Starting phenix.real_space_refine on Sun Aug 4 21:20:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qr0_18610/08_2024/8qr0_18610.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qr0_18610/08_2024/8qr0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qr0_18610/08_2024/8qr0_18610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qr0_18610/08_2024/8qr0_18610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qr0_18610/08_2024/8qr0_18610.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qr0_18610/08_2024/8qr0_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 Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 7.28, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 7.45 Conformation dependent library (CDL) restraints added in 2.2 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: 1.11 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: 3.75 Time building geometry restraints manager: 7.66 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: 95.03 - 102.91: 165 102.91 - 110.79: 3569 110.79 - 118.67: 5669 118.67 - 126.55: 6267 126.55 - 134.43: 226 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: 5.010 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 39.100 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 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:16.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.510 ------------------------------------------------------------------------------- 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= 0.927 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 *********************** 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 fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 1.446 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: 1.7132 time to fit residues: 384.0267 Evaluate side-chains 167 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 1.220 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 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= 0.209 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 *********************** 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 fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.226 Fit side-chains REVERT: A 67 GLN cc_start: 0.8830 (pt0) cc_final: 0.8357 (mt0) REVERT: A 162 GLU cc_start: 0.7743 (pm20) cc_final: 0.7425 (pm20) REVERT: A 259 ARG cc_start: 0.8640 (tpt-90) cc_final: 0.8195 (tpt-90) REVERT: B 67 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: B 149 GLU cc_start: 0.9161 (pt0) cc_final: 0.8864 (pt0) REVERT: B 259 ARG cc_start: 0.8568 (tpt-90) cc_final: 0.8074 (tpt-90) REVERT: C 67 GLN cc_start: 0.8353 (mt0) cc_final: 0.8121 (mm110) REVERT: C 184 ASN cc_start: 0.8004 (t0) cc_final: 0.7457 (m-40) REVERT: C 259 ARG cc_start: 0.8584 (tpt-90) cc_final: 0.8057 (tpt-90) REVERT: D 67 GLN cc_start: 0.8712 (pt0) cc_final: 0.8285 (mt0) REVERT: D 263 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7954 (mt-10) REVERT: E 67 GLN cc_start: 0.8879 (pt0) cc_final: 0.8370 (mt0) REVERT: E 184 ASN cc_start: 0.8019 (t0) cc_final: 0.7541 (m-40) outliers start: 28 outliers final: 16 residues processed: 171 average time/residue: 1.6396 time to fit residues: 299.2205 Evaluate side-chains 162 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 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 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11762 Z= 0.254 Angle : 0.667 11.859 15896 Z= 0.321 Chirality : 0.042 0.219 1735 Planarity : 0.004 0.029 1905 Dihedral : 13.119 75.240 2222 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.43 % Allowed : 8.61 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.22), residues: 1335 helix: 2.37 (0.15), residues: 1020 sheet: 0.68 (0.79), residues: 50 loop : 1.07 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 128 HIS 0.002 0.001 HIS B 20 PHE 0.016 0.002 PHE C 12 TYR 0.016 0.002 TYR C 238 ARG 0.002 0.000 ARG A 92 *********************** 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 184 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 1.217 Fit side-chains REVERT: A 67 GLN cc_start: 0.8796 (pt0) cc_final: 0.8246 (mt0) REVERT: A 162 GLU cc_start: 0.7663 (pm20) cc_final: 0.7313 (pm20) REVERT: A 184 ASN cc_start: 0.8077 (t0) cc_final: 0.7495 (m-40) REVERT: A 259 ARG cc_start: 0.8625 (tpt-90) cc_final: 0.8334 (tpt-90) REVERT: B 67 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8192 (mt0) REVERT: B 259 ARG cc_start: 0.8582 (tpt-90) cc_final: 0.8120 (tpt-90) REVERT: C 67 GLN cc_start: 0.8432 (mt0) cc_final: 0.8167 (mm110) REVERT: C 184 ASN cc_start: 0.8025 (t0) cc_final: 0.7438 (m-40) REVERT: C 259 ARG cc_start: 0.8582 (tpt-90) cc_final: 0.8041 (tpt-90) REVERT: D 67 GLN cc_start: 0.8756 (pt0) cc_final: 0.8244 (mt0) REVERT: D 184 ASN cc_start: 0.7923 (t0) cc_final: 0.7405 (m-40) REVERT: D 259 ARG cc_start: 0.8621 (tpp80) cc_final: 0.8175 (tpt-90) REVERT: D 263 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7948 (mt-10) REVERT: E 67 GLN cc_start: 0.8928 (pt0) cc_final: 0.8359 (mt0) REVERT: E 184 ASN cc_start: 0.8026 (t0) cc_final: 0.7513 (m-40) REVERT: E 259 ARG cc_start: 0.8605 (tpt90) cc_final: 0.8174 (tpt-90) outliers start: 37 outliers final: 19 residues processed: 176 average time/residue: 1.5496 time to fit residues: 290.5457 Evaluate side-chains 166 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 67 GLN 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 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 97 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 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 121 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11762 Z= 0.201 Angle : 0.593 11.376 15896 Z= 0.290 Chirality : 0.039 0.194 1735 Planarity : 0.004 0.032 1905 Dihedral : 11.711 75.580 2218 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.52 % Allowed : 9.44 % Favored : 87.04 % 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: 3.42 (0.21), residues: 1335 helix: 2.58 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.31 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 13 HIS 0.003 0.001 HIS B 20 PHE 0.014 0.002 PHE C 12 TYR 0.012 0.002 TYR B 97 ARG 0.001 0.000 ARG C 125 *********************** 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 183 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 145 time to evaluate : 1.386 Fit side-chains REVERT: A 67 GLN cc_start: 0.8728 (pt0) cc_final: 0.8233 (mt0) REVERT: A 162 GLU cc_start: 0.7650 (pm20) cc_final: 0.7432 (pm20) REVERT: A 184 ASN cc_start: 0.8071 (t0) cc_final: 0.7471 (m-40) REVERT: A 259 ARG cc_start: 0.8620 (tpt-90) cc_final: 0.8358 (tpt-90) REVERT: B 67 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: B 259 ARG cc_start: 0.8561 (tpt-90) cc_final: 0.8059 (tpt-90) REVERT: C 64 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: C 67 GLN cc_start: 0.8389 (mt0) cc_final: 0.8129 (mm-40) REVERT: C 184 ASN cc_start: 0.8033 (t0) cc_final: 0.7429 (m-40) REVERT: C 259 ARG cc_start: 0.8611 (tpt-90) cc_final: 0.8138 (tpt-90) REVERT: D 67 GLN cc_start: 0.8755 (pt0) cc_final: 0.8197 (mt0) REVERT: D 162 GLU cc_start: 0.7817 (pm20) cc_final: 0.7468 (pm20) REVERT: D 184 ASN cc_start: 0.7937 (t0) cc_final: 0.7410 (m-40) REVERT: D 259 ARG cc_start: 0.8609 (tpp80) cc_final: 0.8146 (tpt-90) REVERT: D 263 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7926 (mt-10) REVERT: E 67 GLN cc_start: 0.8949 (pt0) cc_final: 0.8342 (mt0) REVERT: E 184 ASN cc_start: 0.8044 (t0) cc_final: 0.7494 (m-40) REVERT: E 259 ARG cc_start: 0.8577 (tpt90) cc_final: 0.8158 (tpt-90) outliers start: 38 outliers final: 23 residues processed: 173 average time/residue: 1.5653 time to fit residues: 288.3337 Evaluate side-chains 167 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 67 GLN 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 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 D residue 247 LEU 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 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 108 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11762 Z= 0.218 Angle : 0.598 11.502 15896 Z= 0.292 Chirality : 0.040 0.190 1735 Planarity : 0.004 0.033 1905 Dihedral : 11.655 71.010 2218 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.33 % Allowed : 10.00 % Favored : 86.67 % 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: 3.43 (0.21), residues: 1335 helix: 2.59 (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 0.010 0.001 TRP C 13 HIS 0.002 0.001 HIS C 20 PHE 0.014 0.002 PHE C 12 TYR 0.012 0.002 TYR B 97 ARG 0.001 0.000 ARG C 125 *********************** 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 176 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 140 time to evaluate : 1.182 Fit side-chains REVERT: A 67 GLN cc_start: 0.8731 (pt0) cc_final: 0.8229 (mt0) REVERT: A 162 GLU cc_start: 0.7641 (pm20) cc_final: 0.7425 (pm20) REVERT: A 184 ASN cc_start: 0.8095 (t0) cc_final: 0.7484 (m-40) REVERT: A 200 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8261 (mtt180) REVERT: B 67 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8176 (mt0) REVERT: B 259 ARG cc_start: 0.8588 (tpt-90) cc_final: 0.8070 (tpt-90) REVERT: C 64 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: C 67 GLN cc_start: 0.8400 (mt0) cc_final: 0.8136 (mm-40) REVERT: C 184 ASN cc_start: 0.8043 (t0) cc_final: 0.7423 (m-40) REVERT: C 259 ARG cc_start: 0.8606 (tpt-90) cc_final: 0.8127 (tpt-90) REVERT: D 67 GLN cc_start: 0.8736 (pt0) cc_final: 0.8178 (mt0) REVERT: D 162 GLU cc_start: 0.7817 (pm20) cc_final: 0.7454 (pm20) REVERT: D 184 ASN cc_start: 0.7955 (t0) cc_final: 0.7418 (m-40) REVERT: D 259 ARG cc_start: 0.8612 (tpp80) cc_final: 0.8343 (tpt90) REVERT: D 263 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7937 (mt-10) REVERT: E 67 GLN cc_start: 0.8959 (pt0) cc_final: 0.8348 (mt0) REVERT: E 184 ASN cc_start: 0.8061 (t0) cc_final: 0.7505 (m-40) REVERT: E 259 ARG cc_start: 0.8566 (tpt90) cc_final: 0.8146 (tpt-90) outliers start: 36 outliers final: 24 residues processed: 168 average time/residue: 1.6247 time to fit residues: 290.1396 Evaluate side-chains 170 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 67 GLN 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 97 TYR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 247 LEU 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 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 43 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 10 optimal weight: 0.0040 chunk 68 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11762 Z= 0.185 Angle : 0.572 11.043 15896 Z= 0.279 Chirality : 0.039 0.174 1735 Planarity : 0.004 0.034 1905 Dihedral : 11.256 69.892 2216 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.69 % Allowed : 10.93 % 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: 3.58 (0.21), residues: 1335 helix: 2.70 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.34 (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 B 20 PHE 0.013 0.001 PHE C 12 TYR 0.010 0.001 TYR A 219 ARG 0.001 0.000 ARG A 92 *********************** 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 174 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 1.234 Fit side-chains REVERT: A 67 GLN cc_start: 0.8778 (pt0) cc_final: 0.8279 (mt0) REVERT: A 162 GLU cc_start: 0.7637 (pm20) cc_final: 0.7394 (pm20) REVERT: A 184 ASN cc_start: 0.8112 (t0) cc_final: 0.7483 (m-40) REVERT: A 200 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8227 (mtt180) REVERT: B 67 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: B 259 ARG cc_start: 0.8592 (tpt-90) cc_final: 0.8072 (tpt-90) REVERT: C 64 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: C 67 GLN cc_start: 0.8409 (mt0) cc_final: 0.8144 (mm-40) REVERT: C 184 ASN cc_start: 0.8041 (t0) cc_final: 0.7410 (m-40) REVERT: C 259 ARG cc_start: 0.8628 (tpt-90) cc_final: 0.8169 (tpt-90) REVERT: D 67 GLN cc_start: 0.8737 (pt0) cc_final: 0.8168 (mt0) REVERT: D 162 GLU cc_start: 0.7778 (pm20) cc_final: 0.7421 (pm20) REVERT: D 184 ASN cc_start: 0.7971 (t0) cc_final: 0.7431 (m-40) REVERT: D 259 ARG cc_start: 0.8597 (tpp80) cc_final: 0.8129 (tpt-90) REVERT: D 263 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7902 (mt-10) REVERT: E 67 GLN cc_start: 0.8904 (pt0) cc_final: 0.8275 (mt0) REVERT: E 184 ASN cc_start: 0.8019 (t0) cc_final: 0.7440 (m-40) REVERT: E 259 ARG cc_start: 0.8554 (tpt90) cc_final: 0.8157 (tpt-90) outliers start: 29 outliers final: 16 residues processed: 166 average time/residue: 1.7221 time to fit residues: 304.9662 Evaluate side-chains 164 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 67 GLN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 258 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 73 optimal weight: 0.0370 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 80 optimal weight: 0.4980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11762 Z= 0.166 Angle : 0.557 10.772 15896 Z= 0.271 Chirality : 0.038 0.162 1735 Planarity : 0.004 0.034 1905 Dihedral : 10.804 68.700 2209 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.50 % Allowed : 11.48 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.80 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.35 (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 B 20 PHE 0.012 0.001 PHE C 12 TYR 0.011 0.001 TYR A 219 ARG 0.005 0.000 ARG A 259 *********************** 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 176 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.546 Fit side-chains REVERT: A 67 GLN cc_start: 0.8761 (pt0) cc_final: 0.8229 (mt0) REVERT: A 70 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8524 (tp) REVERT: A 162 GLU cc_start: 0.7572 (pm20) cc_final: 0.7340 (pm20) REVERT: A 184 ASN cc_start: 0.8120 (t0) cc_final: 0.7454 (m-40) REVERT: A 200 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8231 (mtt180) REVERT: B 67 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: B 184 ASN cc_start: 0.8082 (t0) cc_final: 0.7494 (m-40) REVERT: B 259 ARG cc_start: 0.8610 (tpt-90) cc_final: 0.8088 (tpt-90) REVERT: C 64 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: C 67 GLN cc_start: 0.8390 (mt0) cc_final: 0.8127 (mm-40) REVERT: C 184 ASN cc_start: 0.8042 (t0) cc_final: 0.7396 (m-40) REVERT: C 259 ARG cc_start: 0.8619 (tpt-90) cc_final: 0.8141 (tpt-90) REVERT: D 67 GLN cc_start: 0.8735 (pt0) cc_final: 0.8152 (mt0) REVERT: D 162 GLU cc_start: 0.7693 (pm20) cc_final: 0.7341 (pm20) REVERT: D 184 ASN cc_start: 0.7964 (t0) cc_final: 0.7414 (m-40) REVERT: D 259 ARG cc_start: 0.8605 (tpp80) cc_final: 0.8331 (tpt90) REVERT: D 263 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7882 (mt-10) REVERT: E 67 GLN cc_start: 0.8883 (pt0) cc_final: 0.8231 (mt0) REVERT: E 70 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8633 (tp) REVERT: E 149 GLU cc_start: 0.9064 (pt0) cc_final: 0.8803 (pt0) REVERT: E 184 ASN cc_start: 0.7991 (t0) cc_final: 0.7403 (m-40) REVERT: E 259 ARG cc_start: 0.8577 (tpt90) cc_final: 0.8201 (tpt-90) outliers start: 27 outliers final: 14 residues processed: 169 average time/residue: 1.6255 time to fit residues: 293.2589 Evaluate side-chains 160 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 A residue 258 LEU Chi-restraints excluded: chain B residue 67 GLN 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 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 152 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 258 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11762 Z= 0.243 Angle : 0.614 11.485 15896 Z= 0.300 Chirality : 0.041 0.190 1735 Planarity : 0.004 0.034 1905 Dihedral : 11.350 71.459 2209 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.50 % Allowed : 11.67 % 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: 3.50 (0.21), residues: 1335 helix: 2.64 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.33 (0.32), residues: 315 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 0.014 0.002 PHE B 7 TYR 0.015 0.002 TYR B 97 ARG 0.004 0.000 ARG A 259 *********************** 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 171 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.320 Fit side-chains REVERT: A 67 GLN cc_start: 0.8763 (pt0) cc_final: 0.8260 (mt0) REVERT: A 70 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8583 (tp) REVERT: A 162 GLU cc_start: 0.7585 (pm20) cc_final: 0.7245 (pm20) REVERT: A 184 ASN cc_start: 0.8168 (t0) cc_final: 0.7522 (m-40) REVERT: A 200 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8267 (mtt180) REVERT: B 67 GLN cc_start: 0.8758 (pt0) cc_final: 0.8175 (mt0) REVERT: B 259 ARG cc_start: 0.8612 (tpt-90) cc_final: 0.8072 (tpt-90) REVERT: C 64 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: C 67 GLN cc_start: 0.8412 (mt0) cc_final: 0.8135 (mm-40) REVERT: C 184 ASN cc_start: 0.8046 (t0) cc_final: 0.7419 (m-40) REVERT: C 259 ARG cc_start: 0.8655 (tpt-90) cc_final: 0.8179 (tpt-90) REVERT: D 67 GLN cc_start: 0.8742 (pt0) cc_final: 0.8172 (mt0) REVERT: D 184 ASN cc_start: 0.7975 (t0) cc_final: 0.7437 (m-40) REVERT: D 259 ARG cc_start: 0.8604 (tpp80) cc_final: 0.8217 (tpt-90) REVERT: D 263 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7922 (mt-10) REVERT: E 67 GLN cc_start: 0.8939 (pt0) cc_final: 0.8318 (mt0) REVERT: E 184 ASN cc_start: 0.8068 (t0) cc_final: 0.7504 (m-40) REVERT: E 259 ARG cc_start: 0.8567 (tpt90) cc_final: 0.8164 (tpt-90) outliers start: 27 outliers final: 18 residues processed: 166 average time/residue: 1.7320 time to fit residues: 305.1790 Evaluate side-chains 161 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 A residue 258 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain 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 Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 258 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11762 Z= 0.222 Angle : 0.602 11.308 15896 Z= 0.294 Chirality : 0.040 0.184 1735 Planarity : 0.004 0.037 1905 Dihedral : 11.303 71.386 2206 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.13 % Allowed : 12.13 % 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: 3.49 (0.21), residues: 1335 helix: 2.65 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.30 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 13 HIS 0.001 0.001 HIS B 20 PHE 0.013 0.002 PHE B 164 TYR 0.014 0.002 TYR B 97 ARG 0.006 0.000 ARG A 259 *********************** 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 161 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.231 Fit side-chains REVERT: A 67 GLN cc_start: 0.8757 (pt0) cc_final: 0.8260 (mt0) REVERT: A 70 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8561 (tp) REVERT: A 162 GLU cc_start: 0.7586 (pm20) cc_final: 0.7264 (pm20) REVERT: A 184 ASN cc_start: 0.8177 (t0) cc_final: 0.7520 (m-40) REVERT: A 200 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8272 (mtt180) REVERT: B 67 GLN cc_start: 0.8758 (pt0) cc_final: 0.8176 (mt0) REVERT: B 259 ARG cc_start: 0.8608 (tpt-90) cc_final: 0.8065 (tpt-90) REVERT: C 64 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: C 67 GLN cc_start: 0.8403 (mt0) cc_final: 0.8133 (mm-40) REVERT: C 184 ASN cc_start: 0.8038 (t0) cc_final: 0.7418 (m-40) REVERT: C 259 ARG cc_start: 0.8657 (tpt-90) cc_final: 0.8164 (tpt-90) REVERT: D 67 GLN cc_start: 0.8740 (pt0) cc_final: 0.8175 (mt0) REVERT: D 184 ASN cc_start: 0.7987 (t0) cc_final: 0.7445 (m-40) REVERT: D 259 ARG cc_start: 0.8606 (tpp80) cc_final: 0.8321 (tpt90) REVERT: D 263 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7953 (mt-10) REVERT: E 67 GLN cc_start: 0.8931 (pt0) cc_final: 0.8324 (mt0) REVERT: E 184 ASN cc_start: 0.8027 (t0) cc_final: 0.7450 (m-40) REVERT: E 259 ARG cc_start: 0.8561 (tpt90) cc_final: 0.8155 (tpt-90) outliers start: 23 outliers final: 18 residues processed: 157 average time/residue: 1.7783 time to fit residues: 295.7198 Evaluate side-chains 159 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 A residue 258 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain 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 Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 123 optimal weight: 0.0570 chunk 107 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 11762 Z= 0.158 Angle : 0.558 10.624 15896 Z= 0.270 Chirality : 0.037 0.158 1735 Planarity : 0.004 0.034 1905 Dihedral : 10.569 68.535 2206 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.22 % Allowed : 12.04 % 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: 3.74 (0.21), residues: 1335 helix: 2.86 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.23 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 13 HIS 0.002 0.001 HIS B 20 PHE 0.012 0.001 PHE C 12 TYR 0.013 0.001 TYR B 219 ARG 0.002 0.000 ARG A 259 ********************** 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 167 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 1.218 Fit side-chains REVERT: A 67 GLN cc_start: 0.8761 (pt0) cc_final: 0.8232 (mt0) REVERT: A 70 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8482 (tp) REVERT: A 162 GLU cc_start: 0.7519 (pm20) cc_final: 0.7222 (pm20) REVERT: A 184 ASN cc_start: 0.8160 (t0) cc_final: 0.7482 (m-40) REVERT: A 200 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8223 (mtt180) REVERT: A 270 ARG cc_start: 0.7631 (mtp85) cc_final: 0.7392 (mtt-85) REVERT: B 67 GLN cc_start: 0.8755 (pt0) cc_final: 0.8146 (mt0) REVERT: B 184 ASN cc_start: 0.8082 (t0) cc_final: 0.7492 (m-40) REVERT: B 259 ARG cc_start: 0.8583 (tpt-90) cc_final: 0.8065 (tpt-90) REVERT: C 64 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: C 67 GLN cc_start: 0.8394 (mt0) cc_final: 0.8134 (mm-40) REVERT: C 184 ASN cc_start: 0.8021 (t0) cc_final: 0.7396 (m-40) REVERT: C 259 ARG cc_start: 0.8637 (tpt-90) cc_final: 0.8150 (tpt-90) REVERT: D 67 GLN cc_start: 0.8735 (pt0) cc_final: 0.8154 (mt0) REVERT: D 162 GLU cc_start: 0.7677 (pm20) cc_final: 0.7326 (pm20) REVERT: D 184 ASN cc_start: 0.7968 (t0) cc_final: 0.7414 (m-40) REVERT: D 259 ARG cc_start: 0.8602 (tpp80) cc_final: 0.8131 (tpt-90) REVERT: D 263 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7835 (mt-10) REVERT: E 67 GLN cc_start: 0.8890 (pt0) cc_final: 0.8270 (mt0) REVERT: E 70 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8594 (tp) REVERT: E 184 ASN cc_start: 0.8046 (t0) cc_final: 0.7435 (m-40) REVERT: E 259 ARG cc_start: 0.8594 (tpt90) cc_final: 0.8223 (tpt-90) REVERT: E 270 ARG cc_start: 0.7719 (mtp85) cc_final: 0.7478 (mtp85) outliers start: 24 outliers final: 15 residues processed: 163 average time/residue: 1.8591 time to fit residues: 323.7788 Evaluate side-chains 162 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 A residue 258 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain 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 Chi-restraints excluded: chain E residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3012 r_free = 0.3012 target = 0.097619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.085376 restraints weight = 12872.053| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.00 r_work: 0.2747 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2339 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= 0.180 Angle : 0.573 10.913 15896 Z= 0.278 Chirality : 0.039 0.162 1735 Planarity : 0.004 0.033 1905 Dihedral : 10.643 70.813 2206 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.85 % Allowed : 12.69 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.82 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : 1.21 (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 B 20 PHE 0.013 0.001 PHE B 164 TYR 0.010 0.001 TYR A 219 ARG 0.003 0.000 ARG A 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4864.02 seconds wall clock time: 86 minutes 23.52 seconds (5183.52 seconds total)