Starting phenix.real_space_refine on Wed Feb 4 13:15:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pch_13320/02_2026/7pch_13320.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pch_13320/02_2026/7pch_13320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pch_13320/02_2026/7pch_13320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pch_13320/02_2026/7pch_13320.map" model { file = "/net/cci-nas-00/data/ceres_data/7pch_13320/02_2026/7pch_13320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pch_13320/02_2026/7pch_13320.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 32 5.16 5 C 6608 2.51 5 N 1734 2.21 5 O 2420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10798 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1159 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Conformer: "B" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} bond proxies already assigned to first conformer: 1113 Chain: "E" Number of atoms: 2830 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2800 Classifications: {'peptide': 340} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 327} Conformer: "B" Number of residues, atoms: 340, 2800 Classifications: {'peptide': 340} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 327} bond proxies already assigned to first conformer: 2822 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Restraints were copied for chains: C, D, F Residues with excluded nonbonded symmetry interactions: 14 residue: pdb=" N ALYS B 61 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 61 " occ=0.50 residue: pdb=" N ALYS B 65 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 65 " occ=0.50 residue: pdb=" N ALYS B 82 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 82 " occ=0.50 residue: pdb=" N AGLU B 101 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU B 101 " occ=0.50 residue: pdb=" N ALYS E 141 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS E 141 " occ=0.50 residue: pdb=" N ALYS E 210 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS E 210 " occ=0.50 residue: pdb=" N ATYR E 214 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR E 214 " occ=0.50 residue: pdb=" N ALYS D 61 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS D 61 " occ=0.50 residue: pdb=" N ALYS D 65 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS D 65 " occ=0.50 residue: pdb=" N ALYS D 82 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS D 82 " occ=0.50 residue: pdb=" N AGLU D 101 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D 101 " occ=0.50 residue: pdb=" N ALYS F 141 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS F 141 " occ=0.50 ... (remaining 2 not shown) Time building chain proxies: 2.79, per 1000 atoms: 0.26 Number of scatterers: 10798 At special positions: 0 Unit cell: (101.06, 132.356, 93.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 32 16.00 O 2420 8.00 N 1734 7.00 C 6608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 526.9 milliseconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 53.9% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.655A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 removed outlier: 4.219A pdb=" N LYS A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 19 through 35 removed outlier: 4.197A pdb=" N GLY B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLY B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 42 Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 57 through 77 removed outlier: 3.571A pdb=" N ALYS B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 95 removed outlier: 5.334A pdb=" N THR B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.636A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'E' and resid 128 through 134 removed outlier: 4.187A pdb=" N LYS E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 169 Processing helix chain 'E' and resid 269 through 285 Proline residue: E 281 - end of helix Processing helix chain 'E' and resid 287 through 300 removed outlier: 4.572A pdb=" N ASP E 300 " --> pdb=" O ASN E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 332 removed outlier: 4.183A pdb=" N ALA E 308 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 365 Processing helix chain 'E' and resid 451 through 463 removed outlier: 3.673A pdb=" N LYS E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.655A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 99 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 139 removed outlier: 4.219A pdb=" N LYS C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 16 Processing helix chain 'D' and resid 19 through 35 removed outlier: 4.197A pdb=" N GLY D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLY D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 42 Processing helix chain 'D' and resid 50 through 57 Processing helix chain 'D' and resid 57 through 77 removed outlier: 3.571A pdb=" N ALYS D 61 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 95 removed outlier: 5.334A pdb=" N THR D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 119 removed outlier: 3.636A pdb=" N PHE D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 123 through 142 Processing helix chain 'F' and resid 128 through 134 removed outlier: 4.187A pdb=" N LYS F 134 " --> pdb=" O ARG F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 169 Processing helix chain 'F' and resid 269 through 285 Proline residue: F 281 - end of helix Processing helix chain 'F' and resid 287 through 300 removed outlier: 4.572A pdb=" N ASP F 300 " --> pdb=" O ASN F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 332 removed outlier: 4.183A pdb=" N ALA F 308 " --> pdb=" O GLU F 304 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU F 309 " --> pdb=" O LYS F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 365 Processing helix chain 'F' and resid 451 through 463 removed outlier: 3.673A pdb=" N LYS F 456 " --> pdb=" O GLU F 452 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 148 through 151 removed outlier: 3.610A pdb=" N ALA E 174 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL E 171 " --> pdb=" O GLN E 190 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN E 190 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLY E 188 " --> pdb=" O PRO E 173 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG E 224 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU E 211 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N SER E 226 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE E 209 " --> pdb=" O SER E 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 153 through 156 removed outlier: 11.269A pdb=" N MET E 254 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL E 237 " --> pdb=" O MET E 254 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N PHE E 256 " --> pdb=" O LYS E 235 " (cutoff:3.500A) removed outlier: 11.512A pdb=" N LYS E 235 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N GLN E 258 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA E 233 " --> pdb=" O GLN E 258 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR E 231 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS E 241 " --> pdb=" O TRP E 195 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TRP E 195 " --> pdb=" O HIS E 241 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL E 200 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 153 through 156 removed outlier: 11.269A pdb=" N MET E 254 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL E 237 " --> pdb=" O MET E 254 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N PHE E 256 " --> pdb=" O LYS E 235 " (cutoff:3.500A) removed outlier: 11.512A pdb=" N LYS E 235 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N GLN E 258 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA E 233 " --> pdb=" O GLN E 258 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR E 231 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER E 238 " --> pdb=" O TYR E 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 344 through 348 removed outlier: 3.854A pdb=" N ASP E 344 " --> pdb=" O MET E 375 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 375 " --> pdb=" O ASP E 344 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE E 371 " --> pdb=" O THR E 348 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU E 385 " --> pdb=" O PRO E 370 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER E 406 " --> pdb=" O THR E 415 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE E 417 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N THR E 404 " --> pdb=" O ILE E 417 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 350 through 353 removed outlier: 7.274A pdb=" N ASP E 428 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL E 397 " --> pdb=" O ASP E 428 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE E 430 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE E 395 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS E 432 " --> pdb=" O LYS E 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 148 through 151 removed outlier: 3.610A pdb=" N ALA F 174 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL F 171 " --> pdb=" O GLN F 190 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN F 190 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLY F 188 " --> pdb=" O PRO F 173 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG F 224 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU F 211 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N SER F 226 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE F 209 " --> pdb=" O SER F 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 153 through 156 removed outlier: 11.269A pdb=" N MET F 254 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL F 237 " --> pdb=" O MET F 254 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N PHE F 256 " --> pdb=" O LYS F 235 " (cutoff:3.500A) removed outlier: 11.512A pdb=" N LYS F 235 " --> pdb=" O PHE F 256 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N GLN F 258 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA F 233 " --> pdb=" O GLN F 258 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR F 231 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS F 241 " --> pdb=" O TRP F 195 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TRP F 195 " --> pdb=" O HIS F 241 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL F 200 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 153 through 156 removed outlier: 11.269A pdb=" N MET F 254 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL F 237 " --> pdb=" O MET F 254 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N PHE F 256 " --> pdb=" O LYS F 235 " (cutoff:3.500A) removed outlier: 11.512A pdb=" N LYS F 235 " --> pdb=" O PHE F 256 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N GLN F 258 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA F 233 " --> pdb=" O GLN F 258 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR F 231 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER F 238 " --> pdb=" O TYR F 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 344 through 348 removed outlier: 3.854A pdb=" N ASP F 344 " --> pdb=" O MET F 375 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET F 375 " --> pdb=" O ASP F 344 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE F 371 " --> pdb=" O THR F 348 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU F 385 " --> pdb=" O PRO F 370 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER F 406 " --> pdb=" O THR F 415 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE F 417 " --> pdb=" O THR F 404 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N THR F 404 " --> pdb=" O ILE F 417 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 350 through 353 removed outlier: 7.274A pdb=" N ASP F 428 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL F 397 " --> pdb=" O ASP F 428 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE F 430 " --> pdb=" O PHE F 395 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE F 395 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS F 432 " --> pdb=" O LYS F 393 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1714 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: 1.35 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 3334 1.36 - 1.54: 6968 1.54 - 1.72: 184 1.72 - 1.90: 58 1.90 - 2.08: 16 Bond restraints: 10560 Sorted by residual: bond pdb=" C LEU B 88 " pdb=" O LEU B 88 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.19e-02 7.06e+03 2.61e+01 bond pdb=" C LEU D 88 " pdb=" O LEU D 88 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.19e-02 7.06e+03 2.61e+01 bond pdb=" CA SER D 89 " pdb=" CB SER D 89 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.55e-02 4.16e+03 2.13e+01 bond pdb=" CA SER B 89 " pdb=" CB SER B 89 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.55e-02 4.16e+03 2.13e+01 bond pdb=" C ARG F 447 " pdb=" O ARG F 447 " ideal model delta sigma weight residual 1.236 1.183 0.052 1.22e-02 6.72e+03 1.84e+01 ... (remaining 10555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 12108 2.23 - 4.47: 2110 4.47 - 6.70: 106 6.70 - 8.93: 8 8.93 - 11.16: 12 Bond angle restraints: 14344 Sorted by residual: angle pdb=" N HIS E 143 " pdb=" CA HIS E 143 " pdb=" C HIS E 143 " ideal model delta sigma weight residual 113.15 105.67 7.48 1.19e+00 7.06e-01 3.95e+01 angle pdb=" N HIS F 143 " pdb=" CA HIS F 143 " pdb=" C HIS F 143 " ideal model delta sigma weight residual 113.15 105.67 7.48 1.19e+00 7.06e-01 3.95e+01 angle pdb=" N SER E 213 " pdb=" CA SER E 213 " pdb=" C SER E 213 " ideal model delta sigma weight residual 108.99 117.44 -8.45 1.57e+00 4.06e-01 2.90e+01 angle pdb=" N SER F 213 " pdb=" CA SER F 213 " pdb=" C SER F 213 " ideal model delta sigma weight residual 108.99 117.44 -8.45 1.57e+00 4.06e-01 2.90e+01 angle pdb=" CA GLN D 127 " pdb=" C GLN D 127 " pdb=" O GLN D 127 " ideal model delta sigma weight residual 120.55 115.29 5.26 1.06e+00 8.90e-01 2.46e+01 ... (remaining 14339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 5784 17.57 - 35.14: 398 35.14 - 52.70: 94 52.70 - 70.27: 26 70.27 - 87.84: 12 Dihedral angle restraints: 6314 sinusoidal: 2566 harmonic: 3748 Sorted by residual: dihedral pdb=" C2C HEM C 201 " pdb=" C3C HEM C 201 " pdb=" CAC HEM C 201 " pdb=" CBC HEM C 201 " ideal model delta sinusoidal sigma weight residual 0.00 -87.51 87.51 2 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" C2C HEM A 201 " pdb=" C3C HEM A 201 " pdb=" CAC HEM A 201 " pdb=" CBC HEM A 201 " ideal model delta sinusoidal sigma weight residual -0.00 -87.51 87.51 2 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" C2B HEM B 201 " pdb=" C3B HEM B 201 " pdb=" CAB HEM B 201 " pdb=" CBB HEM B 201 " ideal model delta sinusoidal sigma weight residual 180.00 114.03 65.97 2 1.00e+01 1.00e-02 4.00e+01 ... (remaining 6311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 616 0.053 - 0.106: 396 0.106 - 0.159: 336 0.159 - 0.212: 156 0.212 - 0.265: 38 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA VAL D 54 " pdb=" N VAL D 54 " pdb=" C VAL D 54 " pdb=" CB VAL D 54 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA VAL B 54 " pdb=" N VAL B 54 " pdb=" C VAL B 54 " pdb=" CB VAL B 54 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA VAL F 237 " pdb=" N VAL F 237 " pdb=" C VAL F 237 " pdb=" CB VAL F 237 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1539 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 60 " -0.027 2.00e-02 2.50e+03 5.50e-02 3.02e+01 pdb=" C VAL B 60 " 0.095 2.00e-02 2.50e+03 pdb=" O VAL B 60 " -0.035 2.00e-02 2.50e+03 pdb=" N BLYS B 61 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 60 " 0.027 2.00e-02 2.50e+03 5.50e-02 3.02e+01 pdb=" C VAL D 60 " -0.095 2.00e-02 2.50e+03 pdb=" O VAL D 60 " 0.035 2.00e-02 2.50e+03 pdb=" N BLYS D 61 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BLYS B 61 " -0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C BLYS B 61 " 0.094 2.00e-02 2.50e+03 pdb=" O BLYS B 61 " -0.035 2.00e-02 2.50e+03 pdb=" N ALA B 62 " -0.033 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3426 2.85 - 3.37: 10214 3.37 - 3.88: 19380 3.88 - 4.39: 23989 4.39 - 4.90: 37494 Nonbonded interactions: 94503 Sorted by model distance: nonbonded pdb=" OE2 GLU D 43 " pdb=" O HOH D 301 " model vdw 2.343 3.040 nonbonded pdb=" OE2 GLU B 43 " pdb=" O HOH B 301 " model vdw 2.343 3.040 nonbonded pdb=" O THR B 84 " pdb=" O HOH B 302 " model vdw 2.452 3.040 nonbonded pdb=" O THR D 84 " pdb=" O HOH D 302 " model vdw 2.452 3.040 nonbonded pdb=" O VAL E 367 " pdb=" O HOH E 501 " model vdw 2.486 3.040 ... (remaining 94498 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=0.99 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: 3.970 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.320 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.013 0.250 10564 Z= 0.914 Angle : 1.542 11.164 14344 Z= 1.142 Chirality : 0.101 0.265 1542 Planarity : 0.008 0.055 1818 Dihedral : 13.622 87.838 3898 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.55 % Allowed : 6.92 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.23), residues: 1284 helix: 2.20 (0.21), residues: 614 sheet: 0.41 (0.43), residues: 154 loop : -0.80 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 414 TYR 0.017 0.002 TYR F 444 PHE 0.013 0.002 PHE F 454 TRP 0.015 0.003 TRP F 392 HIS 0.004 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.01242 (10560) covalent geometry : angle 1.54155 (14344) hydrogen bonds : bond 0.17366 ( 600) hydrogen bonds : angle 8.11861 ( 1714) Misc. bond : bond 0.21502 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.453 Fit side-chains REVERT: A 27 GLU cc_start: 0.8732 (tt0) cc_final: 0.8409 (tt0) REVERT: B 21 ASP cc_start: 0.8833 (m-30) cc_final: 0.8174 (m-30) REVERT: E 382 MET cc_start: 0.8760 (ttm) cc_final: 0.8466 (ttm) REVERT: E 396 MET cc_start: 0.8244 (mtm) cc_final: 0.7958 (mtm) REVERT: C 27 GLU cc_start: 0.8727 (tt0) cc_final: 0.8402 (tt0) REVERT: D 21 ASP cc_start: 0.8835 (m-30) cc_final: 0.8187 (m-30) REVERT: F 382 MET cc_start: 0.8763 (ttm) cc_final: 0.8467 (ttm) REVERT: F 396 MET cc_start: 0.8244 (mtm) cc_final: 0.7961 (mtm) outliers start: 4 outliers final: 0 residues processed: 127 average time/residue: 0.6524 time to fit residues: 88.1086 Evaluate side-chains 83 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN D 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.063412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.041981 restraints weight = 187970.715| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 7.22 r_work: 0.2407 rms_B_bonded: 6.96 restraints_weight: 2.0000 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2458 r_free = 0.2458 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2454 r_free = 0.2454 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10564 Z= 0.129 Angle : 0.579 9.460 14344 Z= 0.300 Chirality : 0.041 0.144 1542 Planarity : 0.004 0.036 1818 Dihedral : 7.871 82.555 1400 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.09 % Allowed : 12.02 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.23), residues: 1284 helix: 2.87 (0.20), residues: 628 sheet: 0.62 (0.41), residues: 158 loop : -0.35 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 104 TYR 0.014 0.001 TYR F 310 PHE 0.011 0.001 PHE F 225 TRP 0.012 0.001 TRP C 14 HIS 0.007 0.001 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00318 (10560) covalent geometry : angle 0.57889 (14344) hydrogen bonds : bond 0.03935 ( 600) hydrogen bonds : angle 5.30049 ( 1714) Misc. bond : bond 0.01451 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.344 Fit side-chains REVERT: A 27 GLU cc_start: 0.9462 (tt0) cc_final: 0.9178 (tt0) REVERT: B 7 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8656 (mt-10) REVERT: B 22 GLU cc_start: 0.8702 (mp0) cc_final: 0.8494 (mp0) REVERT: B 90 GLU cc_start: 0.9083 (pt0) cc_final: 0.8580 (pp20) REVERT: B 104 ARG cc_start: 0.9150 (ttm-80) cc_final: 0.8517 (ttp-110) REVERT: E 382 MET cc_start: 0.9051 (ttm) cc_final: 0.8777 (ttm) REVERT: E 396 MET cc_start: 0.8623 (mtm) cc_final: 0.8258 (mtt) REVERT: C 27 GLU cc_start: 0.9461 (tt0) cc_final: 0.9177 (tt0) REVERT: D 7 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8668 (mt-10) REVERT: D 22 GLU cc_start: 0.8676 (mp0) cc_final: 0.8471 (mp0) REVERT: D 90 GLU cc_start: 0.9078 (pt0) cc_final: 0.8575 (pp20) REVERT: D 104 ARG cc_start: 0.9158 (ttm-80) cc_final: 0.8551 (ttp-110) REVERT: F 276 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8918 (tm-30) REVERT: F 382 MET cc_start: 0.9055 (ttm) cc_final: 0.8779 (ttm) REVERT: F 396 MET cc_start: 0.8619 (mtm) cc_final: 0.8247 (mtt) outliers start: 10 outliers final: 2 residues processed: 98 average time/residue: 0.6174 time to fit residues: 64.6643 Evaluate side-chains 90 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain C residue 74 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 48 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN C 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.037905 restraints weight = 210649.885| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 6.95 r_work: 0.2321 rms_B_bonded: 6.67 restraints_weight: 2.0000 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2334 r_free = 0.2334 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2333 r_free = 0.2333 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 10564 Z= 0.166 Angle : 0.578 9.238 14344 Z= 0.290 Chirality : 0.042 0.162 1542 Planarity : 0.004 0.036 1818 Dihedral : 6.946 83.515 1400 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.73 % Allowed : 11.93 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.24), residues: 1284 helix: 2.96 (0.21), residues: 622 sheet: 0.70 (0.40), residues: 162 loop : -0.06 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 104 TYR 0.015 0.001 TYR F 310 PHE 0.009 0.001 PHE F 164 TRP 0.012 0.002 TRP C 14 HIS 0.005 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00433 (10560) covalent geometry : angle 0.57779 (14344) hydrogen bonds : bond 0.03752 ( 600) hydrogen bonds : angle 4.73649 ( 1714) Misc. bond : bond 0.08830 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 GLU cc_start: 0.9079 (pt0) cc_final: 0.8715 (pp20) REVERT: B 104 ARG cc_start: 0.9188 (ttm-80) cc_final: 0.8533 (ttp-110) REVERT: E 180 ASP cc_start: 0.9279 (m-30) cc_final: 0.8901 (p0) REVERT: E 375 MET cc_start: 0.9226 (tpp) cc_final: 0.8989 (tpp) REVERT: E 396 MET cc_start: 0.8863 (mtm) cc_final: 0.8505 (mtt) REVERT: C 94 ASP cc_start: 0.9139 (t0) cc_final: 0.8938 (t0) REVERT: D 90 GLU cc_start: 0.9076 (pt0) cc_final: 0.8707 (pp20) REVERT: D 104 ARG cc_start: 0.9190 (ttm-80) cc_final: 0.8552 (ttp-110) REVERT: F 180 ASP cc_start: 0.9284 (m-30) cc_final: 0.8903 (p0) REVERT: F 276 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8970 (tm-30) REVERT: F 375 MET cc_start: 0.9237 (tpp) cc_final: 0.8995 (tpp) REVERT: F 396 MET cc_start: 0.8853 (mtm) cc_final: 0.8494 (mtt) outliers start: 17 outliers final: 4 residues processed: 107 average time/residue: 0.7489 time to fit residues: 85.3657 Evaluate side-chains 92 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 10.0000 chunk 81 optimal weight: 0.0670 chunk 16 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.059941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.038520 restraints weight = 226039.893| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 7.46 r_work: 0.2352 rms_B_bonded: 6.99 restraints_weight: 2.0000 r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2363 r_free = 0.2363 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2363 r_free = 0.2363 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 10564 Z= 0.105 Angle : 0.544 8.378 14344 Z= 0.270 Chirality : 0.039 0.139 1542 Planarity : 0.004 0.038 1818 Dihedral : 6.976 87.671 1400 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.09 % Allowed : 12.57 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.24), residues: 1284 helix: 2.86 (0.21), residues: 624 sheet: 0.67 (0.40), residues: 166 loop : 0.05 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 104 TYR 0.011 0.001 TYR E 444 PHE 0.009 0.001 PHE F 418 TRP 0.010 0.001 TRP A 14 HIS 0.004 0.000 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00269 (10560) covalent geometry : angle 0.54403 (14344) hydrogen bonds : bond 0.03031 ( 600) hydrogen bonds : angle 4.51104 ( 1714) Misc. bond : bond 0.07016 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9131 (m-30) cc_final: 0.8687 (p0) REVERT: B 90 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8731 (pp20) REVERT: E 180 ASP cc_start: 0.9282 (m-30) cc_final: 0.8875 (p0) REVERT: E 375 MET cc_start: 0.9289 (tpp) cc_final: 0.9004 (tpp) REVERT: E 382 MET cc_start: 0.9257 (ttm) cc_final: 0.8996 (ttm) REVERT: E 396 MET cc_start: 0.8891 (mtm) cc_final: 0.8546 (mtt) REVERT: E 403 ARG cc_start: 0.9484 (mtp180) cc_final: 0.9104 (mtp-110) REVERT: C 6 ASP cc_start: 0.9128 (m-30) cc_final: 0.8684 (p0) REVERT: D 90 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8734 (pp20) REVERT: F 180 ASP cc_start: 0.9292 (m-30) cc_final: 0.8883 (p0) REVERT: F 276 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8973 (tm-30) REVERT: F 375 MET cc_start: 0.9303 (tpp) cc_final: 0.9011 (tpp) REVERT: F 382 MET cc_start: 0.9263 (ttm) cc_final: 0.9003 (ttm) REVERT: F 396 MET cc_start: 0.8892 (mtm) cc_final: 0.8549 (mtt) REVERT: F 403 ARG cc_start: 0.9491 (mtp180) cc_final: 0.9114 (mtp-110) outliers start: 10 outliers final: 2 residues processed: 97 average time/residue: 0.6783 time to fit residues: 70.1170 Evaluate side-chains 93 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain D residue 90 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS D 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.038027 restraints weight = 225885.699| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 7.30 r_work: 0.2366 rms_B_bonded: 6.91 restraints_weight: 2.0000 r_work (final): 0.2366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2379 r_free = 0.2379 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2379 r_free = 0.2379 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10564 Z= 0.114 Angle : 0.546 11.121 14344 Z= 0.270 Chirality : 0.039 0.142 1542 Planarity : 0.004 0.038 1818 Dihedral : 6.969 87.955 1400 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.73 % Allowed : 12.66 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.24), residues: 1284 helix: 2.96 (0.21), residues: 616 sheet: 0.72 (0.41), residues: 166 loop : 0.04 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.012 0.001 TYR F 444 PHE 0.008 0.001 PHE F 418 TRP 0.009 0.001 TRP A 14 HIS 0.003 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00304 (10560) covalent geometry : angle 0.54555 (14344) hydrogen bonds : bond 0.03022 ( 600) hydrogen bonds : angle 4.40496 ( 1714) Misc. bond : bond 0.06710 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.9548 (t0) cc_final: 0.9292 (t0) REVERT: B 90 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8765 (pp20) REVERT: E 124 MET cc_start: 0.7846 (pp-130) cc_final: 0.7472 (ppp) REVERT: E 180 ASP cc_start: 0.9269 (m-30) cc_final: 0.8902 (p0) REVERT: E 382 MET cc_start: 0.9276 (ttm) cc_final: 0.9064 (ttm) REVERT: E 396 MET cc_start: 0.8948 (mtm) cc_final: 0.8597 (mtt) REVERT: E 403 ARG cc_start: 0.9504 (mtp180) cc_final: 0.9138 (mtp-110) REVERT: C 78 ASN cc_start: 0.9547 (t0) cc_final: 0.9292 (t0) REVERT: D 90 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8765 (pp20) REVERT: F 124 MET cc_start: 0.7861 (pp-130) cc_final: 0.7486 (ppp) REVERT: F 180 ASP cc_start: 0.9271 (m-30) cc_final: 0.8899 (p0) REVERT: F 276 GLU cc_start: 0.9280 (tm-30) cc_final: 0.8857 (tm-30) REVERT: F 382 MET cc_start: 0.9283 (ttm) cc_final: 0.9072 (ttm) REVERT: F 396 MET cc_start: 0.8947 (mtm) cc_final: 0.8597 (mtt) REVERT: F 403 ARG cc_start: 0.9505 (mtp180) cc_final: 0.9140 (mtp-110) outliers start: 6 outliers final: 2 residues processed: 93 average time/residue: 0.6556 time to fit residues: 64.8076 Evaluate side-chains 93 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain D residue 90 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 72 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.059553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.037813 restraints weight = 226408.239| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 7.34 r_work: 0.2370 rms_B_bonded: 6.92 restraints_weight: 2.0000 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2383 r_free = 0.2383 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2383 r_free = 0.2383 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 10564 Z= 0.109 Angle : 0.562 11.098 14344 Z= 0.276 Chirality : 0.039 0.141 1542 Planarity : 0.004 0.039 1818 Dihedral : 7.019 89.192 1400 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.91 % Allowed : 13.21 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.24), residues: 1284 helix: 2.93 (0.21), residues: 618 sheet: 0.72 (0.41), residues: 166 loop : 0.06 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 104 TYR 0.010 0.001 TYR F 310 PHE 0.008 0.001 PHE F 418 TRP 0.009 0.001 TRP C 14 HIS 0.003 0.001 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00292 (10560) covalent geometry : angle 0.56219 (14344) hydrogen bonds : bond 0.02921 ( 600) hydrogen bonds : angle 4.32078 ( 1714) Misc. bond : bond 0.06270 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9157 (m-30) cc_final: 0.8708 (p0) REVERT: A 78 ASN cc_start: 0.9566 (t0) cc_final: 0.9254 (t0) REVERT: B 21 ASP cc_start: 0.9406 (m-30) cc_final: 0.8884 (p0) REVERT: B 22 GLU cc_start: 0.9191 (pm20) cc_final: 0.8835 (pm20) REVERT: B 90 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8797 (pp20) REVERT: E 124 MET cc_start: 0.7899 (pp-130) cc_final: 0.7678 (ppp) REVERT: E 180 ASP cc_start: 0.9283 (m-30) cc_final: 0.8911 (p0) REVERT: E 375 MET cc_start: 0.9120 (tpp) cc_final: 0.8678 (tpp) REVERT: E 382 MET cc_start: 0.9248 (ttm) cc_final: 0.9041 (ttm) REVERT: E 396 MET cc_start: 0.8985 (mtm) cc_final: 0.8625 (mtt) REVERT: E 403 ARG cc_start: 0.9504 (mtp180) cc_final: 0.9187 (mtp-110) REVERT: C 6 ASP cc_start: 0.9134 (m-30) cc_final: 0.8744 (p0) REVERT: C 78 ASN cc_start: 0.9564 (t0) cc_final: 0.9253 (t0) REVERT: D 21 ASP cc_start: 0.9398 (m-30) cc_final: 0.8873 (p0) REVERT: D 22 GLU cc_start: 0.9178 (pm20) cc_final: 0.8856 (pm20) REVERT: D 90 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8796 (pp20) REVERT: F 124 MET cc_start: 0.7908 (pp-130) cc_final: 0.7686 (ppp) REVERT: F 180 ASP cc_start: 0.9287 (m-30) cc_final: 0.8912 (p0) REVERT: F 276 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8883 (tm-30) REVERT: F 375 MET cc_start: 0.9122 (tpp) cc_final: 0.8679 (tpp) REVERT: F 382 MET cc_start: 0.9256 (ttm) cc_final: 0.9049 (ttm) REVERT: F 396 MET cc_start: 0.8986 (mtm) cc_final: 0.8626 (mtt) REVERT: F 403 ARG cc_start: 0.9510 (mtp180) cc_final: 0.9197 (mtp-110) outliers start: 8 outliers final: 4 residues processed: 93 average time/residue: 0.6117 time to fit residues: 60.7217 Evaluate side-chains 95 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 90 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 0.0010 chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.059705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.037902 restraints weight = 239885.565| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 7.46 r_work: 0.2372 rms_B_bonded: 7.00 restraints_weight: 2.0000 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2387 r_free = 0.2387 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2387 r_free = 0.2387 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10564 Z= 0.106 Angle : 0.550 11.790 14344 Z= 0.270 Chirality : 0.039 0.145 1542 Planarity : 0.004 0.044 1818 Dihedral : 7.030 89.991 1400 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.82 % Allowed : 13.48 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.24), residues: 1284 helix: 2.98 (0.21), residues: 618 sheet: 0.87 (0.42), residues: 160 loop : 0.03 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 104 TYR 0.010 0.001 TYR F 310 PHE 0.009 0.001 PHE F 418 TRP 0.008 0.001 TRP C 14 HIS 0.003 0.000 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00281 (10560) covalent geometry : angle 0.55026 (14344) hydrogen bonds : bond 0.02822 ( 600) hydrogen bonds : angle 4.23527 ( 1714) Misc. bond : bond 0.05889 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9154 (m-30) cc_final: 0.8699 (p0) REVERT: A 78 ASN cc_start: 0.9568 (t0) cc_final: 0.9259 (t0) REVERT: B 21 ASP cc_start: 0.9388 (m-30) cc_final: 0.8798 (p0) REVERT: B 22 GLU cc_start: 0.9175 (pm20) cc_final: 0.8788 (pm20) REVERT: B 90 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8812 (pp20) REVERT: E 124 MET cc_start: 0.7912 (pp-130) cc_final: 0.7595 (ppp) REVERT: E 180 ASP cc_start: 0.9300 (m-30) cc_final: 0.8912 (p0) REVERT: E 375 MET cc_start: 0.9091 (tpp) cc_final: 0.8719 (tpp) REVERT: E 382 MET cc_start: 0.9268 (ttm) cc_final: 0.9049 (ttm) REVERT: E 396 MET cc_start: 0.9005 (mtm) cc_final: 0.8654 (mtt) REVERT: E 403 ARG cc_start: 0.9538 (mtp180) cc_final: 0.9154 (mtp-110) REVERT: C 6 ASP cc_start: 0.9140 (m-30) cc_final: 0.8740 (p0) REVERT: C 78 ASN cc_start: 0.9566 (t0) cc_final: 0.9256 (t0) REVERT: D 21 ASP cc_start: 0.9379 (m-30) cc_final: 0.8817 (p0) REVERT: D 22 GLU cc_start: 0.9159 (pm20) cc_final: 0.8843 (pm20) REVERT: D 90 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8813 (pp20) REVERT: F 124 MET cc_start: 0.7921 (pp-130) cc_final: 0.7603 (ppp) REVERT: F 180 ASP cc_start: 0.9299 (m-30) cc_final: 0.8915 (p0) REVERT: F 276 GLU cc_start: 0.9297 (tm-30) cc_final: 0.8880 (tm-30) REVERT: F 375 MET cc_start: 0.9096 (tpp) cc_final: 0.8724 (tpp) REVERT: F 382 MET cc_start: 0.9274 (ttm) cc_final: 0.9055 (ttm) REVERT: F 396 MET cc_start: 0.9010 (mtm) cc_final: 0.8662 (mtt) REVERT: F 403 ARG cc_start: 0.9546 (mtp180) cc_final: 0.9162 (mtp-110) outliers start: 7 outliers final: 2 residues processed: 93 average time/residue: 0.7537 time to fit residues: 74.5288 Evaluate side-chains 93 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain D residue 90 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.057809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.036967 restraints weight = 218650.293| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 7.30 r_work: 0.2363 rms_B_bonded: 6.90 restraints_weight: 2.0000 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2382 r_free = 0.2382 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2383 r_free = 0.2383 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10564 Z= 0.113 Angle : 0.553 11.999 14344 Z= 0.272 Chirality : 0.039 0.134 1542 Planarity : 0.004 0.037 1818 Dihedral : 6.967 89.363 1400 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.73 % Allowed : 13.75 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.24), residues: 1284 helix: 2.98 (0.21), residues: 618 sheet: 0.54 (0.39), residues: 184 loop : 0.21 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 104 TYR 0.010 0.001 TYR E 310 PHE 0.008 0.001 PHE F 418 TRP 0.008 0.001 TRP C 14 HIS 0.003 0.001 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00303 (10560) covalent geometry : angle 0.55262 (14344) hydrogen bonds : bond 0.02859 ( 600) hydrogen bonds : angle 4.24718 ( 1714) Misc. bond : bond 0.05792 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9169 (m-30) cc_final: 0.8710 (p0) REVERT: A 78 ASN cc_start: 0.9579 (t0) cc_final: 0.9297 (t0) REVERT: B 21 ASP cc_start: 0.9338 (m-30) cc_final: 0.8793 (p0) REVERT: B 22 GLU cc_start: 0.9150 (pm20) cc_final: 0.8865 (pm20) REVERT: B 90 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8814 (pp20) REVERT: E 124 MET cc_start: 0.7941 (pp-130) cc_final: 0.7650 (ppp) REVERT: E 180 ASP cc_start: 0.9293 (m-30) cc_final: 0.8904 (p0) REVERT: E 375 MET cc_start: 0.9125 (tpp) cc_final: 0.8774 (tpp) REVERT: E 382 MET cc_start: 0.9246 (ttm) cc_final: 0.8963 (ttm) REVERT: E 396 MET cc_start: 0.8988 (mtm) cc_final: 0.8718 (mtt) REVERT: E 403 ARG cc_start: 0.9549 (mtp180) cc_final: 0.9226 (mtp-110) REVERT: C 6 ASP cc_start: 0.9145 (m-30) cc_final: 0.8748 (p0) REVERT: C 78 ASN cc_start: 0.9578 (t0) cc_final: 0.9295 (t0) REVERT: D 21 ASP cc_start: 0.9335 (m-30) cc_final: 0.8774 (p0) REVERT: D 22 GLU cc_start: 0.9136 (pm20) cc_final: 0.8865 (pm20) REVERT: D 90 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8820 (pp20) REVERT: F 124 MET cc_start: 0.7949 (pp-130) cc_final: 0.7657 (ppp) REVERT: F 180 ASP cc_start: 0.9290 (m-30) cc_final: 0.8902 (p0) REVERT: F 276 GLU cc_start: 0.9302 (tm-30) cc_final: 0.8853 (tm-30) REVERT: F 375 MET cc_start: 0.9129 (tpp) cc_final: 0.8778 (tpp) REVERT: F 382 MET cc_start: 0.9247 (ttm) cc_final: 0.8965 (ttm) REVERT: F 396 MET cc_start: 0.8998 (mtm) cc_final: 0.8732 (mtt) REVERT: F 403 ARG cc_start: 0.9557 (mtp180) cc_final: 0.9240 (mtp-110) outliers start: 6 outliers final: 4 residues processed: 91 average time/residue: 0.7496 time to fit residues: 72.6502 Evaluate side-chains 95 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 90 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 29 optimal weight: 0.0070 chunk 30 optimal weight: 5.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.057659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.037123 restraints weight = 213432.333| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 7.21 r_work: 0.2376 rms_B_bonded: 6.82 restraints_weight: 2.0000 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2405 r_free = 0.2405 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2405 r_free = 0.2405 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10564 Z= 0.114 Angle : 0.550 11.724 14344 Z= 0.270 Chirality : 0.039 0.131 1542 Planarity : 0.004 0.037 1818 Dihedral : 6.934 88.949 1400 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.73 % Allowed : 13.48 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.24), residues: 1284 helix: 3.00 (0.21), residues: 618 sheet: 0.45 (0.39), residues: 186 loop : 0.25 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 104 TYR 0.010 0.001 TYR E 310 PHE 0.009 0.001 PHE F 418 TRP 0.008 0.001 TRP C 14 HIS 0.003 0.000 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00308 (10560) covalent geometry : angle 0.55032 (14344) hydrogen bonds : bond 0.02812 ( 600) hydrogen bonds : angle 4.14428 ( 1714) Misc. bond : bond 0.05714 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.9589 (t0) cc_final: 0.9311 (t0) REVERT: B 21 ASP cc_start: 0.9317 (m-30) cc_final: 0.8778 (p0) REVERT: B 22 GLU cc_start: 0.9164 (pm20) cc_final: 0.8871 (pm20) REVERT: B 90 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8812 (pp20) REVERT: E 124 MET cc_start: 0.7902 (pp-130) cc_final: 0.7618 (ppp) REVERT: E 180 ASP cc_start: 0.9285 (m-30) cc_final: 0.8897 (p0) REVERT: E 375 MET cc_start: 0.9144 (tpp) cc_final: 0.8800 (tpp) REVERT: E 382 MET cc_start: 0.9218 (ttm) cc_final: 0.8990 (ttm) REVERT: E 396 MET cc_start: 0.9018 (mtm) cc_final: 0.8667 (mtt) REVERT: E 403 ARG cc_start: 0.9540 (mtp180) cc_final: 0.9205 (mtp-110) REVERT: C 6 ASP cc_start: 0.9148 (m-30) cc_final: 0.8754 (p0) REVERT: C 78 ASN cc_start: 0.9584 (t0) cc_final: 0.9304 (t0) REVERT: D 21 ASP cc_start: 0.9312 (m-30) cc_final: 0.8772 (p0) REVERT: D 22 GLU cc_start: 0.9156 (pm20) cc_final: 0.8877 (pm20) REVERT: D 90 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8817 (pp20) REVERT: F 124 MET cc_start: 0.7927 (pp-130) cc_final: 0.7638 (ppp) REVERT: F 180 ASP cc_start: 0.9261 (m-30) cc_final: 0.8883 (p0) REVERT: F 276 GLU cc_start: 0.9311 (tm-30) cc_final: 0.8861 (tm-30) REVERT: F 375 MET cc_start: 0.9154 (tpp) cc_final: 0.8890 (tpp) REVERT: F 382 MET cc_start: 0.9216 (ttm) cc_final: 0.8987 (ttm) REVERT: F 396 MET cc_start: 0.9023 (mtm) cc_final: 0.8671 (mtt) REVERT: F 403 ARG cc_start: 0.9544 (mtp180) cc_final: 0.9211 (mtp-110) outliers start: 6 outliers final: 2 residues processed: 89 average time/residue: 0.7749 time to fit residues: 73.4708 Evaluate side-chains 93 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain D residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.0050 chunk 72 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.058406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.037766 restraints weight = 240147.830| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 7.56 r_work: 0.2390 rms_B_bonded: 6.98 restraints_weight: 2.0000 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2420 r_free = 0.2420 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10564 Z= 0.103 Angle : 0.554 11.956 14344 Z= 0.273 Chirality : 0.039 0.128 1542 Planarity : 0.004 0.038 1818 Dihedral : 6.814 87.460 1400 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.55 % Allowed : 13.84 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.24), residues: 1284 helix: 3.00 (0.21), residues: 618 sheet: 0.30 (0.39), residues: 190 loop : 0.23 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 104 TYR 0.010 0.001 TYR F 444 PHE 0.009 0.001 PHE F 418 TRP 0.008 0.001 TRP C 14 HIS 0.003 0.000 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00275 (10560) covalent geometry : angle 0.55427 (14344) hydrogen bonds : bond 0.02673 ( 600) hydrogen bonds : angle 4.08587 ( 1714) Misc. bond : bond 0.05399 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.9137 (m-30) cc_final: 0.8740 (p0) REVERT: A 78 ASN cc_start: 0.9593 (t0) cc_final: 0.9338 (t0) REVERT: B 21 ASP cc_start: 0.9293 (m-30) cc_final: 0.8748 (p0) REVERT: B 22 GLU cc_start: 0.9139 (pm20) cc_final: 0.8863 (pm20) REVERT: B 90 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8821 (pp20) REVERT: E 124 MET cc_start: 0.7917 (pp-130) cc_final: 0.7650 (ppp) REVERT: E 180 ASP cc_start: 0.9271 (m-30) cc_final: 0.8866 (p0) REVERT: E 375 MET cc_start: 0.9124 (tpp) cc_final: 0.8786 (tpp) REVERT: E 382 MET cc_start: 0.9263 (ttm) cc_final: 0.9007 (ttm) REVERT: E 396 MET cc_start: 0.9013 (mtm) cc_final: 0.8652 (mtt) REVERT: E 403 ARG cc_start: 0.9535 (mtp180) cc_final: 0.9209 (mtp-110) REVERT: C 6 ASP cc_start: 0.9134 (m-30) cc_final: 0.8754 (p0) REVERT: C 78 ASN cc_start: 0.9587 (t0) cc_final: 0.9328 (t0) REVERT: D 21 ASP cc_start: 0.9285 (m-30) cc_final: 0.8709 (p0) REVERT: D 22 GLU cc_start: 0.9146 (pm20) cc_final: 0.8861 (pm20) REVERT: D 90 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8819 (pp20) REVERT: F 124 MET cc_start: 0.7927 (pp-130) cc_final: 0.7660 (ppp) REVERT: F 180 ASP cc_start: 0.9261 (m-30) cc_final: 0.8867 (p0) REVERT: F 276 GLU cc_start: 0.9308 (tm-30) cc_final: 0.8896 (tm-30) REVERT: F 375 MET cc_start: 0.9121 (tpp) cc_final: 0.8782 (tpp) REVERT: F 382 MET cc_start: 0.9265 (ttm) cc_final: 0.9049 (ttm) REVERT: F 396 MET cc_start: 0.9010 (mtm) cc_final: 0.8648 (mtt) REVERT: F 403 ARG cc_start: 0.9538 (mtp180) cc_final: 0.9214 (mtp-110) outliers start: 4 outliers final: 2 residues processed: 91 average time/residue: 0.7975 time to fit residues: 77.1194 Evaluate side-chains 95 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain D residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 66 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.058393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.037717 restraints weight = 212485.237| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 7.26 r_work: 0.2396 rms_B_bonded: 6.84 restraints_weight: 2.0000 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2426 r_free = 0.2426 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2426 r_free = 0.2426 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10564 Z= 0.103 Angle : 0.545 11.970 14344 Z= 0.268 Chirality : 0.039 0.125 1542 Planarity : 0.004 0.038 1818 Dihedral : 6.724 86.602 1400 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.55 % Allowed : 13.84 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.24), residues: 1284 helix: 3.02 (0.21), residues: 618 sheet: 0.33 (0.40), residues: 186 loop : 0.26 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 104 TYR 0.011 0.001 TYR E 444 PHE 0.008 0.001 PHE F 418 TRP 0.007 0.001 TRP C 14 HIS 0.003 0.000 HIS E 369 Details of bonding type rmsd covalent geometry : bond 0.00276 (10560) covalent geometry : angle 0.54472 (14344) hydrogen bonds : bond 0.02646 ( 600) hydrogen bonds : angle 4.00441 ( 1714) Misc. bond : bond 0.05067 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3609.98 seconds wall clock time: 62 minutes 16.07 seconds (3736.07 seconds total)