Starting phenix.real_space_refine on Thu Mar 14 19:59:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmy_29300/03_2024/8fmy_29300.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmy_29300/03_2024/8fmy_29300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmy_29300/03_2024/8fmy_29300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmy_29300/03_2024/8fmy_29300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmy_29300/03_2024/8fmy_29300.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmy_29300/03_2024/8fmy_29300.pdb" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 6036 2.51 5 N 1611 2.21 5 O 1893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9597 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3199 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 13, 'TRANS': 406} Chain: "B" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3199 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 13, 'TRANS': 406} Chain: "C" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3199 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 13, 'TRANS': 406} Time building chain proxies: 5.32, per 1000 atoms: 0.55 Number of scatterers: 9597 At special positions: 0 Unit cell: (103, 104, 98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1893 8.00 N 1611 7.00 C 6036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 362 " distance=2.04 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 391 " distance=2.04 Simple disulfide: pdb=" SG CYS A 393 " - pdb=" SG CYS A 416 " distance=2.04 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 339 " distance=2.04 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 362 " distance=2.04 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 391 " distance=2.04 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 416 " distance=2.04 Simple disulfide: pdb=" SG CYS C 330 " - pdb=" SG CYS C 339 " distance=2.03 Simple disulfide: pdb=" SG CYS C 354 " - pdb=" SG CYS C 362 " distance=2.04 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 391 " distance=2.04 Simple disulfide: pdb=" SG CYS C 393 " - pdb=" SG CYS C 416 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.9 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2358 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 40.0% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 28 through 33 removed outlier: 3.556A pdb=" N LEU A 32 " --> pdb=" O HIS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 71 through 105 removed outlier: 3.500A pdb=" N GLU A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.930A pdb=" N MET A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.650A pdb=" N HIS A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 removed outlier: 3.619A pdb=" N ALA A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 152 Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.628A pdb=" N GLY A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 186 removed outlier: 3.565A pdb=" N ILE A 186 " --> pdb=" O ILE A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 186' Processing helix chain 'A' and resid 190 through 219 removed outlier: 3.668A pdb=" N ILE A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.521A pdb=" N GLN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 232 through 235 removed outlier: 4.100A pdb=" N ASN A 235 " --> pdb=" O SER A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.763A pdb=" N LEU A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.619A pdb=" N SER A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'B' and resid 28 through 33 removed outlier: 3.557A pdb=" N LEU B 32 " --> pdb=" O HIS B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 70 Processing helix chain 'B' and resid 71 through 105 removed outlier: 3.751A pdb=" N ASN B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.930A pdb=" N MET B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 124 through 136 removed outlier: 3.650A pdb=" N HIS B 134 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.619A pdb=" N ALA B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.628A pdb=" N GLY B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 removed outlier: 3.565A pdb=" N ILE B 186 " --> pdb=" O ILE B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 186' Processing helix chain 'B' and resid 190 through 219 removed outlier: 3.667A pdb=" N ILE B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 201 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Proline residue: B 215 - end of helix removed outlier: 3.521A pdb=" N GLN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 232 through 235 removed outlier: 4.101A pdb=" N ASN B 235 " --> pdb=" O SER B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 237 through 245 removed outlier: 3.762A pdb=" N LEU B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.620A pdb=" N SER B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 330 Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.557A pdb=" N LEU C 32 " --> pdb=" O HIS C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 70 Processing helix chain 'C' and resid 71 through 105 removed outlier: 3.750A pdb=" N ASN C 80 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 3.931A pdb=" N MET C 91 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.651A pdb=" N HIS C 134 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.618A pdb=" N ALA C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.628A pdb=" N GLY C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 186 removed outlier: 3.565A pdb=" N ILE C 186 " --> pdb=" O ILE C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 186' Processing helix chain 'C' and resid 190 through 219 removed outlier: 3.667A pdb=" N ILE C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 203 " --> pdb=" O GLY C 199 " (cutoff:3.500A) Proline residue: C 215 - end of helix removed outlier: 3.521A pdb=" N GLN C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'C' and resid 232 through 235 removed outlier: 4.100A pdb=" N ASN C 235 " --> pdb=" O SER C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 237 through 245 removed outlier: 3.762A pdb=" N LEU C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.619A pdb=" N SER C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 330 Processing helix chain 'C' and resid 348 through 356 Processing helix chain 'C' and resid 358 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332 removed outlier: 3.643A pdb=" N LYS A 48 " --> pdb=" O CYS A 339 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU A 294 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR A 42 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 292 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASN A 44 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ALA A 290 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N LYS A 46 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LYS A 48 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU A 286 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N PHE A 314 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE A 325 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 161 removed outlier: 8.404A pdb=" N THR A 167 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU A 55 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 267 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU A 278 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE A 265 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU A 280 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLY A 263 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 411 Processing sheet with id=AA7, first strand: chain 'A' and resid 398 through 399 removed outlier: 7.065A pdb=" N LEU A 425 " --> pdb=" O MET B 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 331 through 332 removed outlier: 3.643A pdb=" N LYS B 48 " --> pdb=" O CYS B 339 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU B 294 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR B 42 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 292 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASN B 44 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ALA B 290 " --> pdb=" O ASN B 44 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N LYS B 46 " --> pdb=" O PRO B 288 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LYS B 48 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU B 286 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N PHE B 314 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 325 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 157 through 161 removed outlier: 8.403A pdb=" N THR B 167 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU B 55 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 267 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU B 278 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE B 265 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU B 280 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLY B 263 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 300 through 302 Processing sheet with id=AB2, first strand: chain 'B' and resid 409 through 411 Processing sheet with id=AB3, first strand: chain 'B' and resid 398 through 399 removed outlier: 7.080A pdb=" N LEU B 425 " --> pdb=" O MET C 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 331 through 332 removed outlier: 3.642A pdb=" N LYS C 48 " --> pdb=" O CYS C 339 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU C 294 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR C 42 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 292 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASN C 44 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ALA C 290 " --> pdb=" O ASN C 44 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N LYS C 46 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LYS C 48 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU C 286 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N PHE C 314 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE C 325 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 161 removed outlier: 8.403A pdb=" N THR C 167 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU C 55 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 267 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU C 278 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE C 265 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU C 280 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLY C 263 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 300 through 302 424 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2997 1.34 - 1.46: 1888 1.46 - 1.59: 4757 1.59 - 1.72: 0 1.72 - 1.84: 84 Bond restraints: 9726 Sorted by residual: bond pdb=" N ASP C 172 " pdb=" CA ASP C 172 " ideal model delta sigma weight residual 1.460 1.496 -0.037 2.20e-02 2.07e+03 2.76e+00 bond pdb=" N ASP A 172 " pdb=" CA ASP A 172 " ideal model delta sigma weight residual 1.460 1.496 -0.036 2.20e-02 2.07e+03 2.75e+00 bond pdb=" N ASP B 172 " pdb=" CA ASP B 172 " ideal model delta sigma weight residual 1.460 1.496 -0.036 2.20e-02 2.07e+03 2.67e+00 bond pdb=" CA THR B 173 " pdb=" C THR B 173 " ideal model delta sigma weight residual 1.524 1.542 -0.019 1.27e-02 6.20e+03 2.12e+00 bond pdb=" CA THR C 173 " pdb=" C THR C 173 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.27e-02 6.20e+03 2.02e+00 ... (remaining 9721 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.14: 195 106.14 - 113.12: 5136 113.12 - 120.11: 3722 120.11 - 127.09: 4114 127.09 - 134.07: 57 Bond angle restraints: 13224 Sorted by residual: angle pdb=" N THR B 173 " pdb=" CA THR B 173 " pdb=" C THR B 173 " ideal model delta sigma weight residual 111.07 115.94 -4.87 1.07e+00 8.73e-01 2.07e+01 angle pdb=" N THR C 173 " pdb=" CA THR C 173 " pdb=" C THR C 173 " ideal model delta sigma weight residual 111.07 115.93 -4.86 1.07e+00 8.73e-01 2.06e+01 angle pdb=" N THR A 173 " pdb=" CA THR A 173 " pdb=" C THR A 173 " ideal model delta sigma weight residual 111.07 115.89 -4.82 1.07e+00 8.73e-01 2.03e+01 angle pdb=" N LYS B 68 " pdb=" CA LYS B 68 " pdb=" C LYS B 68 " ideal model delta sigma weight residual 111.33 116.31 -4.98 1.21e+00 6.83e-01 1.70e+01 angle pdb=" N LYS C 68 " pdb=" CA LYS C 68 " pdb=" C LYS C 68 " ideal model delta sigma weight residual 111.33 116.29 -4.96 1.21e+00 6.83e-01 1.68e+01 ... (remaining 13219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 5514 15.33 - 30.65: 342 30.65 - 45.98: 62 45.98 - 61.31: 31 61.31 - 76.64: 18 Dihedral angle restraints: 5967 sinusoidal: 2298 harmonic: 3669 Sorted by residual: dihedral pdb=" CB CYS B 393 " pdb=" SG CYS B 393 " pdb=" SG CYS B 416 " pdb=" CB CYS B 416 " ideal model delta sinusoidal sigma weight residual 93.00 153.09 -60.09 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CB CYS C 393 " pdb=" SG CYS C 393 " pdb=" SG CYS C 416 " pdb=" CB CYS C 416 " ideal model delta sinusoidal sigma weight residual 93.00 153.09 -60.09 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CB CYS A 393 " pdb=" SG CYS A 393 " pdb=" SG CYS A 416 " pdb=" CB CYS A 416 " ideal model delta sinusoidal sigma weight residual 93.00 153.08 -60.08 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 5964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 782 0.039 - 0.077: 496 0.077 - 0.116: 233 0.116 - 0.155: 85 0.155 - 0.193: 18 Chirality restraints: 1614 Sorted by residual: chirality pdb=" CA ILE C 183 " pdb=" N ILE C 183 " pdb=" C ILE C 183 " pdb=" CB ILE C 183 " both_signs ideal model delta sigma weight residual False 2.43 2.24 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ILE A 183 " pdb=" N ILE A 183 " pdb=" C ILE A 183 " pdb=" CB ILE A 183 " both_signs ideal model delta sigma weight residual False 2.43 2.24 0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CA ILE B 183 " pdb=" N ILE B 183 " pdb=" C ILE B 183 " pdb=" CB ILE B 183 " both_signs ideal model delta sigma weight residual False 2.43 2.24 0.19 2.00e-01 2.50e+01 9.00e-01 ... (remaining 1611 not shown) Planarity restraints: 1695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 210 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ILE A 210 " 0.060 2.00e-02 2.50e+03 pdb=" O ILE A 210 " -0.022 2.00e-02 2.50e+03 pdb=" N THR A 211 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 210 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C ILE B 210 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE B 210 " -0.022 2.00e-02 2.50e+03 pdb=" N THR B 211 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 210 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ILE C 210 " -0.059 2.00e-02 2.50e+03 pdb=" O ILE C 210 " 0.022 2.00e-02 2.50e+03 pdb=" N THR C 211 " 0.020 2.00e-02 2.50e+03 ... (remaining 1692 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 3594 2.91 - 3.41: 8340 3.41 - 3.91: 14234 3.91 - 4.40: 15737 4.40 - 4.90: 27878 Nonbonded interactions: 69783 Sorted by model distance: nonbonded pdb=" O THR A 319 " pdb=" OG1 THR A 320 " model vdw 2.417 2.440 nonbonded pdb=" O THR B 319 " pdb=" OG1 THR B 320 " model vdw 2.417 2.440 nonbonded pdb=" O THR C 319 " pdb=" OG1 THR C 320 " model vdw 2.417 2.440 nonbonded pdb=" OD1 ASN A 44 " pdb=" OG SER A 336 " model vdw 2.505 2.440 nonbonded pdb=" OD1 ASN B 44 " pdb=" OG SER B 336 " model vdw 2.505 2.440 ... (remaining 69778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.000 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.180 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 : 0.008 0.050 9726 Z= 0.542 Angle : 1.159 7.388 13224 Z= 0.715 Chirality : 0.062 0.193 1614 Planarity : 0.007 0.049 1695 Dihedral : 12.096 76.635 3573 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1254 helix: -1.03 (0.21), residues: 402 sheet: 0.31 (0.31), residues: 258 loop : -0.98 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.007 TRP B 307 HIS 0.006 0.002 HIS B 257 PHE 0.023 0.005 PHE C 281 TYR 0.042 0.006 TYR A 45 ARG 0.013 0.002 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.905 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.7443 time to fit residues: 105.3459 Evaluate side-chains 32 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 HIS C 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9726 Z= 0.187 Angle : 0.584 5.087 13224 Z= 0.334 Chirality : 0.044 0.137 1614 Planarity : 0.004 0.046 1695 Dihedral : 4.964 17.817 1350 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.83 % Allowed : 4.04 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1254 helix: 1.18 (0.25), residues: 405 sheet: 0.34 (0.32), residues: 255 loop : -0.40 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 307 HIS 0.002 0.001 HIS B 257 PHE 0.008 0.001 PHE A 234 TYR 0.012 0.002 TYR A 45 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.985 Fit side-chains REVERT: B 349 HIS cc_start: 0.6960 (OUTLIER) cc_final: 0.6700 (t-90) REVERT: B 426 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8552 (tt) outliers start: 9 outliers final: 2 residues processed: 38 average time/residue: 1.2229 time to fit residues: 51.0605 Evaluate side-chains 34 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9726 Z= 0.338 Angle : 0.625 7.042 13224 Z= 0.351 Chirality : 0.046 0.164 1614 Planarity : 0.004 0.037 1695 Dihedral : 4.907 17.600 1350 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.92 % Allowed : 4.96 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1254 helix: 1.86 (0.27), residues: 387 sheet: 0.16 (0.32), residues: 249 loop : -0.48 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 307 HIS 0.010 0.001 HIS B 349 PHE 0.013 0.002 PHE A 234 TYR 0.015 0.002 TYR A 274 ARG 0.003 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 1.195 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 38 average time/residue: 1.2729 time to fit residues: 53.1006 Evaluate side-chains 31 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9726 Z= 0.188 Angle : 0.510 5.311 13224 Z= 0.288 Chirality : 0.043 0.142 1614 Planarity : 0.003 0.037 1695 Dihedral : 4.599 17.166 1350 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.64 % Allowed : 5.97 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1254 helix: 2.27 (0.27), residues: 372 sheet: 0.11 (0.32), residues: 249 loop : -0.56 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 307 HIS 0.002 0.001 HIS C 134 PHE 0.008 0.001 PHE B 238 TYR 0.011 0.001 TYR A 274 ARG 0.002 0.000 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 1.052 Fit side-chains REVERT: B 426 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8624 (tt) outliers start: 7 outliers final: 2 residues processed: 34 average time/residue: 1.2014 time to fit residues: 44.9235 Evaluate side-chains 31 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 84 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9726 Z= 0.129 Angle : 0.454 4.747 13224 Z= 0.255 Chirality : 0.042 0.134 1614 Planarity : 0.003 0.033 1695 Dihedral : 4.243 17.174 1350 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.73 % Allowed : 6.80 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1254 helix: 2.47 (0.27), residues: 375 sheet: 0.18 (0.31), residues: 258 loop : -0.51 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 307 HIS 0.001 0.000 HIS C 134 PHE 0.006 0.001 PHE B 375 TYR 0.009 0.001 TYR C 274 ARG 0.002 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 1.238 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 37 average time/residue: 1.1798 time to fit residues: 48.1971 Evaluate side-chains 31 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9726 Z= 0.315 Angle : 0.565 4.969 13224 Z= 0.319 Chirality : 0.045 0.144 1614 Planarity : 0.004 0.039 1695 Dihedral : 4.568 17.555 1350 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.73 % Allowed : 7.71 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1254 helix: 2.48 (0.28), residues: 372 sheet: 0.09 (0.33), residues: 246 loop : -0.58 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 307 HIS 0.003 0.001 HIS A 134 PHE 0.013 0.002 PHE C 238 TYR 0.016 0.002 TYR A 274 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 1.204 Fit side-chains REVERT: B 426 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8685 (tt) outliers start: 8 outliers final: 5 residues processed: 35 average time/residue: 1.2830 time to fit residues: 49.4091 Evaluate side-chains 34 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9726 Z= 0.151 Angle : 0.465 5.457 13224 Z= 0.261 Chirality : 0.042 0.126 1614 Planarity : 0.003 0.032 1695 Dihedral : 4.304 17.433 1350 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.64 % Allowed : 8.08 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1254 helix: 2.52 (0.28), residues: 375 sheet: 0.09 (0.32), residues: 258 loop : -0.63 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 307 HIS 0.002 0.001 HIS C 134 PHE 0.005 0.001 PHE A 281 TYR 0.009 0.001 TYR A 274 ARG 0.001 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 1.070 Fit side-chains REVERT: B 426 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8622 (tt) outliers start: 7 outliers final: 3 residues processed: 34 average time/residue: 1.2677 time to fit residues: 47.3889 Evaluate side-chains 32 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9726 Z= 0.208 Angle : 0.489 5.666 13224 Z= 0.276 Chirality : 0.043 0.134 1614 Planarity : 0.003 0.036 1695 Dihedral : 4.301 17.386 1350 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.64 % Allowed : 8.08 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.24), residues: 1254 helix: 2.65 (0.28), residues: 372 sheet: 0.04 (0.32), residues: 258 loop : -0.67 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 307 HIS 0.002 0.001 HIS C 134 PHE 0.010 0.002 PHE B 238 TYR 0.012 0.001 TYR A 274 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 1.225 Fit side-chains REVERT: A 146 MET cc_start: 0.7991 (mmm) cc_final: 0.7741 (mtp) REVERT: B 426 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8647 (tt) outliers start: 7 outliers final: 5 residues processed: 34 average time/residue: 1.3405 time to fit residues: 49.9784 Evaluate side-chains 34 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9726 Z= 0.238 Angle : 0.507 6.029 13224 Z= 0.286 Chirality : 0.043 0.135 1614 Planarity : 0.003 0.034 1695 Dihedral : 4.390 17.649 1350 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.83 % Allowed : 8.17 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1254 helix: 2.62 (0.28), residues: 372 sheet: 0.02 (0.32), residues: 258 loop : -0.69 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 307 HIS 0.002 0.001 HIS C 134 PHE 0.012 0.002 PHE B 238 TYR 0.013 0.001 TYR A 274 ARG 0.001 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 1.091 Fit side-chains REVERT: A 146 MET cc_start: 0.8006 (mmm) cc_final: 0.7728 (mtp) REVERT: B 426 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8661 (tt) outliers start: 9 outliers final: 6 residues processed: 36 average time/residue: 1.2698 time to fit residues: 50.1176 Evaluate side-chains 35 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 0.0020 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9726 Z= 0.128 Angle : 0.440 6.185 13224 Z= 0.247 Chirality : 0.042 0.125 1614 Planarity : 0.003 0.032 1695 Dihedral : 4.143 17.556 1350 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.55 % Allowed : 8.54 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1254 helix: 2.68 (0.28), residues: 372 sheet: 0.30 (0.31), residues: 288 loop : -0.53 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 307 HIS 0.001 0.000 HIS C 134 PHE 0.005 0.001 PHE B 375 TYR 0.009 0.001 TYR B 274 ARG 0.001 0.000 ARG C 415 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 1.083 Fit side-chains REVERT: B 426 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8565 (tt) outliers start: 6 outliers final: 1 residues processed: 36 average time/residue: 1.2463 time to fit residues: 49.2405 Evaluate side-chains 31 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 0.0270 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3126 r_free = 0.3126 target = 0.071414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.057675 restraints weight = 21806.389| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.49 r_work: 0.2716 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9726 Z= 0.116 Angle : 0.440 11.262 13224 Z= 0.241 Chirality : 0.041 0.124 1614 Planarity : 0.003 0.031 1695 Dihedral : 3.957 17.026 1350 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.37 % Allowed : 9.00 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1254 helix: 2.77 (0.28), residues: 372 sheet: 0.44 (0.33), residues: 258 loop : -0.57 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 307 HIS 0.001 0.000 HIS C 134 PHE 0.005 0.001 PHE C 375 TYR 0.008 0.001 TYR C 274 ARG 0.001 0.000 ARG C 415 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.29 seconds wall clock time: 38 minutes 43.24 seconds (2323.24 seconds total)