Starting phenix.real_space_refine on Fri Jul 3 09:48:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xoh_33348/07_2026/7xoh_33348_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xoh_33348/07_2026/7xoh_33348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xoh_33348/07_2026/7xoh_33348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xoh_33348/07_2026/7xoh_33348.map" model { file = "/net/cci-nas-00/data/ceres_data/7xoh_33348/07_2026/7xoh_33348_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xoh_33348/07_2026/7xoh_33348_trim.cif" } resolution = 3.6 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= 0.011 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 P 4 5.49 5 S 60 5.16 5 C 8484 2.51 5 N 2336 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13524 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "A" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "C" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "D" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.29, per 1000 atoms: 0.17 Number of scatterers: 13524 At special positions: 0 Unit cell: (84.53, 146.59, 84.53, 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) S 60 16.00 P 4 15.00 O 2640 8.00 N 2336 7.00 C 8484 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: 0.90 Conformation dependent library (CDL) restraints added in 572.0 milliseconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 20 sheets defined 37.4% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.869A pdb=" N VAL B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.929A pdb=" N ARG B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 109 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 139 removed outlier: 3.506A pdb=" N VAL B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 161 through 168 removed outlier: 3.768A pdb=" N ILE B 165 " --> pdb=" O THR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.512A pdb=" N ARG B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 262 removed outlier: 3.519A pdb=" N SER B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 281 removed outlier: 3.924A pdb=" N GLY B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.655A pdb=" N MET B 302 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 303 " --> pdb=" O GLY B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 450 through 458 Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.753A pdb=" N LEU A 10 " --> pdb=" O ILE A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 58 Processing helix chain 'A' and resid 74 through 87 removed outlier: 4.127A pdb=" N GLY A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.653A pdb=" N ARG A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.580A pdb=" N VAL A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.680A pdb=" N THR A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.792A pdb=" N GLY A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 262 Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.827A pdb=" N GLY A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.883A pdb=" N TYR A 314 " --> pdb=" O TRP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 392 through 397 removed outlier: 3.874A pdb=" N PHE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 397' Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.695A pdb=" N ALA A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 44 through 58 removed outlier: 3.697A pdb=" N LYS C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.855A pdb=" N VAL C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.893A pdb=" N ARG C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 139 removed outlier: 3.506A pdb=" N VAL C 131 " --> pdb=" O SER C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 161 through 168 removed outlier: 3.646A pdb=" N ILE C 165 " --> pdb=" O THR C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 247 through 262 removed outlier: 3.561A pdb=" N SER C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 removed outlier: 3.902A pdb=" N GLY C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 303 removed outlier: 3.671A pdb=" N MET C 302 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 303' Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 422 through 430 Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.511A pdb=" N GLY C 455 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 removed outlier: 3.749A pdb=" N LEU D 10 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 58 removed outlier: 3.802A pdb=" N LYS D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 removed outlier: 4.422A pdb=" N GLY D 78 " --> pdb=" O ASN D 74 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 109 removed outlier: 3.647A pdb=" N ARG D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 139 removed outlier: 3.577A pdb=" N VAL D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 161 through 170 removed outlier: 3.704A pdb=" N THR D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 196 Processing helix chain 'D' and resid 247 through 262 Processing helix chain 'D' and resid 267 through 281 removed outlier: 3.756A pdb=" N GLY D 271 " --> pdb=" O GLY D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 352 through 364 removed outlier: 3.685A pdb=" N TYR D 363 " --> pdb=" O ILE D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 409 Processing helix chain 'D' and resid 422 through 430 removed outlier: 3.918A pdb=" N ALA D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.591A pdb=" N GLY D 455 " --> pdb=" O TYR D 451 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 19 removed outlier: 4.778A pdb=" N VAL B 30 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 116 removed outlier: 6.536A pdb=" N CYS B 90 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL B 114 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE B 92 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N CYS B 116 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS B 94 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 67 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL B 93 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU B 69 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP B 143 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 205 Processing sheet with id=AA4, first strand: chain 'B' and resid 367 through 370 removed outlier: 3.506A pdb=" N GLY B 384 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 416 through 418 removed outlier: 6.318A pdb=" N ILE B 417 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY B 446 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU B 440 " --> pdb=" O PRO B 444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 16 through 18 Processing sheet with id=AA7, first strand: chain 'A' and resid 111 through 116 removed outlier: 3.531A pdb=" N VAL A 114 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE A 67 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A 93 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU A 69 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP A 143 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 68 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.580A pdb=" N ALA A 178 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.619A pdb=" N GLY A 384 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 416 through 418 removed outlier: 4.134A pdb=" N GLY A 446 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLU A 440 " --> pdb=" O PRO A 444 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 19 removed outlier: 4.806A pdb=" N VAL C 30 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 116 removed outlier: 6.537A pdb=" N CYS C 90 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL C 114 " --> pdb=" O CYS C 90 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE C 92 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N CYS C 116 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS C 94 " --> pdb=" O CYS C 116 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 67 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL C 93 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU C 69 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP C 143 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.679A pdb=" N PHE C 176 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU C 242 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 367 through 368 Processing sheet with id=AB6, first strand: chain 'C' and resid 416 through 418 removed outlier: 6.363A pdb=" N ILE C 417 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY C 446 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU C 440 " --> pdb=" O PRO C 444 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 16 through 18 Processing sheet with id=AB8, first strand: chain 'D' and resid 111 through 116 removed outlier: 3.535A pdb=" N VAL D 114 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE D 67 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL D 93 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU D 69 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP D 143 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 68 " --> pdb=" O TRP D 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 178 through 179 removed outlier: 3.705A pdb=" N ALA D 178 " --> pdb=" O VAL D 204 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 367 through 370 removed outlier: 3.521A pdb=" N GLY D 384 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 416 through 418 removed outlier: 4.146A pdb=" N GLY D 446 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU D 440 " --> pdb=" O PRO D 444 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1311 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: 2.11 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4589 1.34 - 1.46: 2670 1.46 - 1.58: 6429 1.58 - 1.69: 4 1.69 - 1.81: 104 Bond restraints: 13796 Sorted by residual: bond pdb=" CA GLY A 297 " pdb=" C GLY A 297 " ideal model delta sigma weight residual 1.520 1.486 0.034 7.30e-03 1.88e+04 2.23e+01 bond pdb=" C4 PLP D 501 " pdb=" C4A PLP D 501 " ideal model delta sigma weight residual 1.462 1.527 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C4 PLP C 501 " pdb=" C4A PLP C 501 " ideal model delta sigma weight residual 1.462 1.527 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C4 PLP A 501 " pdb=" C5 PLP A 501 " ideal model delta sigma weight residual 1.410 1.348 0.062 2.00e-02 2.50e+03 9.67e+00 bond pdb=" N ILE A 180 " pdb=" CA ILE A 180 " ideal model delta sigma weight residual 1.457 1.492 -0.036 1.15e-02 7.56e+03 9.63e+00 ... (remaining 13791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 18244 1.65 - 3.30: 443 3.30 - 4.94: 64 4.94 - 6.59: 13 6.59 - 8.24: 4 Bond angle restraints: 18768 Sorted by residual: angle pdb=" N SER D 313 " pdb=" CA SER D 313 " pdb=" C SER D 313 " ideal model delta sigma weight residual 112.54 105.53 7.01 1.22e+00 6.72e-01 3.30e+01 angle pdb=" N GLY C 183 " pdb=" CA GLY C 183 " pdb=" C GLY C 183 " ideal model delta sigma weight residual 114.46 108.38 6.08 1.81e+00 3.05e-01 1.13e+01 angle pdb=" C LYS C 44 " pdb=" N ASP C 45 " pdb=" CA ASP C 45 " ideal model delta sigma weight residual 120.38 116.06 4.32 1.37e+00 5.33e-01 9.94e+00 angle pdb=" N SER C 43 " pdb=" CA SER C 43 " pdb=" C SER C 43 " ideal model delta sigma weight residual 113.23 109.44 3.79 1.24e+00 6.50e-01 9.34e+00 angle pdb=" C GLN B 367 " pdb=" N MET B 368 " pdb=" CA MET B 368 " ideal model delta sigma weight residual 122.08 116.81 5.27 1.83e+00 2.99e-01 8.28e+00 ... (remaining 18763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 7579 16.73 - 33.46: 500 33.46 - 50.20: 107 50.20 - 66.93: 32 66.93 - 83.66: 14 Dihedral angle restraints: 8232 sinusoidal: 3136 harmonic: 5096 Sorted by residual: dihedral pdb=" CA GLY A 339 " pdb=" C GLY A 339 " pdb=" N ALA A 340 " pdb=" CA ALA A 340 " ideal model delta harmonic sigma weight residual 180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLY D 339 " pdb=" C GLY D 339 " pdb=" N ALA D 340 " pdb=" CA ALA D 340 " ideal model delta harmonic sigma weight residual 180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA LEU B 321 " pdb=" C LEU B 321 " pdb=" N ASP B 322 " pdb=" CA ASP B 322 " ideal model delta harmonic sigma weight residual -180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 8229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1325 0.035 - 0.070: 524 0.070 - 0.105: 205 0.105 - 0.140: 48 0.140 - 0.175: 2 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CA ILE A 180 " pdb=" N ILE A 180 " pdb=" C ILE A 180 " pdb=" CB ILE A 180 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE C 47 " pdb=" N ILE C 47 " pdb=" C ILE C 47 " pdb=" CB ILE C 47 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 2101 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 180 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C ILE C 180 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE C 180 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY C 181 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 294 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO B 295 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 313 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C SER C 313 " 0.027 2.00e-02 2.50e+03 pdb=" O SER C 313 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR C 314 " -0.009 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 143 2.58 - 3.16: 12621 3.16 - 3.74: 19431 3.74 - 4.32: 28236 4.32 - 4.90: 46895 Nonbonded interactions: 107326 Sorted by model distance: nonbonded pdb=" OH TYR D 158 " pdb=" OE1 GLU D 195 " model vdw 2.005 3.040 nonbonded pdb=" O LEU D 193 " pdb=" OG SER D 197 " model vdw 2.013 3.040 nonbonded pdb=" OG1 THR D 14 " pdb=" O VAL D 34 " model vdw 2.068 3.040 nonbonded pdb=" OH TYR A 158 " pdb=" OE1 GLU A 195 " model vdw 2.081 3.040 nonbonded pdb=" O LEU A 193 " pdb=" OG SER A 197 " model vdw 2.096 3.040 ... (remaining 107321 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.890 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.300 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.265 13800 Z= 0.308 Angle : 0.614 8.238 18768 Z= 0.326 Chirality : 0.044 0.175 2104 Planarity : 0.004 0.040 2472 Dihedral : 12.593 83.660 5024 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 32.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.64 % Favored : 89.31 % Rotamer: Outliers : 4.34 % Allowed : 3.06 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.16 (0.18), residues: 1824 helix: -1.69 (0.19), residues: 648 sheet: -4.45 (0.25), residues: 200 loop : -3.22 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.015 0.001 TYR D 36 PHE 0.007 0.001 PHE D 230 TRP 0.007 0.001 TRP B 310 HIS 0.002 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.21 (13796) covalent geometry : angle 0.61430 / 0.33 (18768) hydrogen bonds : bond 0.17269 / 11.11 ( 454) hydrogen bonds : angle 6.94894 / 4.91 ( 1311) Misc. bond : bond 0.13428 / 6.36 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 281 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 GLN cc_start: 0.7381 (tt0) cc_final: 0.7157 (tt0) REVERT: B 172 LYS cc_start: 0.7080 (ttpt) cc_final: 0.6662 (tptt) REVERT: B 200 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.7227 (ptm160) REVERT: B 287 ASP cc_start: 0.7236 (t0) cc_final: 0.6863 (t0) REVERT: B 401 LYS cc_start: 0.8474 (mttp) cc_final: 0.8210 (mtpt) REVERT: A 260 ARG cc_start: 0.8161 (tpt-90) cc_final: 0.7485 (ttm110) REVERT: A 363 TYR cc_start: 0.8061 (m-80) cc_final: 0.7689 (m-80) REVERT: C 58 SER cc_start: 0.8274 (m) cc_final: 0.7955 (p) REVERT: C 60 GLN cc_start: 0.7385 (tt0) cc_final: 0.7171 (tt0) REVERT: C 200 ARG cc_start: 0.7823 (mtp-110) cc_final: 0.7233 (ptm160) REVERT: C 287 ASP cc_start: 0.7246 (t0) cc_final: 0.6848 (t0) REVERT: D 260 ARG cc_start: 0.8144 (tpt-90) cc_final: 0.7455 (ttm110) REVERT: D 362 GLU cc_start: 0.8026 (tt0) cc_final: 0.7692 (tt0) REVERT: D 431 ARG cc_start: 0.8496 (ttt-90) cc_final: 0.7754 (tmt-80) REVERT: D 437 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7829 (mtm) outliers start: 61 outliers final: 23 residues processed: 325 average time/residue: 0.1129 time to fit residues: 52.6592 Evaluate side-chains 214 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 437 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN C 5 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.131362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.107824 restraints weight = 17142.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.110334 restraints weight = 11758.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.112100 restraints weight = 9101.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.113289 restraints weight = 7670.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.114140 restraints weight = 6826.664| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13800 Z= 0.209 Angle : 0.710 8.036 18768 Z= 0.359 Chirality : 0.049 0.369 2104 Planarity : 0.005 0.043 2472 Dihedral : 7.848 59.255 2058 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.56 % Allowed : 9.97 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.46 (0.18), residues: 1824 helix: -1.39 (0.20), residues: 692 sheet: -3.61 (0.28), residues: 200 loop : -2.72 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 260 TYR 0.020 0.002 TYR D 36 PHE 0.014 0.002 PHE C 230 TRP 0.014 0.001 TRP B 310 HIS 0.009 0.002 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.21 (13796) covalent geometry : angle 0.70967 / 0.36 (18768) hydrogen bonds : bond 0.04550 / 3.00 ( 454) hydrogen bonds : angle 5.12483 / 3.61 ( 1311) Misc. bond : bond 0.00091 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 SER cc_start: 0.8233 (m) cc_final: 0.7917 (p) REVERT: B 60 GLN cc_start: 0.7432 (tt0) cc_final: 0.7077 (tt0) REVERT: B 182 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8357 (t) REVERT: B 200 ARG cc_start: 0.7600 (mtp-110) cc_final: 0.7198 (ptm160) REVERT: B 401 LYS cc_start: 0.8474 (mttp) cc_final: 0.8155 (mtpt) REVERT: A 228 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7722 (mm-30) REVERT: A 260 ARG cc_start: 0.7933 (tpt-90) cc_final: 0.7446 (ttm110) REVERT: A 363 TYR cc_start: 0.8054 (m-80) cc_final: 0.7713 (m-80) REVERT: C 58 SER cc_start: 0.8209 (m) cc_final: 0.7906 (p) REVERT: C 200 ARG cc_start: 0.7621 (mtp-110) cc_final: 0.7243 (ptm160) REVERT: D 18 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7938 (ttt-90) REVERT: D 35 GLU cc_start: 0.8017 (tt0) cc_final: 0.7722 (tt0) REVERT: D 147 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8153 (pm20) REVERT: D 228 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7674 (mm-30) REVERT: D 362 GLU cc_start: 0.7992 (tt0) cc_final: 0.7785 (tt0) REVERT: D 454 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7637 (mp) outliers start: 36 outliers final: 22 residues processed: 223 average time/residue: 0.0984 time to fit residues: 33.1836 Evaluate side-chains 199 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 454 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 40 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN C 6 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.132038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.108554 restraints weight = 17197.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.111076 restraints weight = 11680.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.112867 restraints weight = 9057.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.114088 restraints weight = 7580.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.114616 restraints weight = 6737.697| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13800 Z= 0.171 Angle : 0.652 7.430 18768 Z= 0.327 Chirality : 0.047 0.306 2104 Planarity : 0.005 0.041 2472 Dihedral : 7.155 57.873 2041 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.13 % Allowed : 13.60 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.01 (0.19), residues: 1824 helix: -1.13 (0.20), residues: 696 sheet: -2.98 (0.32), residues: 200 loop : -2.47 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.018 0.001 TYR D 36 PHE 0.015 0.001 PHE C 230 TRP 0.011 0.001 TRP B 310 HIS 0.008 0.002 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (13796) covalent geometry : angle 0.65216 / 0.33 (18768) hydrogen bonds : bond 0.04124 / 2.72 ( 454) hydrogen bonds : angle 4.80425 / 3.40 ( 1311) Misc. bond : bond 0.00069 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: B 58 SER cc_start: 0.8120 (m) cc_final: 0.7884 (p) REVERT: B 182 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8573 (t) REVERT: B 200 ARG cc_start: 0.7539 (mtp-110) cc_final: 0.7139 (ptm160) REVERT: B 401 LYS cc_start: 0.8470 (mttp) cc_final: 0.8123 (mtpt) REVERT: A 228 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7771 (mm-30) REVERT: A 260 ARG cc_start: 0.7927 (tpt-90) cc_final: 0.7366 (ttm110) REVERT: A 363 TYR cc_start: 0.8116 (m-80) cc_final: 0.7814 (m-80) REVERT: A 404 ASP cc_start: 0.7762 (m-30) cc_final: 0.7393 (m-30) REVERT: A 452 ASP cc_start: 0.7518 (t0) cc_final: 0.7197 (t0) REVERT: C 58 SER cc_start: 0.8138 (m) cc_final: 0.7909 (p) REVERT: C 152 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7497 (mt-10) REVERT: C 200 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.7216 (ptm160) REVERT: D 18 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7851 (ttt-90) REVERT: D 35 GLU cc_start: 0.7981 (tt0) cc_final: 0.7695 (tt0) REVERT: D 84 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: D 147 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: D 228 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7713 (mm-30) outliers start: 44 outliers final: 26 residues processed: 219 average time/residue: 0.0937 time to fit residues: 31.1807 Evaluate side-chains 201 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN D 123 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.130516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.107070 restraints weight = 17223.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.109587 restraints weight = 11715.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.111223 restraints weight = 9091.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.112517 restraints weight = 7655.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.113297 restraints weight = 6802.981| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13800 Z= 0.201 Angle : 0.666 7.304 18768 Z= 0.333 Chirality : 0.048 0.315 2104 Planarity : 0.005 0.043 2472 Dihedral : 7.001 55.600 2035 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 3.21 % Allowed : 15.60 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.80 (0.19), residues: 1824 helix: -1.07 (0.20), residues: 700 sheet: -2.54 (0.33), residues: 204 loop : -2.33 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 260 TYR 0.020 0.002 TYR D 36 PHE 0.017 0.001 PHE C 230 TRP 0.011 0.001 TRP B 310 HIS 0.008 0.002 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.20 (13796) covalent geometry : angle 0.66579 / 0.33 (18768) hydrogen bonds : bond 0.04323 / 2.85 ( 454) hydrogen bonds : angle 4.82845 / 3.42 ( 1311) Misc. bond : bond 0.00076 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7468 (mp0) REVERT: B 58 SER cc_start: 0.8128 (m) cc_final: 0.7913 (p) REVERT: B 152 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7462 (mt-10) REVERT: B 401 LYS cc_start: 0.8501 (mttp) cc_final: 0.8132 (mtpt) REVERT: B 404 ASP cc_start: 0.8141 (t0) cc_final: 0.7922 (t0) REVERT: A 84 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8084 (pt0) REVERT: A 228 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 363 TYR cc_start: 0.8125 (m-80) cc_final: 0.7814 (m-80) REVERT: A 404 ASP cc_start: 0.7779 (m-30) cc_final: 0.7435 (m-30) REVERT: A 452 ASP cc_start: 0.7569 (t0) cc_final: 0.7257 (t0) REVERT: C 58 SER cc_start: 0.8081 (m) cc_final: 0.7873 (p) REVERT: C 152 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7546 (mt-10) REVERT: C 424 SER cc_start: 0.9024 (t) cc_final: 0.8716 (p) REVERT: D 35 GLU cc_start: 0.8001 (tt0) cc_final: 0.7768 (tt0) REVERT: D 69 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8285 (tp30) REVERT: D 147 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: D 228 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7696 (mm-30) REVERT: D 404 ASP cc_start: 0.7751 (m-30) cc_final: 0.7398 (m-30) outliers start: 45 outliers final: 32 residues processed: 204 average time/residue: 0.0873 time to fit residues: 27.6956 Evaluate side-chains 192 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 122 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 110 optimal weight: 0.0970 chunk 177 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN A 123 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.132135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.108277 restraints weight = 17174.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.110868 restraints weight = 11680.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.112541 restraints weight = 9038.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.113889 restraints weight = 7621.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.114668 restraints weight = 6761.395| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13800 Z= 0.161 Angle : 0.632 6.733 18768 Z= 0.315 Chirality : 0.047 0.393 2104 Planarity : 0.005 0.041 2472 Dihedral : 6.635 56.332 2034 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.63 % Allowed : 17.38 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.48 (0.19), residues: 1824 helix: -0.89 (0.20), residues: 700 sheet: -2.12 (0.35), residues: 204 loop : -2.14 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.018 0.001 TYR D 36 PHE 0.016 0.001 PHE C 230 TRP 0.009 0.001 TRP B 310 HIS 0.007 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (13796) covalent geometry : angle 0.63224 / 0.32 (18768) hydrogen bonds : bond 0.03958 / 2.61 ( 454) hydrogen bonds : angle 4.65925 / 3.31 ( 1311) Misc. bond : bond 0.00065 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: B 152 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7497 (mt-10) REVERT: B 401 LYS cc_start: 0.8494 (mttp) cc_final: 0.8120 (mtpt) REVERT: B 404 ASP cc_start: 0.8169 (t0) cc_final: 0.7958 (t0) REVERT: B 436 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7967 (pp) REVERT: A 84 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8104 (pt0) REVERT: A 135 LEU cc_start: 0.7900 (tp) cc_final: 0.7544 (mp) REVERT: A 228 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7740 (mm-30) REVERT: A 332 ASP cc_start: 0.8391 (t0) cc_final: 0.8086 (m-30) REVERT: A 363 TYR cc_start: 0.8131 (m-80) cc_final: 0.7804 (m-80) REVERT: A 404 ASP cc_start: 0.7808 (m-30) cc_final: 0.7476 (m-30) REVERT: A 452 ASP cc_start: 0.7604 (t0) cc_final: 0.7227 (t0) REVERT: C 152 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7566 (mt-10) REVERT: C 378 MET cc_start: 0.7926 (pmm) cc_final: 0.6727 (mmm) REVERT: C 424 SER cc_start: 0.9021 (t) cc_final: 0.8728 (p) REVERT: D 35 GLU cc_start: 0.7976 (tt0) cc_final: 0.7771 (tt0) REVERT: D 147 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: D 296 ASP cc_start: 0.8344 (t0) cc_final: 0.7710 (m-30) REVERT: D 332 ASP cc_start: 0.8393 (t0) cc_final: 0.8105 (m-30) REVERT: D 404 ASP cc_start: 0.7769 (m-30) cc_final: 0.7430 (m-30) outliers start: 51 outliers final: 37 residues processed: 211 average time/residue: 0.0914 time to fit residues: 31.0252 Evaluate side-chains 200 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 41 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN A 6 HIS A 84 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.134210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.110331 restraints weight = 17018.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.112992 restraints weight = 11524.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.114806 restraints weight = 8883.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.115977 restraints weight = 7457.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.116930 restraints weight = 6621.948| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13800 Z= 0.130 Angle : 0.608 6.634 18768 Z= 0.303 Chirality : 0.046 0.330 2104 Planarity : 0.005 0.041 2472 Dihedral : 6.449 58.590 2034 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.56 % Allowed : 18.45 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.17 (0.20), residues: 1824 helix: -0.69 (0.20), residues: 700 sheet: -1.70 (0.37), residues: 200 loop : -1.97 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.016 0.001 TYR D 36 PHE 0.014 0.001 PHE C 230 TRP 0.007 0.001 TRP B 310 HIS 0.006 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (13796) covalent geometry : angle 0.60758 / 0.30 (18768) hydrogen bonds : bond 0.03578 / 2.36 ( 454) hydrogen bonds : angle 4.53368 / 3.22 ( 1311) Misc. bond : bond 0.00033 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7238 (mp0) REVERT: B 152 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7464 (mt-10) REVERT: B 200 ARG cc_start: 0.7363 (mtp-110) cc_final: 0.6918 (ptm160) REVERT: B 401 LYS cc_start: 0.8474 (mttp) cc_final: 0.8091 (mtpt) REVERT: B 404 ASP cc_start: 0.8169 (t0) cc_final: 0.7855 (t0) REVERT: B 436 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7975 (pp) REVERT: A 135 LEU cc_start: 0.7873 (tp) cc_final: 0.7546 (mp) REVERT: A 158 TYR cc_start: 0.8213 (t80) cc_final: 0.7870 (t80) REVERT: A 228 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 332 ASP cc_start: 0.8364 (t0) cc_final: 0.8089 (m-30) REVERT: A 363 TYR cc_start: 0.8124 (m-80) cc_final: 0.7846 (m-80) REVERT: A 404 ASP cc_start: 0.7831 (m-30) cc_final: 0.7533 (m-30) REVERT: A 452 ASP cc_start: 0.7551 (t0) cc_final: 0.7181 (t0) REVERT: C 152 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7540 (mt-10) REVERT: C 207 ASP cc_start: 0.8430 (t0) cc_final: 0.8219 (t0) REVERT: C 424 SER cc_start: 0.9053 (t) cc_final: 0.8721 (p) REVERT: D 35 GLU cc_start: 0.8016 (tt0) cc_final: 0.7801 (tt0) REVERT: D 147 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: D 158 TYR cc_start: 0.8270 (t80) cc_final: 0.7906 (t80) REVERT: D 296 ASP cc_start: 0.8372 (t0) cc_final: 0.7731 (m-30) REVERT: D 301 TYR cc_start: 0.8688 (m-80) cc_final: 0.8406 (m-80) REVERT: D 332 ASP cc_start: 0.8357 (t0) cc_final: 0.8087 (m-30) REVERT: D 404 ASP cc_start: 0.7786 (m-30) cc_final: 0.7490 (m-30) outliers start: 50 outliers final: 37 residues processed: 217 average time/residue: 0.0910 time to fit residues: 30.9520 Evaluate side-chains 205 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 153 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 131 optimal weight: 0.0670 chunk 24 optimal weight: 4.9990 overall best weight: 1.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN A 84 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.133917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.110108 restraints weight = 17069.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112724 restraints weight = 11611.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.114533 restraints weight = 8971.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.115579 restraints weight = 7542.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.116541 restraints weight = 6744.286| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13800 Z= 0.142 Angle : 0.613 7.728 18768 Z= 0.305 Chirality : 0.046 0.289 2104 Planarity : 0.005 0.041 2472 Dihedral : 6.309 59.224 2033 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.49 % Allowed : 18.95 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.01 (0.20), residues: 1824 helix: -0.62 (0.20), residues: 700 sheet: -1.48 (0.37), residues: 204 loop : -1.87 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 85 TYR 0.016 0.001 TYR D 36 PHE 0.013 0.001 PHE C 230 TRP 0.007 0.001 TRP C 310 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (13796) covalent geometry : angle 0.61349 / 0.30 (18768) hydrogen bonds : bond 0.03700 / 2.43 ( 454) hydrogen bonds : angle 4.50030 / 3.20 ( 1311) Misc. bond : bond 0.00046 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7502 (mt-10) REVERT: B 200 ARG cc_start: 0.7348 (mtp-110) cc_final: 0.6981 (ptm160) REVERT: B 401 LYS cc_start: 0.8501 (mttp) cc_final: 0.8116 (mtpt) REVERT: B 404 ASP cc_start: 0.8156 (t0) cc_final: 0.7838 (t0) REVERT: B 436 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8043 (pp) REVERT: A 135 LEU cc_start: 0.7878 (tp) cc_final: 0.7548 (mp) REVERT: A 158 TYR cc_start: 0.8174 (t80) cc_final: 0.7845 (t80) REVERT: A 228 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7670 (mm-30) REVERT: A 332 ASP cc_start: 0.8350 (t0) cc_final: 0.8058 (m-30) REVERT: A 363 TYR cc_start: 0.8142 (m-80) cc_final: 0.7847 (m-80) REVERT: A 404 ASP cc_start: 0.7847 (m-30) cc_final: 0.7553 (m-30) REVERT: A 452 ASP cc_start: 0.7366 (t0) cc_final: 0.6992 (t0) REVERT: C 152 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7558 (mt-10) REVERT: C 200 ARG cc_start: 0.7556 (mtp-110) cc_final: 0.7080 (ptm160) REVERT: C 207 ASP cc_start: 0.8441 (t0) cc_final: 0.8213 (t0) REVERT: C 424 SER cc_start: 0.9058 (t) cc_final: 0.8736 (p) REVERT: D 147 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: D 158 TYR cc_start: 0.8257 (t80) cc_final: 0.7906 (t80) REVERT: D 296 ASP cc_start: 0.8398 (t0) cc_final: 0.7763 (m-30) REVERT: D 301 TYR cc_start: 0.8694 (m-80) cc_final: 0.8413 (m-80) REVERT: D 332 ASP cc_start: 0.8349 (t0) cc_final: 0.8070 (m-30) REVERT: D 404 ASP cc_start: 0.7807 (m-30) cc_final: 0.7516 (m-30) REVERT: D 452 ASP cc_start: 0.7435 (t0) cc_final: 0.7116 (t0) outliers start: 49 outliers final: 41 residues processed: 214 average time/residue: 0.0889 time to fit residues: 29.5853 Evaluate side-chains 211 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 163 optimal weight: 0.7980 chunk 23 optimal weight: 0.0370 chunk 126 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 overall best weight: 1.2860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.133919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.110199 restraints weight = 16956.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112786 restraints weight = 11547.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.114565 restraints weight = 8919.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.115635 restraints weight = 7510.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.116593 restraints weight = 6708.587| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13800 Z= 0.139 Angle : 0.613 8.257 18768 Z= 0.303 Chirality : 0.046 0.272 2104 Planarity : 0.005 0.041 2472 Dihedral : 6.164 57.997 2033 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.35 % Allowed : 19.16 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.86 (0.20), residues: 1824 helix: -0.50 (0.20), residues: 696 sheet: -1.29 (0.37), residues: 204 loop : -1.79 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 260 TYR 0.015 0.001 TYR D 36 PHE 0.012 0.001 PHE C 230 TRP 0.007 0.001 TRP B 310 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (13796) covalent geometry : angle 0.61327 / 0.30 (18768) hydrogen bonds : bond 0.03633 / 2.39 ( 454) hydrogen bonds : angle 4.48161 / 3.19 ( 1311) Misc. bond : bond 0.00045 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7521 (mt-10) REVERT: B 200 ARG cc_start: 0.7335 (mtp-110) cc_final: 0.6888 (ptm160) REVERT: B 287 ASP cc_start: 0.7041 (t0) cc_final: 0.6761 (t0) REVERT: B 401 LYS cc_start: 0.8502 (mttp) cc_final: 0.8109 (mtpt) REVERT: B 404 ASP cc_start: 0.8151 (t0) cc_final: 0.7837 (t0) REVERT: B 436 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8020 (pp) REVERT: A 84 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8415 (pt0) REVERT: A 135 LEU cc_start: 0.7870 (tp) cc_final: 0.7539 (mp) REVERT: A 158 TYR cc_start: 0.8139 (t80) cc_final: 0.7801 (t80) REVERT: A 228 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 332 ASP cc_start: 0.8312 (t0) cc_final: 0.8035 (m-30) REVERT: A 363 TYR cc_start: 0.8178 (m-80) cc_final: 0.7905 (m-80) REVERT: A 404 ASP cc_start: 0.7858 (m-30) cc_final: 0.7562 (m-30) REVERT: A 452 ASP cc_start: 0.7337 (t0) cc_final: 0.6962 (t0) REVERT: C 152 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7568 (mt-10) REVERT: C 200 ARG cc_start: 0.7562 (mtp-110) cc_final: 0.7110 (ptm160) REVERT: C 287 ASP cc_start: 0.7019 (t0) cc_final: 0.6724 (t0) REVERT: C 424 SER cc_start: 0.9062 (t) cc_final: 0.8743 (p) REVERT: C 436 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8002 (pp) REVERT: D 147 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: D 158 TYR cc_start: 0.8245 (t80) cc_final: 0.7935 (t80) REVERT: D 296 ASP cc_start: 0.8416 (t0) cc_final: 0.7790 (m-30) REVERT: D 301 TYR cc_start: 0.8691 (m-80) cc_final: 0.8409 (m-80) REVERT: D 332 ASP cc_start: 0.8318 (t0) cc_final: 0.8051 (m-30) REVERT: D 404 ASP cc_start: 0.7805 (m-30) cc_final: 0.7510 (m-30) REVERT: D 452 ASP cc_start: 0.7431 (t0) cc_final: 0.7107 (t0) outliers start: 47 outliers final: 41 residues processed: 210 average time/residue: 0.0904 time to fit residues: 29.6909 Evaluate side-chains 212 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 121 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 HIS A 84 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.132450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.108775 restraints weight = 17162.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.111310 restraints weight = 11681.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.113088 restraints weight = 9033.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.114187 restraints weight = 7605.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115097 restraints weight = 6777.377| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13800 Z= 0.166 Angle : 0.633 7.536 18768 Z= 0.314 Chirality : 0.047 0.316 2104 Planarity : 0.005 0.042 2472 Dihedral : 5.984 59.997 2030 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.49 % Allowed : 19.16 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.20), residues: 1824 helix: -0.33 (0.20), residues: 672 sheet: -1.13 (0.37), residues: 204 loop : -1.73 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 260 TYR 0.016 0.001 TYR A 36 PHE 0.017 0.001 PHE C 230 TRP 0.009 0.001 TRP B 310 HIS 0.006 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (13796) covalent geometry : angle 0.63297 / 0.31 (18768) hydrogen bonds : bond 0.03896 / 2.55 ( 454) hydrogen bonds : angle 4.54764 / 3.24 ( 1311) Misc. bond : bond 0.00060 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: B 152 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7541 (mt-10) REVERT: B 287 ASP cc_start: 0.7316 (t0) cc_final: 0.6991 (t0) REVERT: B 401 LYS cc_start: 0.8517 (mttp) cc_final: 0.8135 (mtpt) REVERT: B 404 ASP cc_start: 0.8134 (t0) cc_final: 0.7924 (t0) REVERT: B 436 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8030 (pp) REVERT: A 84 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8169 (pt0) REVERT: A 135 LEU cc_start: 0.7948 (tp) cc_final: 0.7582 (mp) REVERT: A 158 TYR cc_start: 0.8154 (t80) cc_final: 0.7821 (t80) REVERT: A 228 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 332 ASP cc_start: 0.8311 (t0) cc_final: 0.8024 (m-30) REVERT: A 363 TYR cc_start: 0.8188 (m-80) cc_final: 0.7914 (m-80) REVERT: A 404 ASP cc_start: 0.7842 (m-30) cc_final: 0.7558 (m-30) REVERT: A 452 ASP cc_start: 0.7369 (t0) cc_final: 0.7001 (t0) REVERT: C 152 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7577 (mt-10) REVERT: C 200 ARG cc_start: 0.7575 (mtp-110) cc_final: 0.7118 (ptm160) REVERT: C 287 ASP cc_start: 0.7077 (t0) cc_final: 0.6832 (t0) REVERT: C 424 SER cc_start: 0.9077 (t) cc_final: 0.8758 (p) REVERT: C 436 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8083 (pp) REVERT: D 84 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8426 (pt0) REVERT: D 147 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: D 158 TYR cc_start: 0.8265 (t80) cc_final: 0.7951 (t80) REVERT: D 296 ASP cc_start: 0.8341 (t0) cc_final: 0.7728 (m-30) REVERT: D 332 ASP cc_start: 0.8300 (t0) cc_final: 0.8021 (m-30) REVERT: D 404 ASP cc_start: 0.7801 (m-30) cc_final: 0.7517 (m-30) REVERT: D 452 ASP cc_start: 0.7424 (t0) cc_final: 0.7107 (t0) outliers start: 49 outliers final: 41 residues processed: 201 average time/residue: 0.0995 time to fit residues: 31.8335 Evaluate side-chains 207 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 23 optimal weight: 0.0970 chunk 100 optimal weight: 0.8980 chunk 74 optimal weight: 0.0040 chunk 82 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 131 optimal weight: 0.0470 chunk 52 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.3888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.138025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.114587 restraints weight = 16903.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.117230 restraints weight = 11358.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.119022 restraints weight = 8694.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.120201 restraints weight = 7281.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.121093 restraints weight = 6442.457| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13800 Z= 0.102 Angle : 0.583 7.460 18768 Z= 0.289 Chirality : 0.045 0.260 2104 Planarity : 0.004 0.043 2472 Dihedral : 5.624 57.652 2030 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.64 % Allowed : 19.80 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.40 (0.20), residues: 1824 helix: -0.07 (0.21), residues: 672 sheet: -0.84 (0.37), residues: 204 loop : -1.59 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 85 TYR 0.013 0.001 TYR C 128 PHE 0.016 0.001 PHE C 230 TRP 0.004 0.001 TRP B 433 HIS 0.004 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (13796) covalent geometry : angle 0.58314 / 0.29 (18768) hydrogen bonds : bond 0.03069 / 2.03 ( 454) hydrogen bonds : angle 4.34232 / 3.09 ( 1311) Misc. bond : bond 0.00014 / 0.01 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 401 LYS cc_start: 0.8487 (mttp) cc_final: 0.8068 (mtpt) REVERT: B 404 ASP cc_start: 0.8159 (t0) cc_final: 0.7841 (t0) REVERT: B 436 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8034 (pp) REVERT: A 84 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8309 (pt0) REVERT: A 135 LEU cc_start: 0.7821 (tp) cc_final: 0.7540 (mp) REVERT: A 158 TYR cc_start: 0.7959 (t80) cc_final: 0.7707 (t80) REVERT: A 228 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7541 (mm-30) REVERT: A 332 ASP cc_start: 0.8313 (t0) cc_final: 0.8038 (m-30) REVERT: A 363 TYR cc_start: 0.8132 (m-80) cc_final: 0.7868 (m-80) REVERT: A 404 ASP cc_start: 0.7886 (m-30) cc_final: 0.7586 (m-30) REVERT: A 452 ASP cc_start: 0.7175 (t0) cc_final: 0.6798 (t0) REVERT: C 152 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7567 (mt-10) REVERT: C 200 ARG cc_start: 0.7375 (mtp-110) cc_final: 0.7017 (ptm160) REVERT: C 424 SER cc_start: 0.9105 (t) cc_final: 0.8811 (p) REVERT: C 436 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8030 (pp) REVERT: D 84 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: D 147 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8070 (pm20) REVERT: D 158 TYR cc_start: 0.8055 (t80) cc_final: 0.7804 (t80) REVERT: D 228 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7328 (mm-30) REVERT: D 296 ASP cc_start: 0.8333 (t0) cc_final: 0.7710 (m-30) REVERT: D 301 TYR cc_start: 0.8631 (m-80) cc_final: 0.8376 (m-80) REVERT: D 332 ASP cc_start: 0.8260 (t0) cc_final: 0.8022 (m-30) REVERT: D 404 ASP cc_start: 0.7816 (m-30) cc_final: 0.7546 (m-30) REVERT: D 452 ASP cc_start: 0.7374 (t0) cc_final: 0.7070 (t0) outliers start: 37 outliers final: 29 residues processed: 219 average time/residue: 0.1029 time to fit residues: 34.8010 Evaluate side-chains 211 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 149 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN A 84 GLN D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.135794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.112289 restraints weight = 17059.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.114902 restraints weight = 11500.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.116576 restraints weight = 8842.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.117920 restraints weight = 7450.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.118599 restraints weight = 6580.231| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13800 Z= 0.128 Angle : 0.607 7.691 18768 Z= 0.298 Chirality : 0.045 0.232 2104 Planarity : 0.004 0.042 2472 Dihedral : 5.536 59.785 2028 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.64 % Allowed : 20.58 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.20), residues: 1824 helix: 0.01 (0.21), residues: 672 sheet: -0.60 (0.39), residues: 200 loop : -1.52 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 260 TYR 0.014 0.001 TYR C 128 PHE 0.016 0.001 PHE C 230 TRP 0.008 0.001 TRP B 310 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (13796) covalent geometry : angle 0.60652 / 0.30 (18768) hydrogen bonds : bond 0.03391 / 2.22 ( 454) hydrogen bonds : angle 4.34204 / 3.11 ( 1311) Misc. bond : bond 0.00037 / 0.02 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1935.84 seconds wall clock time: 34 minutes 22.05 seconds (2062.05 seconds total)