Starting phenix.real_space_refine on Sun Jul 21 06:05:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoh_33348/07_2024/7xoh_33348_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoh_33348/07_2024/7xoh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoh_33348/07_2024/7xoh_33348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoh_33348/07_2024/7xoh_33348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoh_33348/07_2024/7xoh_33348_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoh_33348/07_2024/7xoh_33348_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: 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: 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: 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: 1 Time building chain proxies: 7.99, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 1.46 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: 3.65 Time building geometry restraints manager: 5.90 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=" 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 bond pdb=" N ILE C 47 " pdb=" CA ILE C 47 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.69e+00 bond pdb=" N ASP C 45 " pdb=" CA ASP C 45 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.04e+00 bond pdb=" N THR C 182 " pdb=" CA THR C 182 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.72e+00 ... (remaining 13791 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.34: 539 106.34 - 113.25: 7439 113.25 - 120.17: 4895 120.17 - 127.08: 5720 127.08 - 133.99: 175 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 - 22.33: 7832 22.33 - 44.65: 324 44.65 - 66.98: 51 66.98 - 89.30: 11 89.30 - 111.63: 2 Dihedral angle restraints: 8220 sinusoidal: 3124 harmonic: 5096 Sorted by residual: dihedral pdb=" C5A PLP D 501 " pdb=" O4P PLP D 501 " pdb=" P PLP D 501 " pdb=" O1P PLP D 501 " ideal model delta sinusoidal sigma weight residual 76.43 -171.94 -111.63 1 2.00e+01 2.50e-03 3.28e+01 dihedral pdb=" C5A PLP C 501 " pdb=" O4P PLP C 501 " pdb=" P PLP C 501 " pdb=" O1P PLP C 501 " ideal model delta sinusoidal sigma weight residual 76.43 177.79 -101.36 1 2.00e+01 2.50e-03 2.87e+01 dihedral pdb=" C5 PLP B 501 " pdb=" C5A PLP B 501 " pdb=" O4P PLP B 501 " pdb=" P PLP B 501 " ideal model delta sinusoidal sigma weight residual 188.31 117.64 70.66 1 2.00e+01 2.50e-03 1.61e+01 ... (remaining 8217 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 2.440 nonbonded pdb=" O LEU D 193 " pdb=" OG SER D 197 " model vdw 2.013 2.440 nonbonded pdb=" OG1 THR D 14 " pdb=" O VAL D 34 " model vdw 2.068 2.440 nonbonded pdb=" OH TYR A 158 " pdb=" OE1 GLU A 195 " model vdw 2.081 2.440 nonbonded pdb=" O LEU A 193 " pdb=" OG SER A 197 " model vdw 2.096 2.440 ... (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 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: 0.920 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 38.010 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.004 0.052 13796 Z= 0.238 Angle : 0.581 7.009 18768 Z= 0.319 Chirality : 0.044 0.175 2104 Planarity : 0.004 0.040 2472 Dihedral : 12.554 111.630 5012 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP B 310 HIS 0.002 0.001 HIS A 409 PHE 0.007 0.001 PHE D 230 TYR 0.015 0.001 TYR D 36 ARG 0.003 0.000 ARG A 86 *********************** 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 fitting. rotamer outliers: 61 poor density : 281 time to evaluate : 1.327 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: 0.6862 (t0) REVERT: B 401 LYS cc_start: 0.8474 (mttp) cc_final: 0.8211 (mtpt) REVERT: A 260 ARG cc_start: 0.8162 (tpt-90) cc_final: 0.7484 (ttm110) REVERT: A 363 TYR cc_start: 0.8061 (m-80) cc_final: 0.7700 (m-80) REVERT: C 58 SER cc_start: 0.8274 (m) cc_final: 0.7957 (p) REVERT: C 60 GLN cc_start: 0.7385 (tt0) cc_final: 0.7172 (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: 0.6846 (t0) REVERT: D 260 ARG cc_start: 0.8144 (tpt-90) cc_final: 0.7454 (ttm110) REVERT: D 362 GLU cc_start: 0.8026 (tt0) cc_final: 0.7693 (tt0) REVERT: D 431 ARG cc_start: 0.8496 (ttt-90) cc_final: 0.7751 (tmt-80) outliers start: 61 outliers final: 23 residues processed: 325 average time/residue: 0.2784 time to fit residues: 127.2473 Evaluate side-chains 213 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 74 ASN A 84 GLN C 5 GLN C 6 HIS C 20 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13796 Z= 0.321 Angle : 0.687 7.759 18768 Z= 0.346 Chirality : 0.049 0.384 2104 Planarity : 0.005 0.043 2472 Dihedral : 7.298 77.663 2043 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 2.85 % Allowed : 10.54 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.19), residues: 1824 helix: -1.33 (0.20), residues: 688 sheet: -3.57 (0.28), residues: 204 loop : -2.67 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 310 HIS 0.008 0.002 HIS C 348 PHE 0.014 0.002 PHE C 230 TYR 0.020 0.002 TYR D 36 ARG 0.004 0.000 ARG C 260 *********************** 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 235 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 195 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 SER cc_start: 0.8238 (m) cc_final: 0.7985 (p) REVERT: B 60 GLN cc_start: 0.7416 (tt0) cc_final: 0.7119 (tt0) REVERT: B 182 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8482 (t) REVERT: B 200 ARG cc_start: 0.7544 (mtp-110) cc_final: 0.7146 (ptm160) REVERT: B 401 LYS cc_start: 0.8547 (mttp) cc_final: 0.8223 (mtpt) REVERT: B 452 ASP cc_start: 0.8233 (t0) cc_final: 0.8022 (t0) REVERT: A 84 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: A 260 ARG cc_start: 0.7966 (tpt-90) cc_final: 0.7429 (ttm110) REVERT: A 363 TYR cc_start: 0.8087 (m-80) cc_final: 0.7767 (m-80) REVERT: C 58 SER cc_start: 0.8263 (m) cc_final: 0.8001 (p) REVERT: C 60 GLN cc_start: 0.7400 (tt0) cc_final: 0.7104 (tt0) REVERT: C 200 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.7236 (ptm160) REVERT: C 272 MET cc_start: 0.8858 (ttm) cc_final: 0.8635 (ttp) REVERT: D 18 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8101 (ttt-90) REVERT: D 35 GLU cc_start: 0.7981 (tt0) cc_final: 0.7638 (tt0) REVERT: D 147 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: D 185 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8349 (m) REVERT: D 228 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7733 (mm-30) REVERT: D 260 ARG cc_start: 0.7949 (tpt-90) cc_final: 0.7324 (ttm110) REVERT: D 428 LYS cc_start: 0.8669 (tptm) cc_final: 0.8356 (tttt) REVERT: D 454 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7600 (mp) outliers start: 40 outliers final: 23 residues processed: 219 average time/residue: 0.2329 time to fit residues: 75.6839 Evaluate side-chains 205 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 176 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 45 ASP 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 160 THR 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 185 THR Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 287 ASP 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 90 optimal weight: 0.0970 chunk 50 optimal weight: 5.9990 chunk 136 optimal weight: 0.0870 chunk 111 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13796 Z= 0.248 Angle : 0.627 6.714 18768 Z= 0.314 Chirality : 0.046 0.301 2104 Planarity : 0.004 0.043 2472 Dihedral : 6.288 59.252 2029 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.13 % Allowed : 14.32 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.19), residues: 1824 helix: -1.02 (0.20), residues: 692 sheet: -2.92 (0.31), residues: 204 loop : -2.42 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 310 HIS 0.007 0.002 HIS C 348 PHE 0.015 0.001 PHE C 230 TYR 0.018 0.001 TYR D 36 ARG 0.004 0.000 ARG C 336 *********************** 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 228 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: B 182 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8655 (t) REVERT: B 200 ARG cc_start: 0.7447 (mtp-110) cc_final: 0.7082 (ptm160) REVERT: B 401 LYS cc_start: 0.8522 (mttp) cc_final: 0.8180 (mtpt) REVERT: B 436 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8128 (pp) REVERT: A 228 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 260 ARG cc_start: 0.7924 (tpt-90) cc_final: 0.7307 (ttm110) REVERT: A 363 TYR cc_start: 0.8128 (m-80) cc_final: 0.7802 (m-80) REVERT: A 452 ASP cc_start: 0.7523 (t0) cc_final: 0.7231 (t0) REVERT: C 9 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7793 (mt-10) REVERT: C 152 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7428 (mt-10) REVERT: C 200 ARG cc_start: 0.7530 (mtp-110) cc_final: 0.7157 (ptm160) REVERT: C 272 MET cc_start: 0.8811 (ttm) cc_final: 0.8567 (ttp) REVERT: D 18 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7860 (ttt-90) REVERT: D 35 GLU cc_start: 0.8008 (tt0) cc_final: 0.7753 (tt0) REVERT: D 147 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: D 158 TYR cc_start: 0.8098 (t80) cc_final: 0.7794 (t80) REVERT: D 185 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7761 (m) REVERT: D 260 ARG cc_start: 0.7966 (tpt-90) cc_final: 0.7713 (ttm-80) outliers start: 44 outliers final: 27 residues processed: 214 average time/residue: 0.2346 time to fit residues: 75.2207 Evaluate side-chains 196 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.521 ------------------------------------------------------------------------------- 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 45 ASP Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 177 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 436 LEU 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 185 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 432 ASP 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 161 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN A 74 ASN A 84 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13796 Z= 0.444 Angle : 0.721 8.052 18768 Z= 0.359 Chirality : 0.049 0.151 2104 Planarity : 0.005 0.046 2472 Dihedral : 6.351 58.322 2022 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 4.20 % Allowed : 15.81 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.19), residues: 1824 helix: -1.13 (0.20), residues: 700 sheet: -2.65 (0.33), residues: 204 loop : -2.38 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 310 HIS 0.009 0.002 HIS A 348 PHE 0.019 0.002 PHE C 230 TYR 0.024 0.002 TYR D 36 ARG 0.004 0.001 ARG B 85 *********************** 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 212 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 153 time to evaluate : 1.433 Fit side-chains revert: symmetry clash REVERT: B 9 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7573 (mt-10) REVERT: B 401 LYS cc_start: 0.8568 (mttp) cc_final: 0.8199 (mtpt) REVERT: A 228 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7911 (mm-30) REVERT: A 296 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: A 363 TYR cc_start: 0.8201 (m-80) cc_final: 0.7894 (m-80) REVERT: A 404 ASP cc_start: 0.7813 (m-30) cc_final: 0.7411 (m-30) REVERT: D 18 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8058 (ttt-90) REVERT: D 35 GLU cc_start: 0.8108 (tt0) cc_final: 0.7896 (tt0) REVERT: D 84 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: D 147 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: D 158 TYR cc_start: 0.8209 (t80) cc_final: 0.7911 (t80) REVERT: D 260 ARG cc_start: 0.8043 (tpt-90) cc_final: 0.7749 (ttm-80) REVERT: D 404 ASP cc_start: 0.7858 (m-30) cc_final: 0.7447 (m-30) outliers start: 59 outliers final: 38 residues processed: 194 average time/residue: 0.2162 time to fit residues: 64.1144 Evaluate side-chains 188 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 146 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 58 SER 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 160 THR 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 17 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 45 ASP 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 296 ASP 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 58 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 160 THR 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 84 GLN Chi-restraints excluded: chain D residue 98 VAL 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 287 ASP 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 417 ILE 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 144 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN A 74 ASN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13796 Z= 0.221 Angle : 0.608 6.610 18768 Z= 0.303 Chirality : 0.045 0.179 2104 Planarity : 0.004 0.041 2472 Dihedral : 5.836 51.925 2021 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.99 % Allowed : 17.24 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.19), residues: 1824 helix: -0.81 (0.20), residues: 692 sheet: -2.28 (0.34), residues: 204 loop : -2.12 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 310 HIS 0.007 0.001 HIS C 348 PHE 0.015 0.001 PHE C 230 TYR 0.016 0.001 TYR D 36 ARG 0.004 0.000 ARG A 260 *********************** 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 223 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 167 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7413 (mt-10) REVERT: B 401 LYS cc_start: 0.8531 (mttp) cc_final: 0.8176 (mtpt) REVERT: A 74 ASN cc_start: 0.6965 (OUTLIER) cc_final: 0.6622 (t0) REVERT: A 228 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7830 (mm-30) REVERT: A 296 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: A 363 TYR cc_start: 0.8088 (m-80) cc_final: 0.7791 (m-80) REVERT: A 404 ASP cc_start: 0.7795 (m-30) cc_final: 0.7468 (m-30) REVERT: A 452 ASP cc_start: 0.7631 (t0) cc_final: 0.7294 (t0) REVERT: C 152 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7504 (mt-10) REVERT: C 424 SER cc_start: 0.9060 (t) cc_final: 0.8758 (p) REVERT: D 147 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: D 185 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7687 (m) REVERT: D 260 ARG cc_start: 0.8028 (tpt-90) cc_final: 0.7199 (ttm110) REVERT: D 296 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: D 404 ASP cc_start: 0.7873 (m-30) cc_final: 0.7496 (m-30) outliers start: 56 outliers final: 39 residues processed: 209 average time/residue: 0.2150 time to fit residues: 68.6375 Evaluate side-chains 195 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 151 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 371 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 45 ASP Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 159 VAL 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 296 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 313 SER 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 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 287 ASP Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 432 ASP 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 58 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 174 optimal weight: 0.0040 chunk 144 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN A 74 ASN A 84 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13796 Z= 0.226 Angle : 0.600 6.701 18768 Z= 0.298 Chirality : 0.045 0.159 2104 Planarity : 0.004 0.041 2472 Dihedral : 5.596 51.875 2021 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 4.06 % Allowed : 18.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.20), residues: 1824 helix: -0.68 (0.20), residues: 692 sheet: -1.95 (0.34), residues: 204 loop : -2.03 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.006 0.001 HIS C 348 PHE 0.013 0.001 PHE C 230 TYR 0.015 0.001 TYR B 36 ARG 0.005 0.000 ARG C 260 *********************** 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 216 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 159 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: B 9 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7383 (mt-10) REVERT: B 152 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7434 (mt-10) REVERT: B 401 LYS cc_start: 0.8523 (mttp) cc_final: 0.8171 (mtpt) REVERT: B 436 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8084 (pp) REVERT: A 228 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 296 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: A 363 TYR cc_start: 0.8092 (m-80) cc_final: 0.7825 (m-80) REVERT: A 404 ASP cc_start: 0.7841 (m-30) cc_final: 0.7520 (m-30) REVERT: A 452 ASP cc_start: 0.7555 (t0) cc_final: 0.7190 (t0) REVERT: C 152 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7541 (mt-10) REVERT: C 200 ARG cc_start: 0.7536 (mtp-110) cc_final: 0.7135 (ptm160) REVERT: C 424 SER cc_start: 0.9063 (t) cc_final: 0.8778 (p) REVERT: C 436 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8123 (pp) REVERT: D 147 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: D 260 ARG cc_start: 0.8008 (tpt-90) cc_final: 0.7726 (ttm-80) REVERT: D 296 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: D 404 ASP cc_start: 0.7898 (m-30) cc_final: 0.7533 (m-30) outliers start: 57 outliers final: 42 residues processed: 202 average time/residue: 0.2083 time to fit residues: 65.4157 Evaluate side-chains 204 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 157 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 58 SER 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 160 THR 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 45 ASP 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 196 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 ASP 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 58 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 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 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 432 ASP 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 167 optimal weight: 10.0000 chunk 19 optimal weight: 0.0010 chunk 99 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN A 74 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13796 Z= 0.268 Angle : 0.616 6.598 18768 Z= 0.306 Chirality : 0.046 0.144 2104 Planarity : 0.005 0.041 2472 Dihedral : 5.489 53.784 2020 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.27 % Allowed : 18.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.20), residues: 1824 helix: -0.67 (0.20), residues: 692 sheet: -1.70 (0.35), residues: 204 loop : -1.94 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 310 HIS 0.006 0.001 HIS B 348 PHE 0.013 0.001 PHE C 230 TYR 0.016 0.001 TYR A 36 ARG 0.004 0.000 ARG B 85 *********************** 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 218 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 158 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: B 152 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7448 (mt-10) REVERT: B 374 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.5558 (tt0) REVERT: B 401 LYS cc_start: 0.8535 (mttp) cc_final: 0.8171 (mtpt) REVERT: B 436 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8032 (pp) REVERT: A 228 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7809 (mm-30) REVERT: A 296 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: A 363 TYR cc_start: 0.8168 (m-80) cc_final: 0.7901 (m-80) REVERT: A 404 ASP cc_start: 0.7840 (m-30) cc_final: 0.7519 (m-30) REVERT: A 452 ASP cc_start: 0.7462 (t0) cc_final: 0.7093 (t0) REVERT: C 152 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7526 (mt-10) REVERT: C 424 SER cc_start: 0.9115 (t) cc_final: 0.8796 (p) REVERT: C 436 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8098 (pp) REVERT: D 147 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8184 (pm20) REVERT: D 260 ARG cc_start: 0.8030 (tpt-90) cc_final: 0.7771 (ttm-80) REVERT: D 296 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: D 404 ASP cc_start: 0.7902 (m-30) cc_final: 0.7547 (m-30) outliers start: 60 outliers final: 46 residues processed: 205 average time/residue: 0.2086 time to fit residues: 66.4826 Evaluate side-chains 205 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 153 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 58 SER 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 160 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 374 GLU 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 45 ASP 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 196 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 ASP 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 58 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 160 THR 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 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 296 ASP 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 432 ASP 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 107 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 84 GLN ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13796 Z= 0.272 Angle : 0.623 8.225 18768 Z= 0.308 Chirality : 0.046 0.159 2104 Planarity : 0.005 0.042 2472 Dihedral : 5.480 56.920 2020 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 4.49 % Allowed : 18.30 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.20), residues: 1824 helix: -0.65 (0.20), residues: 692 sheet: -1.52 (0.35), residues: 204 loop : -1.88 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 310 HIS 0.007 0.001 HIS B 6 PHE 0.012 0.001 PHE C 230 TYR 0.016 0.002 TYR D 36 ARG 0.005 0.000 ARG D 85 *********************** 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 216 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 153 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: B 152 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7474 (mt-10) REVERT: B 374 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5589 (tt0) REVERT: B 401 LYS cc_start: 0.8541 (mttp) cc_final: 0.8175 (mtpt) REVERT: B 430 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8309 (mp) REVERT: B 436 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8073 (pp) REVERT: A 228 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7805 (mm-30) REVERT: A 296 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: A 363 TYR cc_start: 0.8169 (m-80) cc_final: 0.7920 (m-80) REVERT: A 404 ASP cc_start: 0.7836 (m-30) cc_final: 0.7515 (m-30) REVERT: A 452 ASP cc_start: 0.7374 (t0) cc_final: 0.7056 (t0) REVERT: C 152 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7534 (mt-10) REVERT: C 424 SER cc_start: 0.9117 (t) cc_final: 0.8797 (p) REVERT: C 436 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8127 (pp) REVERT: D 147 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: D 260 ARG cc_start: 0.8031 (tpt-90) cc_final: 0.7745 (ttm-80) REVERT: D 296 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: D 404 ASP cc_start: 0.7907 (m-30) cc_final: 0.7555 (m-30) outliers start: 63 outliers final: 50 residues processed: 200 average time/residue: 0.2047 time to fit residues: 63.7897 Evaluate side-chains 208 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 151 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER 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 160 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 430 LEU 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 45 ASP 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 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 296 ASP 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 A residue 449 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 160 THR 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 287 ASP Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 296 ASP 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 157 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13796 Z= 0.249 Angle : 0.611 7.909 18768 Z= 0.302 Chirality : 0.046 0.145 2104 Planarity : 0.004 0.042 2472 Dihedral : 5.321 57.590 2018 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.99 % Allowed : 18.95 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.20), residues: 1824 helix: -0.60 (0.20), residues: 692 sheet: -1.34 (0.36), residues: 204 loop : -1.81 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 310 HIS 0.006 0.001 HIS B 348 PHE 0.011 0.001 PHE C 230 TYR 0.015 0.001 TYR C 128 ARG 0.006 0.000 ARG D 85 *********************** 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 205 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 149 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: B 152 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7519 (mt-10) REVERT: B 287 ASP cc_start: 0.7215 (t0) cc_final: 0.6940 (t0) REVERT: B 374 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5164 (tt0) REVERT: B 401 LYS cc_start: 0.8537 (mttp) cc_final: 0.8172 (mtpt) REVERT: B 436 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8082 (pp) REVERT: A 228 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 296 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: A 363 TYR cc_start: 0.8159 (m-80) cc_final: 0.7901 (m-80) REVERT: A 404 ASP cc_start: 0.7831 (m-30) cc_final: 0.7531 (m-30) REVERT: A 452 ASP cc_start: 0.7388 (t0) cc_final: 0.7069 (t0) REVERT: C 152 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7559 (mt-10) REVERT: C 424 SER cc_start: 0.9116 (t) cc_final: 0.8799 (p) REVERT: C 436 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8135 (pp) REVERT: D 147 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: D 260 ARG cc_start: 0.8022 (tpt-90) cc_final: 0.7756 (ttm-80) REVERT: D 296 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: D 404 ASP cc_start: 0.7907 (m-30) cc_final: 0.7545 (m-30) outliers start: 56 outliers final: 49 residues processed: 193 average time/residue: 0.1985 time to fit residues: 60.6134 Evaluate side-chains 205 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 150 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 58 SER 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 160 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 374 GLU 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 45 ASP 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 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 296 ASP 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 A residue 449 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 160 THR 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 287 ASP Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 296 ASP 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 432 ASP 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 170 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 118 optimal weight: 0.0270 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 0.0970 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN A 74 ASN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13796 Z= 0.179 Angle : 0.581 7.100 18768 Z= 0.287 Chirality : 0.044 0.144 2104 Planarity : 0.004 0.042 2472 Dihedral : 5.086 51.860 2018 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.70 % Allowed : 19.09 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.20), residues: 1824 helix: -0.25 (0.21), residues: 672 sheet: -1.08 (0.36), residues: 204 loop : -1.69 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 310 HIS 0.005 0.001 HIS C 348 PHE 0.011 0.001 PHE C 230 TYR 0.015 0.001 TYR B 36 ARG 0.004 0.000 ARG A 85 ********************** 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 220 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 168 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: B 152 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7504 (mt-10) REVERT: B 200 ARG cc_start: 0.7291 (mtp-110) cc_final: 0.6837 (ptm160) REVERT: B 374 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.3883 (tt0) REVERT: B 401 LYS cc_start: 0.8508 (mttp) cc_final: 0.8134 (mtpt) REVERT: B 436 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8020 (pp) REVERT: A 228 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 296 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7772 (m-30) REVERT: A 332 ASP cc_start: 0.8455 (t0) cc_final: 0.8063 (m-30) REVERT: A 363 TYR cc_start: 0.8112 (m-80) cc_final: 0.7853 (m-80) REVERT: A 404 ASP cc_start: 0.7838 (m-30) cc_final: 0.7537 (m-30) REVERT: A 452 ASP cc_start: 0.7385 (t0) cc_final: 0.7056 (t0) REVERT: C 152 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7540 (mt-10) REVERT: C 200 ARG cc_start: 0.7382 (mtp-110) cc_final: 0.7016 (ptm160) REVERT: C 424 SER cc_start: 0.9120 (t) cc_final: 0.8806 (p) REVERT: C 436 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8154 (pp) REVERT: D 147 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: D 260 ARG cc_start: 0.7943 (tpt-90) cc_final: 0.7493 (tpp-160) REVERT: D 296 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7741 (m-30) REVERT: D 332 ASP cc_start: 0.8373 (t0) cc_final: 0.8029 (m-30) REVERT: D 404 ASP cc_start: 0.7918 (m-30) cc_final: 0.7584 (m-30) outliers start: 52 outliers final: 44 residues processed: 206 average time/residue: 0.2098 time to fit residues: 67.4915 Evaluate side-chains 210 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 160 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 374 GLU 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 45 ASP 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 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 296 ASP 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 A residue 449 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 160 THR 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 196 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 296 ASP 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 432 ASP 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 152 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 chunk 131 optimal weight: 0.0370 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 59 optimal weight: 0.0060 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 0.0070 overall best weight: 0.2692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN A 84 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** 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 = 0.3484 r_free = 0.3484 target = 0.139920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.116512 restraints weight = 16649.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.119222 restraints weight = 11124.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.121078 restraints weight = 8515.423| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13796 Z= 0.149 Angle : 0.563 7.045 18768 Z= 0.278 Chirality : 0.044 0.142 2104 Planarity : 0.004 0.043 2472 Dihedral : 4.803 50.291 2016 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.99 % Allowed : 20.30 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.20), residues: 1824 helix: -0.09 (0.21), residues: 676 sheet: -0.75 (0.38), residues: 204 loop : -1.60 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 433 HIS 0.004 0.001 HIS D 157 PHE 0.010 0.001 PHE C 230 TYR 0.014 0.001 TYR B 36 ARG 0.006 0.000 ARG D 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2508.25 seconds wall clock time: 45 minutes 47.48 seconds (2747.48 seconds total)