Starting phenix.real_space_refine on Sat Mar 16 21:51:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amw_15527/03_2024/8amw_15527.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amw_15527/03_2024/8amw_15527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amw_15527/03_2024/8amw_15527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amw_15527/03_2024/8amw_15527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amw_15527/03_2024/8amw_15527.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amw_15527/03_2024/8amw_15527.pdb" } resolution = 3.0 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= 0.032 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 104 5.16 5 C 10454 2.51 5 N 2553 2.21 5 O 2681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15792 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1965 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 1956 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Conformer: "B" Number of residues, atoms: 254, 1956 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} bond proxies already assigned to first conformer: 2003 Chain: "B" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "C" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1956 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Chain: "D" Number of atoms: 1974 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1969 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Conformer: "B" Number of residues, atoms: 256, 1969 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} bond proxies already assigned to first conformer: 2020 Chain: "E" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "F" Number of atoms: 1978 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1969 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Conformer: "B" Number of residues, atoms: 256, 1969 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} bond proxies already assigned to first conformer: 2016 Chain: "G" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "H" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {'GOL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 30 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 24 Unusual residues: {'GOL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 24 Unusual residues: {'GOL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 15 Chain: "D" Number of atoms: 12 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Conformer: "C" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 12 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {'GOL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 12 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AGLN A 145 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 145 " occ=0.50 residue: pdb=" N AALA D 23 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA D 23 " occ=0.50 residue: pdb=" N AGLN F 145 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN F 145 " occ=0.50 residue: pdb=" C1 AGOL C 402 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BGOL C 402 " occ=0.50 residue: pdb=" C1 AGOL D 401 " occ=0.38 ... (10 atoms not shown) pdb=" O3 CGOL D 401 " occ=0.62 residue: pdb=" C1 AGOL E 401 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BGOL E 401 " occ=0.50 residue: pdb=" C1 AGOL F 401 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BGOL F 401 " occ=0.50 residue: pdb=" C1 AGOL H 401 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BGOL H 401 " occ=0.50 Time building chain proxies: 11.18, per 1000 atoms: 0.71 Number of scatterers: 15792 At special positions: 0 Unit cell: (93.104, 100.722, 121.035, 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 104 16.00 O 2681 8.00 N 2553 7.00 C 10454 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: 6.02 Conformation dependent library (CDL) restraints added in 3.8 seconds 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3574 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 0 sheets defined 78.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 27 through 30 Processing helix chain 'A' and resid 31 through 61 removed outlier: 3.561A pdb=" N PHE A 37 " --> pdb=" O MET A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 86 removed outlier: 3.806A pdb=" N VAL A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.640A pdb=" N PHE A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 190 Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.939A pdb=" N VAL A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 Proline residue: A 232 - end of helix removed outlier: 3.536A pdb=" N GLY A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.712A pdb=" N VAL A 246 " --> pdb=" O GLY A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 255 through 276 Proline residue: A 261 - end of helix Processing helix chain 'B' and resid 27 through 30 Processing helix chain 'B' and resid 31 through 61 Processing helix chain 'B' and resid 66 through 86 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.560A pdb=" N ILE B 157 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 158 " --> pdb=" O ALA B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 158' Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.925A pdb=" N LEU B 173 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 218 removed outlier: 3.872A pdb=" N VAL B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.566A pdb=" N ASP B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Proline residue: B 232 - end of helix removed outlier: 3.508A pdb=" N GLY B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.958A pdb=" N VAL B 246 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 255 through 276 Proline residue: B 261 - end of helix Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 32 through 61 removed outlier: 3.562A pdb=" N PHE C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 86 removed outlier: 4.347A pdb=" N VAL C 78 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.572A pdb=" N PHE C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 190 removed outlier: 3.508A pdb=" N THR C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 218 removed outlier: 3.811A pdb=" N VAL C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 Proline residue: C 232 - end of helix Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.747A pdb=" N VAL C 246 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 255 through 276 Proline residue: C 261 - end of helix Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 31 through 61 Processing helix chain 'D' and resid 66 through 90 removed outlier: 4.183A pdb=" N VAL D 78 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ARG D 87 " --> pdb=" O HIS D 83 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE D 88 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 134 removed outlier: 3.557A pdb=" N TYR D 115 " --> pdb=" O LYS D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.643A pdb=" N PHE D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 190 removed outlier: 3.513A pdb=" N GLY D 171 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 218 removed outlier: 3.889A pdb=" N VAL D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 240 Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.941A pdb=" N VAL D 246 " --> pdb=" O GLY D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 254 No H-bonds generated for 'chain 'D' and resid 252 through 254' Processing helix chain 'D' and resid 255 through 276 Proline residue: D 261 - end of helix Processing helix chain 'E' and resid 31 through 61 removed outlier: 3.559A pdb=" N PHE E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 86 Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 111 through 134 removed outlier: 3.523A pdb=" N TYR E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 154 through 158 removed outlier: 3.618A pdb=" N PHE E 158 " --> pdb=" O ALA E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 191 removed outlier: 3.509A pdb=" N THR E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 217 removed outlier: 3.736A pdb=" N VAL E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 240 removed outlier: 3.662A pdb=" N ASP E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Proline residue: E 232 - end of helix Processing helix chain 'E' and resid 243 through 247 removed outlier: 3.991A pdb=" N VAL E 246 " --> pdb=" O GLY E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 254 No H-bonds generated for 'chain 'E' and resid 252 through 254' Processing helix chain 'E' and resid 255 through 276 Proline residue: E 261 - end of helix Processing helix chain 'F' and resid 24 through 30 Processing helix chain 'F' and resid 31 through 61 removed outlier: 3.796A pdb=" N ARG F 35 " --> pdb=" O ARG F 31 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU F 36 " --> pdb=" O LYS F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 86 removed outlier: 3.635A pdb=" N MET F 80 " --> pdb=" O PHE F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 134 through 143 Processing helix chain 'F' and resid 154 through 158 removed outlier: 3.555A pdb=" N ILE F 157 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE F 158 " --> pdb=" O ALA F 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 154 through 158' Processing helix chain 'F' and resid 167 through 190 removed outlier: 3.511A pdb=" N THR F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 217 removed outlier: 3.875A pdb=" N VAL F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 241 Proline residue: F 232 - end of helix removed outlier: 3.578A pdb=" N GLY F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.744A pdb=" N SER F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 254 No H-bonds generated for 'chain 'F' and resid 252 through 254' Processing helix chain 'F' and resid 255 through 276 Proline residue: F 261 - end of helix Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 31 through 61 Processing helix chain 'G' and resid 66 through 86 Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'G' and resid 154 through 158 removed outlier: 3.573A pdb=" N PHE G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 190 Processing helix chain 'G' and resid 201 through 218 removed outlier: 3.764A pdb=" N VAL G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 240 Proline residue: G 232 - end of helix Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.839A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 254 No H-bonds generated for 'chain 'G' and resid 252 through 254' Processing helix chain 'G' and resid 255 through 276 Proline residue: G 261 - end of helix Processing helix chain 'H' and resid 26 through 30 Processing helix chain 'H' and resid 31 through 61 Processing helix chain 'H' and resid 66 through 86 removed outlier: 4.028A pdb=" N VAL H 78 " --> pdb=" O PHE H 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 111 through 134 Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 154 through 158 removed outlier: 3.602A pdb=" N ILE H 157 " --> pdb=" O THR H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 190 Processing helix chain 'H' and resid 201 through 218 removed outlier: 3.754A pdb=" N VAL H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY H 218 " --> pdb=" O GLY H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 241 Proline residue: H 232 - end of helix removed outlier: 3.591A pdb=" N GLY H 241 " --> pdb=" O THR H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 249 removed outlier: 3.741A pdb=" N SER H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 254 No H-bonds generated for 'chain 'H' and resid 252 through 254' Processing helix chain 'H' and resid 255 through 276 Proline residue: H 261 - end of helix 1057 hydrogen bonds defined for protein. 3120 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: 4.20 Time building geometry restraints manager: 6.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4763 1.34 - 1.46: 3124 1.46 - 1.57: 8146 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 16225 Sorted by residual: bond pdb=" C1 AGOL E 401 " pdb=" C2 AGOL E 401 " ideal model delta sigma weight residual 1.514 1.549 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" C2 GOL G 401 " pdb=" O2 GOL G 401 " ideal model delta sigma weight residual 1.410 1.378 0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" C2 AGOL E 401 " pdb=" O2 AGOL E 401 " ideal model delta sigma weight residual 1.410 1.378 0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" C2 BGOL H 401 " pdb=" O2 BGOL H 401 " ideal model delta sigma weight residual 1.410 1.378 0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" C2 GOL B 401 " pdb=" O2 GOL B 401 " ideal model delta sigma weight residual 1.410 1.378 0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 16220 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.66: 416 105.66 - 112.75: 8342 112.75 - 119.85: 5559 119.85 - 126.94: 7483 126.94 - 134.04: 265 Bond angle restraints: 22065 Sorted by residual: angle pdb=" N VAL H 258 " pdb=" CA VAL H 258 " pdb=" C VAL H 258 " ideal model delta sigma weight residual 112.96 109.54 3.42 1.00e+00 1.00e+00 1.17e+01 angle pdb=" CA TYR A 223 " pdb=" CB TYR A 223 " pdb=" CG TYR A 223 " ideal model delta sigma weight residual 113.90 118.69 -4.79 1.80e+00 3.09e-01 7.07e+00 angle pdb=" CA TYR D 223 " pdb=" CB TYR D 223 " pdb=" CG TYR D 223 " ideal model delta sigma weight residual 113.90 118.67 -4.77 1.80e+00 3.09e-01 7.02e+00 angle pdb=" CA TYR C 223 " pdb=" CB TYR C 223 " pdb=" CG TYR C 223 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 6.99e+00 angle pdb=" CA TYR G 223 " pdb=" CB TYR G 223 " pdb=" CG TYR G 223 " ideal model delta sigma weight residual 113.90 118.61 -4.71 1.80e+00 3.09e-01 6.85e+00 ... (remaining 22060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8573 17.89 - 35.78: 435 35.78 - 53.66: 81 53.66 - 71.55: 3 71.55 - 89.44: 4 Dihedral angle restraints: 9096 sinusoidal: 3412 harmonic: 5684 Sorted by residual: dihedral pdb=" CA PHE A 76 " pdb=" C PHE A 76 " pdb=" N GLY A 77 " pdb=" CA GLY A 77 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE F 76 " pdb=" C PHE F 76 " pdb=" N GLY F 77 " pdb=" CA GLY F 77 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE C 76 " pdb=" C PHE C 76 " pdb=" N GLY C 77 " pdb=" CA GLY C 77 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 9093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1317 0.030 - 0.060: 805 0.060 - 0.090: 255 0.090 - 0.120: 62 0.120 - 0.150: 22 Chirality restraints: 2461 Sorted by residual: chirality pdb=" CA TYR C 223 " pdb=" N TYR C 223 " pdb=" C TYR C 223 " pdb=" CB TYR C 223 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA TYR A 223 " pdb=" N TYR A 223 " pdb=" C TYR A 223 " pdb=" CB TYR A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA TYR H 223 " pdb=" N TYR H 223 " pdb=" C TYR H 223 " pdb=" CB TYR H 223 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2458 not shown) Planarity restraints: 2728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 226 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO E 227 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 227 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 227 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 162 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO D 163 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 163 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 163 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 231 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO G 232 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 232 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 232 " -0.022 5.00e-02 4.00e+02 ... (remaining 2725 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3421 2.78 - 3.31: 14371 3.31 - 3.84: 26054 3.84 - 4.37: 30116 4.37 - 4.90: 55260 Nonbonded interactions: 129222 Sorted by model distance: nonbonded pdb=" OD1 ASN C 101 " pdb=" O2 GOL C 403 " model vdw 2.245 2.440 nonbonded pdb=" OG SER F 142 " pdb=" O AGLN F 145 " model vdw 2.257 2.440 nonbonded pdb=" O3 GOL G 401 " pdb=" O1 GOL G 402 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR A 160 " pdb=" OD1 ASP A 230 " model vdw 2.279 2.440 nonbonded pdb=" O1 GOL C 401 " pdb=" O1 BGOL C 402 " model vdw 2.283 2.440 ... (remaining 129217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'B' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'C' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'D' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'E' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'F' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'G' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'H' and (resid 25 through 144 or resid 146 through 277)) } 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=0.38 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: 4.340 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: 13.900 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 45.210 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.070 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.005 0.040 16225 Z= 0.316 Angle : 0.610 5.978 22065 Z= 0.317 Chirality : 0.042 0.150 2461 Planarity : 0.005 0.050 2728 Dihedral : 11.059 89.440 5522 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.44 % Allowed : 5.56 % Favored : 94.00 % 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: 1.57 (0.19), residues: 2024 helix: 1.92 (0.14), residues: 1428 sheet: None (None), residues: 0 loop : -1.18 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 169 HIS 0.003 0.001 HIS G 57 PHE 0.012 0.002 PHE F 134 TYR 0.021 0.002 TYR C 223 ARG 0.002 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 1.615 Fit side-chains REVERT: A 63 LYS cc_start: 0.8675 (ptpt) cc_final: 0.8431 (ptmm) REVERT: A 74 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.7527 (t80) REVERT: A 193 GLU cc_start: 0.8288 (mp0) cc_final: 0.8066 (mp0) REVERT: A 270 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8119 (tp) REVERT: B 28 ILE cc_start: 0.7382 (tt) cc_final: 0.6863 (mm) REVERT: B 63 LYS cc_start: 0.8424 (ptpt) cc_final: 0.8034 (pttm) REVERT: C 63 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8121 (pttm) REVERT: C 74 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.7777 (t80) REVERT: E 245 GLN cc_start: 0.8459 (mt0) cc_final: 0.8211 (mt0) REVERT: F 33 MET cc_start: 0.6828 (mmm) cc_final: 0.6511 (ptm) REVERT: G 244 LYS cc_start: 0.8266 (pttp) cc_final: 0.7748 (tptp) REVERT: H 74 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7561 (t80) outliers start: 6 outliers final: 2 residues processed: 193 average time/residue: 1.4195 time to fit residues: 299.6718 Evaluate side-chains 170 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain H residue 74 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 0.2980 chunk 181 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS F 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16225 Z= 0.168 Angle : 0.523 5.966 22065 Z= 0.280 Chirality : 0.039 0.138 2461 Planarity : 0.005 0.048 2728 Dihedral : 5.355 56.567 2228 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.62 % Allowed : 10.25 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.17 (0.19), residues: 2024 helix: 2.41 (0.14), residues: 1424 sheet: None (None), residues: 0 loop : -1.05 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 169 HIS 0.008 0.001 HIS F 140 PHE 0.010 0.001 PHE A 37 TYR 0.019 0.001 TYR D 223 ARG 0.003 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.539 Fit side-chains REVERT: A 63 LYS cc_start: 0.8663 (ptpt) cc_final: 0.8407 (ptmm) REVERT: A 74 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7607 (t80) REVERT: A 270 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8099 (tp) REVERT: B 28 ILE cc_start: 0.7310 (tt) cc_final: 0.6762 (mm) REVERT: B 63 LYS cc_start: 0.8424 (ptpt) cc_final: 0.8031 (pttm) REVERT: C 63 LYS cc_start: 0.8416 (ptpt) cc_final: 0.8170 (pttm) REVERT: C 74 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7552 (t80) REVERT: E 48 MET cc_start: 0.9068 (mmp) cc_final: 0.8840 (mmt) REVERT: E 245 GLN cc_start: 0.8389 (mt0) cc_final: 0.8153 (mt0) REVERT: F 33 MET cc_start: 0.6663 (mmm) cc_final: 0.6356 (ptm) REVERT: G 87 ARG cc_start: 0.7693 (tmm-80) cc_final: 0.7424 (ttt90) REVERT: G 244 LYS cc_start: 0.8212 (pttp) cc_final: 0.7699 (tptp) REVERT: H 74 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7682 (t80) outliers start: 25 outliers final: 6 residues processed: 183 average time/residue: 1.4448 time to fit residues: 288.7783 Evaluate side-chains 171 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 74 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16225 Z= 0.370 Angle : 0.622 6.592 22065 Z= 0.333 Chirality : 0.044 0.156 2461 Planarity : 0.005 0.052 2728 Dihedral : 5.801 54.525 2226 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.69 % Allowed : 12.00 % Favored : 86.31 % 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: 1.70 (0.19), residues: 2024 helix: 2.13 (0.14), residues: 1412 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 169 HIS 0.005 0.001 HIS G 57 PHE 0.011 0.002 PHE A 134 TYR 0.023 0.002 TYR C 223 ARG 0.006 0.001 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.617 Fit side-chains REVERT: A 63 LYS cc_start: 0.8693 (ptpt) cc_final: 0.8262 (ptmm) REVERT: A 74 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.7677 (t80) REVERT: A 270 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8138 (tp) REVERT: B 28 ILE cc_start: 0.7551 (tt) cc_final: 0.7027 (mm) REVERT: B 63 LYS cc_start: 0.8465 (ptpt) cc_final: 0.8028 (pttm) REVERT: C 63 LYS cc_start: 0.8469 (ptpt) cc_final: 0.8188 (pttm) REVERT: C 74 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.7793 (t80) REVERT: E 245 GLN cc_start: 0.8431 (mt0) cc_final: 0.8139 (mt0) REVERT: F 33 MET cc_start: 0.6917 (mmm) cc_final: 0.6571 (ptm) REVERT: G 87 ARG cc_start: 0.7810 (tmm-80) cc_final: 0.7541 (tmm-80) REVERT: G 244 LYS cc_start: 0.8188 (pttp) cc_final: 0.7701 (tptp) REVERT: H 74 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7729 (t80) outliers start: 26 outliers final: 9 residues processed: 181 average time/residue: 1.5385 time to fit residues: 303.1442 Evaluate side-chains 175 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 248 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16225 Z= 0.194 Angle : 0.527 6.132 22065 Z= 0.282 Chirality : 0.039 0.141 2461 Planarity : 0.005 0.044 2728 Dihedral : 5.497 57.501 2226 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.69 % Allowed : 13.69 % Favored : 84.62 % 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: 2.12 (0.19), residues: 2024 helix: 2.42 (0.14), residues: 1418 sheet: None (None), residues: 0 loop : -1.16 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 169 HIS 0.005 0.001 HIS D 57 PHE 0.010 0.001 PHE A 37 TYR 0.018 0.001 TYR D 223 ARG 0.004 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 1.399 Fit side-chains REVERT: A 63 LYS cc_start: 0.8646 (ptpt) cc_final: 0.8226 (ptmm) REVERT: A 74 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7721 (t80) REVERT: A 193 GLU cc_start: 0.8370 (mp0) cc_final: 0.8111 (mp0) REVERT: A 270 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8107 (tp) REVERT: B 28 ILE cc_start: 0.7455 (tt) cc_final: 0.6904 (mm) REVERT: B 63 LYS cc_start: 0.8395 (ptpt) cc_final: 0.7981 (pttm) REVERT: C 63 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8140 (pttm) REVERT: C 74 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7555 (t80) REVERT: E 244 LYS cc_start: 0.8435 (ptmt) cc_final: 0.8054 (pttm) REVERT: E 245 GLN cc_start: 0.8412 (mt0) cc_final: 0.8128 (mt0) REVERT: G 87 ARG cc_start: 0.7781 (tmm-80) cc_final: 0.7450 (ttt90) REVERT: G 244 LYS cc_start: 0.8181 (pttp) cc_final: 0.7694 (tptp) REVERT: H 74 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7642 (t80) outliers start: 26 outliers final: 10 residues processed: 180 average time/residue: 1.4802 time to fit residues: 290.5075 Evaluate side-chains 176 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16225 Z= 0.226 Angle : 0.542 6.182 22065 Z= 0.289 Chirality : 0.040 0.142 2461 Planarity : 0.005 0.048 2728 Dihedral : 5.500 56.805 2226 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.94 % Allowed : 13.81 % Favored : 84.25 % 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: 2.08 (0.19), residues: 2024 helix: 2.53 (0.14), residues: 1388 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 169 HIS 0.005 0.001 HIS D 57 PHE 0.010 0.001 PHE A 37 TYR 0.020 0.002 TYR C 223 ARG 0.003 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 1.468 Fit side-chains REVERT: A 63 LYS cc_start: 0.8639 (ptpt) cc_final: 0.8215 (ptmm) REVERT: A 74 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.7747 (t80) REVERT: A 193 GLU cc_start: 0.8411 (mp0) cc_final: 0.8046 (mp0) REVERT: A 270 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8118 (tp) REVERT: B 28 ILE cc_start: 0.7517 (tt) cc_final: 0.6979 (mm) REVERT: B 63 LYS cc_start: 0.8406 (ptpt) cc_final: 0.7945 (pttm) REVERT: C 63 LYS cc_start: 0.8456 (ptpt) cc_final: 0.8128 (pttm) REVERT: C 74 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7689 (t80) REVERT: E 244 LYS cc_start: 0.8476 (ptmt) cc_final: 0.8085 (pttm) REVERT: E 245 GLN cc_start: 0.8405 (mt0) cc_final: 0.8105 (mt0) REVERT: F 33 MET cc_start: 0.6936 (mmt) cc_final: 0.6183 (ptm) REVERT: G 87 ARG cc_start: 0.7794 (tmm-80) cc_final: 0.7464 (ttt90) REVERT: G 244 LYS cc_start: 0.8182 (pttp) cc_final: 0.7695 (tptp) REVERT: H 74 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.7687 (t80) outliers start: 30 outliers final: 16 residues processed: 183 average time/residue: 1.5498 time to fit residues: 310.1940 Evaluate side-chains 181 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 248 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 113 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16225 Z= 0.162 Angle : 0.503 6.225 22065 Z= 0.267 Chirality : 0.038 0.134 2461 Planarity : 0.004 0.043 2728 Dihedral : 5.242 59.098 2226 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.69 % Allowed : 14.25 % Favored : 84.06 % 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: 2.41 (0.20), residues: 2024 helix: 2.70 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -1.16 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 169 HIS 0.005 0.001 HIS D 57 PHE 0.010 0.001 PHE A 37 TYR 0.017 0.001 TYR D 223 ARG 0.003 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 1.518 Fit side-chains REVERT: A 63 LYS cc_start: 0.8599 (ptpt) cc_final: 0.8197 (ptmm) REVERT: A 74 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7761 (t80) REVERT: A 270 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8117 (tp) REVERT: B 28 ILE cc_start: 0.7464 (tt) cc_final: 0.6915 (mm) REVERT: B 63 LYS cc_start: 0.8349 (ptpt) cc_final: 0.7898 (pttm) REVERT: C 63 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8089 (pttm) REVERT: C 74 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7468 (t80) REVERT: E 244 LYS cc_start: 0.8472 (ptmt) cc_final: 0.8071 (pttm) REVERT: E 245 GLN cc_start: 0.8372 (mt0) cc_final: 0.8059 (mt0) REVERT: F 33 MET cc_start: 0.6730 (mmt) cc_final: 0.6008 (ptm) REVERT: G 244 LYS cc_start: 0.8169 (pttp) cc_final: 0.7685 (tptp) REVERT: H 74 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.7570 (t80) outliers start: 26 outliers final: 13 residues processed: 184 average time/residue: 1.4662 time to fit residues: 295.0359 Evaluate side-chains 181 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 162 optimal weight: 0.0470 chunk 108 optimal weight: 0.6980 chunk 192 optimal weight: 0.7980 chunk 120 optimal weight: 0.0670 chunk 117 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16225 Z= 0.149 Angle : 0.490 7.555 22065 Z= 0.257 Chirality : 0.037 0.129 2461 Planarity : 0.004 0.039 2728 Dihedral : 4.962 59.564 2226 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.56 % Allowed : 15.38 % Favored : 83.06 % 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: 2.60 (0.20), residues: 2024 helix: 2.94 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 169 HIS 0.005 0.001 HIS D 57 PHE 0.009 0.001 PHE A 37 TYR 0.016 0.001 TYR D 223 ARG 0.009 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.807 Fit side-chains REVERT: A 63 LYS cc_start: 0.8545 (ptpt) cc_final: 0.8325 (ptmm) REVERT: A 74 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7715 (t80) REVERT: A 270 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8073 (tp) REVERT: B 28 ILE cc_start: 0.7415 (tt) cc_final: 0.6849 (mm) REVERT: B 63 LYS cc_start: 0.8269 (ptpt) cc_final: 0.7838 (pttm) REVERT: C 63 LYS cc_start: 0.8348 (ptpt) cc_final: 0.8012 (pttm) REVERT: C 74 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7370 (t80) REVERT: E 230 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7449 (t0) REVERT: E 244 LYS cc_start: 0.8471 (ptmt) cc_final: 0.8065 (pttm) REVERT: G 244 LYS cc_start: 0.8159 (pttp) cc_final: 0.7671 (tptp) REVERT: H 74 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7536 (t80) outliers start: 24 outliers final: 11 residues processed: 190 average time/residue: 1.3909 time to fit residues: 290.1833 Evaluate side-chains 185 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.0060 chunk 151 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16225 Z= 0.287 Angle : 0.583 9.861 22065 Z= 0.308 Chirality : 0.042 0.147 2461 Planarity : 0.005 0.043 2728 Dihedral : 5.457 56.011 2226 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.00 % Allowed : 15.06 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.12 (0.19), residues: 2024 helix: 2.53 (0.14), residues: 1394 sheet: None (None), residues: 0 loop : -1.30 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 169 HIS 0.005 0.001 HIS F 57 PHE 0.011 0.002 PHE A 236 TYR 0.023 0.002 TYR C 223 ARG 0.007 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.658 Fit side-chains REVERT: A 63 LYS cc_start: 0.8621 (ptpt) cc_final: 0.8188 (ptmm) REVERT: A 74 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.7696 (t80) REVERT: A 270 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8137 (tp) REVERT: B 28 ILE cc_start: 0.7602 (tt) cc_final: 0.7060 (mm) REVERT: B 63 LYS cc_start: 0.8324 (ptpt) cc_final: 0.7886 (pttm) REVERT: C 63 LYS cc_start: 0.8409 (ptpt) cc_final: 0.8070 (pttm) REVERT: C 74 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7735 (t80) REVERT: D 132 SER cc_start: 0.8730 (t) cc_final: 0.8450 (m) REVERT: E 244 LYS cc_start: 0.8537 (ptmt) cc_final: 0.8123 (pttm) REVERT: E 245 GLN cc_start: 0.8422 (mt0) cc_final: 0.8048 (mt0) REVERT: F 33 MET cc_start: 0.6889 (mmt) cc_final: 0.6174 (ptm) REVERT: G 244 LYS cc_start: 0.8195 (pttp) cc_final: 0.7694 (tptp) REVERT: H 74 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.7748 (t80) outliers start: 31 outliers final: 14 residues processed: 188 average time/residue: 1.5477 time to fit residues: 319.3463 Evaluate side-chains 182 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 248 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 162 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16225 Z= 0.175 Angle : 0.516 10.449 22065 Z= 0.273 Chirality : 0.038 0.136 2461 Planarity : 0.005 0.042 2728 Dihedral : 5.282 58.932 2226 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.50 % Allowed : 15.88 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.20), residues: 2024 helix: 2.77 (0.14), residues: 1388 sheet: None (None), residues: 0 loop : -1.28 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 169 HIS 0.005 0.001 HIS D 57 PHE 0.010 0.001 PHE A 37 TYR 0.017 0.001 TYR D 223 ARG 0.008 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.762 Fit side-chains REVERT: A 63 LYS cc_start: 0.8586 (ptpt) cc_final: 0.8277 (ptmm) REVERT: A 74 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.7767 (t80) REVERT: A 270 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8122 (tp) REVERT: B 28 ILE cc_start: 0.7502 (tt) cc_final: 0.6957 (mm) REVERT: B 63 LYS cc_start: 0.8331 (ptpt) cc_final: 0.7880 (pttm) REVERT: C 63 LYS cc_start: 0.8406 (ptpt) cc_final: 0.8070 (pttm) REVERT: C 74 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7464 (t80) REVERT: E 244 LYS cc_start: 0.8506 (ptmt) cc_final: 0.8082 (pttm) REVERT: E 245 GLN cc_start: 0.8389 (mt0) cc_final: 0.8017 (mt0) REVERT: F 33 MET cc_start: 0.6726 (mmt) cc_final: 0.6038 (ptm) REVERT: G 244 LYS cc_start: 0.8177 (pttp) cc_final: 0.7682 (tptp) REVERT: H 74 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7614 (t80) outliers start: 23 outliers final: 15 residues processed: 178 average time/residue: 1.4508 time to fit residues: 282.3967 Evaluate side-chains 179 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 110 ARG Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 248 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 169 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16225 Z= 0.167 Angle : 0.515 10.675 22065 Z= 0.270 Chirality : 0.038 0.134 2461 Planarity : 0.005 0.041 2728 Dihedral : 5.139 59.445 2226 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.38 % Allowed : 16.00 % Favored : 82.62 % 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: 2.48 (0.20), residues: 2024 helix: 2.85 (0.14), residues: 1388 sheet: None (None), residues: 0 loop : -1.25 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 169 HIS 0.005 0.001 HIS D 57 PHE 0.009 0.001 PHE A 37 TYR 0.018 0.001 TYR C 223 ARG 0.009 0.000 ARG D 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 1.631 Fit side-chains REVERT: A 63 LYS cc_start: 0.8553 (ptpt) cc_final: 0.8341 (ptmm) REVERT: A 74 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.7703 (t80) REVERT: A 270 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8086 (tp) REVERT: B 28 ILE cc_start: 0.7501 (tt) cc_final: 0.6950 (mm) REVERT: B 63 LYS cc_start: 0.8289 (ptpt) cc_final: 0.7850 (pttm) REVERT: C 63 LYS cc_start: 0.8378 (ptpt) cc_final: 0.8042 (pttm) REVERT: C 74 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.7405 (t80) REVERT: E 244 LYS cc_start: 0.8511 (ptmt) cc_final: 0.8076 (pttm) REVERT: F 33 MET cc_start: 0.6649 (mmt) cc_final: 0.5992 (ptm) REVERT: G 244 LYS cc_start: 0.8145 (pttp) cc_final: 0.7669 (tptp) REVERT: H 74 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7586 (t80) outliers start: 21 outliers final: 14 residues processed: 179 average time/residue: 1.4447 time to fit residues: 283.4006 Evaluate side-chains 178 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 248 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.3980 chunk 146 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.0370 chunk 158 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.105304 restraints weight = 38355.229| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.50 r_work: 0.3057 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16225 Z= 0.152 Angle : 0.499 10.799 22065 Z= 0.260 Chirality : 0.037 0.132 2461 Planarity : 0.004 0.040 2728 Dihedral : 4.959 59.217 2226 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.12 % Allowed : 16.44 % Favored : 82.44 % 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: 2.64 (0.20), residues: 2024 helix: 2.98 (0.14), residues: 1388 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 169 HIS 0.005 0.001 HIS D 57 PHE 0.010 0.001 PHE A 37 TYR 0.016 0.001 TYR G 223 ARG 0.008 0.000 ARG D 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5126.31 seconds wall clock time: 91 minutes 34.50 seconds (5494.50 seconds total)