72.110 2211 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 3.33 % Allowed : 10.46 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.21), residues: 1335 helix: 2.49 (0.15), residues: 1020 sheet: 1.06 (0.77), residues: 50 loop : 1.11 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 13 HIS 0.002 0.001 HIS B 20 PHE 0.016 0.002 PHE B 7 TYR 0.016 0.002 TYR B 97 ARG 0.002 0.000 ARG C 125 Details of bonding type rmsd hydrogen bonds : bond 0.06399 ( 840) hydrogen bonds : angle 3.87078 ( 2475) covalent geometry : bond 0.00439 (11762) covalent geometry : angle 0.63591 (15896) *********************** 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 184 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 1.125 Fit side-chains REVERT: A 67 GLN cc_start: 0.8499 (pt0) cc_final: 0.7936 (mt0) REVERT: A 162 GLU cc_start: 0.7403 (pm20) cc_final: 0.7143 (pm20) REVERT: A 184 ASN cc_start: 0.7921 (t0) cc_final: 0.7462 (m-40) REVERT: A 200 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7959 (mtt180) REVERT: A 259 ARG cc_start: 0.8299 (tpt-90) cc_final: 0.7966 (tpt-90) REVERT: B 67 GLN cc_start: 0.8492 (pt0) cc_final: 0.7910 (mt0) REVERT: B 259 ARG cc_start: 0.8257 (tpt-90) cc_final: 0.7621 (tpt-90) REVERT: C 64 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: C 184 ASN cc_start: 0.7750 (t0) cc_final: 0.7341 (m-40) REVERT: C 259 ARG cc_start: 0.8300 (tpt-90) cc_final: 0.7690 (tpt-90) REVERT: D 67 GLN cc_start: 0.8456 (pt0) cc_final: 0.7902 (mt0) REVERT: D 70 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8727 (tp) REVERT: D 184 ASN cc_start: 0.7649 (t0) cc_final: 0.7320 (m-40) REVERT: D 259 ARG cc_start: 0.8340 (tpp80) cc_final: 0.7970 (tpt90) REVERT: D 263 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7677 (mt-10) REVERT: E 67 GLN cc_start: 0.8662 (pt0) cc_final: 0.8022 (mt0) REVERT: E 184 ASN cc_start: 0.7741 (t0) cc_final: 0.7409 (m-40) REVERT: E 259 ARG cc_start: 0.8255 (tpt90) cc_final: 0.7732 (tpt-90) outliers start: 36 outliers final: 22 residues processed: 177 average time/residue: 1.6484 time to fit residues: 309.8069 Evaluate side-chains 170 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 122 THR Chi-restraints excluded: chain B residue 152 VAL 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 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 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 D residue 258 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 130 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 101 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.095206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.083232 restraints weight = 13011.671| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 0.97 r_work: 0.2712 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2135 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= 0.147 Angle : 0.588 11.281 15896 Z= 0.288 Chirality : 0.039 0.188 1735 Planarity : 0.004 0.036 1905 Dihedral : 11.535 69.363 2211 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.24 % Allowed : 10.65 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.21), residues: 1335 helix: 2.64 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.27 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 13 HIS 0.002 0.001 HIS C 20 PHE 0.014 0.002 PHE C 12 TYR 0.014 0.001 TYR B 97 ARG 0.001 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.05640 ( 840) hydrogen bonds : angle 3.79514 ( 2475) covalent geometry : bond 0.00324 (11762) covalent geometry : angle 0.58777 (15896) *********************** 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 177 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 1.146 Fit side-chains REVERT: A 67 GLN cc_start: 0.8441 (pt0) cc_final: 0.7969 (mt0) REVERT: A 162 GLU cc_start: 0.7340 (pm20) cc_final: 0.7049 (pm20) REVERT: A 184 ASN cc_start: 0.7902 (t0) cc_final: 0.7407 (m-40) REVERT: A 200 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7850 (mtt180) REVERT: A 259 ARG cc_start: 0.8251 (tpt-90) cc_final: 0.7863 (tpt-90) REVERT: B 67 GLN cc_start: 0.8480 (pt0) cc_final: 0.7878 (mt0) REVERT: B 259 ARG cc_start: 0.8238 (tpt-90) cc_final: 0.7599 (tpt-90) REVERT: C 64 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: C 184 ASN cc_start: 0.7725 (t0) cc_final: 0.7285 (m-40) REVERT: C 200 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7711 (mtt180) REVERT: C 259 ARG cc_start: 0.8299 (tpt-90) cc_final: 0.7712 (tpt-90) REVERT: D 67 GLN cc_start: 0.8411 (pt0) cc_final: 0.7844 (mt0) REVERT: D 184 ASN cc_start: 0.7644 (t0) cc_final: 0.7282 (m-40) REVERT: D 259 ARG cc_start: 0.8316 (tpp80) cc_final: 0.7929 (tpt90) REVERT: D 263 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7672 (mt-10) REVERT: E 67 GLN cc_start: 0.8633 (pt0) cc_final: 0.7972 (mt0) REVERT: E 184 ASN cc_start: 0.7704 (t0) cc_final: 0.7340 (m-40) REVERT: E 259 ARG cc_start: 0.8211 (tpt90) cc_final: 0.7708 (tpt-90) outliers start: 35 outliers final: 21 residues processed: 170 average time/residue: 1.7157 time to fit residues: 309.1070 Evaluate side-chains 167 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 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 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 200 ARG 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 D residue 258 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 41 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 0.0040 chunk 129 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.098895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.086825 restraints weight = 12968.374| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 0.99 r_work: 0.2771 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11762 Z= 0.120 Angle : 0.553 10.779 15896 Z= 0.268 Chirality : 0.037 0.167 1735 Planarity : 0.004 0.035 1905 Dihedral : 10.675 68.008 2209 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.22 % Allowed : 11.57 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.21), residues: 1335 helix: 2.85 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.28 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 13 HIS 0.002 0.001 HIS C 20 PHE 0.012 0.001 PHE C 12 TYR 0.013 0.001 TYR A 219 ARG 0.001 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.04816 ( 840) hydrogen bonds : angle 3.69534 ( 2475) covalent geometry : bond 0.00244 (11762) covalent geometry : angle 0.55317 (15896) *********************** 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 174 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.254 Fit side-chains REVERT: A 67 GLN cc_start: 0.8436 (pt0) cc_final: 0.7894 (mt0) REVERT: A 70 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8473 (tp) REVERT: A 162 GLU cc_start: 0.7238 (pm20) cc_final: 0.6901 (pm20) REVERT: A 184 ASN cc_start: 0.7911 (t0) cc_final: 0.7340 (m-40) REVERT: A 200 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7837 (mtt180) REVERT: A 259 ARG cc_start: 0.8180 (tpt-90) cc_final: 0.7727 (tpt-90) REVERT: B 67 GLN cc_start: 0.8468 (pt0) cc_final: 0.7814 (mt0) REVERT: B 184 ASN cc_start: 0.7785 (t0) cc_final: 0.7337 (m-40) REVERT: B 259 ARG cc_start: 0.8194 (tpt-90) cc_final: 0.7564 (tpt-90) REVERT: C 64 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: C 184 ASN cc_start: 0.7686 (t0) cc_final: 0.7172 (m-40) REVERT: C 200 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7681 (mtt180) REVERT: C 259 ARG cc_start: 0.8237 (tpt-90) cc_final: 0.7671 (tpt-90) REVERT: D 67 GLN cc_start: 0.8398 (pt0) cc_final: 0.7790 (mt0) REVERT: D 162 GLU cc_start: 0.7485 (pm20) cc_final: 0.7088 (pm20) REVERT: D 184 ASN cc_start: 0.7644 (t0) cc_final: 0.7194 (m-40) REVERT: D 259 ARG cc_start: 0.8282 (tpp80) cc_final: 0.7693 (tpt-90) REVERT: D 263 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7418 (mt-10) REVERT: E 64 GLU cc_start: 0.8690 (tt0) cc_final: 0.8453 (pt0) REVERT: E 67 GLN cc_start: 0.8557 (pt0) cc_final: 0.7813 (mt0) REVERT: E 70 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8563 (tp) REVERT: E 184 ASN cc_start: 0.7653 (t0) cc_final: 0.7225 (m-40) REVERT: E 259 ARG cc_start: 0.8229 (tpt90) cc_final: 0.7752 (tpt-90) outliers start: 24 outliers final: 12 residues processed: 169 average time/residue: 1.6533 time to fit residues: 296.6637 Evaluate side-chains 161 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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 200 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 0.0050 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.097225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.085042 restraints weight = 12976.970| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 0.99 r_work: 0.2742 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2309 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= 0.135 Angle : 0.575 11.050 15896 Z= 0.279 Chirality : 0.039 0.171 1735 Planarity : 0.004 0.034 1905 Dihedral : 10.753 69.896 2206 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.04 % Allowed : 12.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.68 (0.21), residues: 1335 helix: 2.81 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.24 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 13 HIS 0.002 0.001 HIS C 20 PHE 0.012 0.001 PHE A 164 TYR 0.010 0.001 TYR B 97 ARG 0.001 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.05231 ( 840) hydrogen bonds : angle 3.70542 ( 2475) covalent geometry : bond 0.00289 (11762) covalent geometry : angle 0.57500 (15896) *********************** 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 164 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.205 Fit side-chains REVERT: A 67 GLN cc_start: 0.8422 (pt0) cc_final: 0.7863 (mt0) REVERT: A 70 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8476 (tp) REVERT: A 162 GLU cc_start: 0.7236 (pm20) cc_final: 0.6906 (pm20) REVERT: A 184 ASN cc_start: 0.7920 (t0) cc_final: 0.7339 (m-40) REVERT: A 200 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7848 (mtt180) REVERT: A 259 ARG cc_start: 0.8189 (tpt-90) cc_final: 0.7736 (tpt-90) REVERT: B 67 GLN cc_start: 0.8468 (pt0) cc_final: 0.7776 (mt0) REVERT: B 184 ASN cc_start: 0.7789 (t0) cc_final: 0.7345 (m-40) REVERT: B 259 ARG cc_start: 0.8209 (tpt-90) cc_final: 0.7575 (tpt-90) REVERT: C 64 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: C 184 ASN cc_start: 0.7689 (t0) cc_final: 0.7178 (m-40) REVERT: C 200 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7707 (mtt180) REVERT: C 259 ARG cc_start: 0.8264 (tpt-90) cc_final: 0.7660 (tpt-90) REVERT: D 67 GLN cc_start: 0.8403 (pt0) cc_final: 0.7784 (mt0) REVERT: D 162 GLU cc_start: 0.7499 (pm20) cc_final: 0.7086 (pm20) REVERT: D 184 ASN cc_start: 0.7667 (t0) cc_final: 0.7208 (m-40) REVERT: D 259 ARG cc_start: 0.8286 (tpp80) cc_final: 0.7677 (tpt-90) REVERT: D 263 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7442 (mt-10) REVERT: E 64 GLU cc_start: 0.8734 (tt0) cc_final: 0.8515 (pt0) REVERT: E 67 GLN cc_start: 0.8567 (pt0) cc_final: 0.7827 (mt0) REVERT: E 70 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8587 (tp) REVERT: E 184 ASN cc_start: 0.7706 (t0) cc_final: 0.7269 (m-40) REVERT: E 259 ARG cc_start: 0.8160 (tpt90) cc_final: 0.7673 (tpt-90) outliers start: 22 outliers final: 13 residues processed: 161 average time/residue: 1.8022 time to fit residues: 306.7535 Evaluate side-chains 160 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 200 ARG 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 3 SER 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 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 chunk 80 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3015 r_free = 0.3015 target = 0.097892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.085988 restraints weight = 12941.391| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 0.95 r_work: 0.2759 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11762 Z= 0.128 Angle : 0.565 10.873 15896 Z= 0.274 Chirality : 0.038 0.166 1735 Planarity : 0.004 0.034 1905 Dihedral : 10.617 69.822 2206 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.67 % Allowed : 12.69 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.21), residues: 1335 helix: 2.85 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.20 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 13 HIS 0.002 0.001 HIS C 20 PHE 0.012 0.001 PHE C 12 TYR 0.010 0.001 TYR A 219 ARG 0.001 0.000 ARG C 125 Details of bonding type rmsd hydrogen bonds : bond 0.05084 ( 840) hydrogen bonds : angle 3.68623 ( 2475) covalent geometry : bond 0.00269 (11762) covalent geometry : angle 0.56539 (15896) ********************** 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 161 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 2.161 Fit side-chains REVERT: A 67 GLN cc_start: 0.8405 (pt0) cc_final: 0.7859 (mt0) REVERT: A 70 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8496 (tp) REVERT: A 162 GLU cc_start: 0.7231 (pm20) cc_final: 0.6903 (pm20) REVERT: A 184 ASN cc_start: 0.7877 (t0) cc_final: 0.7331 (m-40) REVERT: A 200 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7868 (mtt180) REVERT: A 259 ARG cc_start: 0.8204 (tpt-90) cc_final: 0.7764 (tpt-90) REVERT: B 67 GLN cc_start: 0.8486 (pt0) cc_final: 0.7848 (mt0) REVERT: B 184 ASN cc_start: 0.7805 (t0) cc_final: 0.7381 (m-40) REVERT: B 259 ARG cc_start: 0.8222 (tpt-90) cc_final: 0.7609 (tpt-90) REVERT: C 64 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: C 184 ASN cc_start: 0.7693 (t0) cc_final: 0.7223 (m-40) REVERT: C 200 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7706 (mtt180) REVERT: C 259 ARG cc_start: 0.8278 (tpt-90) cc_final: 0.7698 (tpt-90) REVERT: D 67 GLN cc_start: 0.8402 (pt0) cc_final: 0.7809 (mt0) REVERT: D 162 GLU cc_start: 0.7511 (pm20) cc_final: 0.7112 (pm20) REVERT: D 184 ASN cc_start: 0.7680 (t0) cc_final: 0.7240 (m-40) REVERT: D 259 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7718 (tpt-90) REVERT: D 263 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7384 (mt-10) REVERT: E 67 GLN cc_start: 0.8573 (pt0) cc_final: 0.7853 (mt0) REVERT: E 70 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8595 (tp) REVERT: E 184 ASN cc_start: 0.7709 (t0) cc_final: 0.7303 (m-40) REVERT: E 259 ARG cc_start: 0.8214 (tpt90) cc_final: 0.7748 (tpt-90) outliers start: 18 outliers final: 11 residues processed: 158 average time/residue: 2.7908 time to fit residues: 466.3956 Evaluate side-chains 152 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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 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 200 ARG 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 57 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3049 r_free = 0.3049 target = 0.099305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.087854 restraints weight = 12689.332| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 0.94 r_work: 0.2798 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11762 Z= 0.122 Angle : 0.558 10.732 15896 Z= 0.270 Chirality : 0.038 0.159 1735 Planarity : 0.004 0.034 1905 Dihedral : 10.424 69.755 2206 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.76 % Allowed : 12.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.21), residues: 1335 helix: 2.90 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.18 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 13 HIS 0.002 0.001 HIS C 20 PHE 0.012 0.001 PHE C 12 TYR 0.011 0.001 TYR C 219 ARG 0.001 0.000 ARG C 125 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 840) hydrogen bonds : angle 3.65797 ( 2475) covalent geometry : bond 0.00253 (11762) covalent geometry : angle 0.55813 (15896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9545.59 seconds wall clock time: 170 minutes 33.27 seconds (10233.27 seconds total)