Starting phenix.real_space_refine on Wed Feb 14 14:49:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xdg_22137/02_2024/6xdg_22137.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xdg_22137/02_2024/6xdg_22137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xdg_22137/02_2024/6xdg_22137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xdg_22137/02_2024/6xdg_22137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xdg_22137/02_2024/6xdg_22137.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xdg_22137/02_2024/6xdg_22137.pdb" } resolution = 3.9 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1514 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5058 2.51 5 N 1320 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "E PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8004 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} bond proxies already assigned to first conformer: 1572 Chain: "D" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain: "B" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1603 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Chain breaks: 1 Chain: "C" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1604 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 1 Chain: "A" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1565 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 MAN F 4 " occ=0.70 ... (9 atoms not shown) pdb=" O6 MAN F 4 " occ=0.70 Time building chain proxies: 5.68, per 1000 atoms: 0.71 Number of scatterers: 8004 At special positions: 0 Unit cell: (72.25, 119.85, 150.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1594 8.00 N 1320 7.00 C 5058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 197 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG F 1 " - " ASN E 343 " Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 1.8 seconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 21 sheets defined 8.8% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 383 through 389 removed outlier: 3.753A pdb=" N ASP E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.489A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 183 through 189 Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.257A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.728A pdb=" N SER B 195 " --> pdb=" O PRO B 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.823A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 192 through 196 removed outlier: 3.975A pdb=" N LEU C 196 " --> pdb=" O SER C 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.798A pdb=" N GLN A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 removed outlier: 3.996A pdb=" N HIS A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.820A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.758A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.431A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 34 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN D 89 " --> pdb=" O ASN D 34 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.513A pdb=" N SER D 114 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 162 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 153 through 155 removed outlier: 3.730A pdb=" N GLN D 155 " --> pdb=" O TRP D 148 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 192 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS D 207 " --> pdb=" O CYS D 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.755A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR B 80 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER B 71 " --> pdb=" O TYR B 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.739A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 99 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 94 removed outlier: 3.658A pdb=" N THR B 114 " --> pdb=" O TYR B 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 131 removed outlier: 3.738A pdb=" N SER B 127 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 143 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 187 " --> pdb=" O CYS B 147 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 149 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 185 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER B 184 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA B 175 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER B 186 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.717A pdb=" N THR B 158 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.922A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.578A pdb=" N TYR C 59 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 50 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 93 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 127 through 131 removed outlier: 4.472A pdb=" N SER C 127 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 150 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 145 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 187 " --> pdb=" O CYS C 147 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR C 183 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 205 through 206 removed outlier: 3.515A pdb=" N VAL C 205 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 214 " --> pdb=" O VAL C 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.737A pdb=" N VAL A 10 " --> pdb=" O THR A 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 17 through 23 Processing sheet with id=AB9, first strand: chain 'A' and resid 47 through 51 removed outlier: 5.444A pdb=" N LEU A 48 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN A 39 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 40 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP A 87 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 92 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 100 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 118 through 122 removed outlier: 3.573A pdb=" N PHE A 122 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 137 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER A 141 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA A 178 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 169 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 118 through 122 removed outlier: 3.573A pdb=" N PHE A 122 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 137 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 158 through 159 removed outlier: 3.565A pdb=" N TRP A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 198 " --> pdb=" O ALA A 151 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2535 1.35 - 1.47: 2165 1.47 - 1.59: 3460 1.59 - 1.71: 0 1.71 - 1.83: 39 Bond restraints: 8199 Sorted by residual: bond pdb=" C PHE E 497 " pdb=" N GLN E 498 " ideal model delta sigma weight residual 1.329 1.293 0.035 1.60e-02 3.91e+03 4.86e+00 bond pdb=" N VAL B 176 " pdb=" CA VAL B 176 " ideal model delta sigma weight residual 1.459 1.441 0.018 1.25e-02 6.40e+03 2.15e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C5 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.418 1.444 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" CA VAL D 110 " pdb=" CB VAL D 110 " ideal model delta sigma weight residual 1.553 1.544 0.009 7.40e-03 1.83e+04 1.44e+00 ... (remaining 8194 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.10: 283 107.10 - 113.83: 4579 113.83 - 120.55: 2925 120.55 - 127.28: 3295 127.28 - 134.01: 89 Bond angle restraints: 11171 Sorted by residual: angle pdb=" C PHE E 497 " pdb=" N GLN E 498 " pdb=" CA GLN E 498 " ideal model delta sigma weight residual 120.49 113.22 7.27 1.42e+00 4.96e-01 2.62e+01 angle pdb=" C TYR A 51 " pdb=" N ASP A 52 " pdb=" CA ASP A 52 " ideal model delta sigma weight residual 121.54 129.53 -7.99 1.91e+00 2.74e-01 1.75e+01 angle pdb=" C VAL A 53 " pdb=" N SER A 54 " pdb=" CA SER A 54 " ideal model delta sigma weight residual 120.23 127.04 -6.81 1.67e+00 3.59e-01 1.66e+01 angle pdb=" N SER C 100 " pdb=" CA SER C 100 " pdb=" C SER C 100 " ideal model delta sigma weight residual 110.33 114.61 -4.28 1.29e+00 6.01e-01 1.10e+01 angle pdb=" N ASP A 52 " pdb=" CA ASP A 52 " pdb=" C ASP A 52 " ideal model delta sigma weight residual 110.80 117.69 -6.89 2.13e+00 2.20e-01 1.05e+01 ... (remaining 11166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.95: 4633 21.95 - 43.89: 248 43.89 - 65.84: 20 65.84 - 87.78: 13 87.78 - 109.73: 4 Dihedral angle restraints: 4918 sinusoidal: 1898 harmonic: 3020 Sorted by residual: dihedral pdb=" CA CYS E 361 " pdb=" C CYS E 361 " pdb=" N VAL E 362 " pdb=" CA VAL E 362 " ideal model delta harmonic sigma weight residual 180.00 154.06 25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASP A 52 " pdb=" C ASP A 52 " pdb=" N VAL A 53 " pdb=" CA VAL A 53 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ASP B 108 " pdb=" C ASP B 108 " pdb=" N TYR B 109 " pdb=" CA TYR B 109 " ideal model delta harmonic sigma weight residual -180.00 -154.24 -25.76 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 4915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1150 0.081 - 0.162: 109 0.162 - 0.244: 0 0.244 - 0.325: 2 0.325 - 0.406: 1 Chirality restraints: 1262 Sorted by residual: chirality pdb=" C1 MAN F 4 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 4 " pdb=" O5 MAN F 4 " both_signs ideal model delta sigma weight residual False 2.40 1.99 0.41 2.00e-02 2.50e+03 4.12e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.62e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.76e+01 ... (remaining 1259 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 155 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO C 156 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 110 " -0.016 2.00e-02 2.50e+03 9.78e-03 2.39e+00 pdb=" CG TRP B 110 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 110 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP B 110 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 110 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 110 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 110 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 110 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 110 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 110 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 462 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO E 463 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 463 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 463 " 0.020 5.00e-02 4.00e+02 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 317 2.68 - 3.24: 8293 3.24 - 3.79: 12628 3.79 - 4.35: 16251 4.35 - 4.90: 25992 Nonbonded interactions: 63481 Sorted by model distance: nonbonded pdb=" OG SER D 121 " pdb=" O PRO B 130 " model vdw 2.127 2.440 nonbonded pdb=" O PRO C 130 " pdb=" OG SER A 125 " model vdw 2.135 2.440 nonbonded pdb=" O TYR D 186 " pdb=" OH TYR D 192 " model vdw 2.140 2.440 nonbonded pdb=" OG SER D 7 " pdb=" OG1 THR D 22 " model vdw 2.157 2.440 nonbonded pdb=" OD1 ASP A 142 " pdb=" NE2 GLN A 171 " model vdw 2.171 2.520 ... (remaining 63476 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 'B' and (resid 1 through 10 or resid 12 or resid 14 through 15 or resid 1 \ 7 through 30 or resid 32 or resid 34 or resid 36 or resid 38 through 48 or resid \ 51 or resid 53 or resid 55 through 56 or resid 59 through 74 or resid 76 or res \ id 79 through 87 or resid 89 through 97 or resid 109 through 220)) selection = (chain 'C' and (resid 1 through 10 or resid 12 or resid 14 through 15 or resid 1 \ 7 through 30 or resid 32 or resid 34 or resid 36 or resid 38 through 48 or resid \ 51 or resid 53 or resid 55 through 56 or resid 59 through 74 or resid 76 or res \ id 79 through 87 or resid 89 through 97 or resid 109 through 220)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 5.320 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 27.440 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 0.035 8199 Z= 0.267 Angle : 0.701 8.108 11171 Z= 0.375 Chirality : 0.046 0.406 1262 Planarity : 0.004 0.042 1425 Dihedral : 13.904 109.730 2968 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.82 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % 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: -3.87 (0.23), residues: 1030 helix: -3.19 (0.52), residues: 48 sheet: -2.30 (0.24), residues: 377 loop : -2.77 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 110 HIS 0.003 0.001 HIS A 201 PHE 0.013 0.002 PHE C 68 TYR 0.014 0.001 TYR E 495 ARG 0.007 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.9165 (pp20) cc_final: 0.8961 (pp20) REVERT: E 386 LYS cc_start: 0.9132 (mptt) cc_final: 0.8812 (tptt) REVERT: E 406 GLU cc_start: 0.9390 (mt-10) cc_final: 0.8660 (mp0) REVERT: E 432 CYS cc_start: 0.7903 (t) cc_final: 0.7513 (m) REVERT: E 465 GLU cc_start: 0.7124 (tt0) cc_final: 0.6805 (tt0) REVERT: E 471 GLU cc_start: 0.8884 (tp30) cc_final: 0.8616 (tm-30) REVERT: E 515 PHE cc_start: 0.9124 (m-80) cc_final: 0.8896 (m-80) REVERT: D 93 ASN cc_start: 0.8525 (m110) cc_final: 0.8140 (t0) REVERT: D 105 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8107 (pt0) REVERT: D 142 ARG cc_start: 0.8989 (tmt170) cc_final: 0.8500 (ttp80) REVERT: D 187 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8841 (mm-30) REVERT: B 199 GLN cc_start: 0.8327 (mt0) cc_final: 0.8068 (tp40) REVERT: B 216 LYS cc_start: 0.9052 (ttmm) cc_final: 0.8790 (ttpp) REVERT: C 4 LEU cc_start: 0.8118 (mt) cc_final: 0.7853 (mt) REVERT: A 49 MET cc_start: 0.8318 (mmm) cc_final: 0.7818 (mmm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2841 time to fit residues: 46.9572 Evaluate side-chains 87 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 93 optimal weight: 30.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 388 ASN E 474 GLN E 487 ASN D 38 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS D 210 ASN B 82 GLN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 1 GLN C 162 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN C 204 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8199 Z= 0.364 Angle : 0.756 11.067 11171 Z= 0.390 Chirality : 0.046 0.184 1262 Planarity : 0.005 0.070 1425 Dihedral : 8.680 87.564 1210 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.30 % Favored : 89.31 % Rotamer: Outliers : 1.91 % Allowed : 14.03 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % 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: -3.25 (0.24), residues: 1030 helix: -2.68 (0.52), residues: 54 sheet: -1.67 (0.26), residues: 374 loop : -2.50 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 110 HIS 0.003 0.001 HIS D 198 PHE 0.022 0.002 PHE E 400 TYR 0.020 0.002 TYR E 365 ARG 0.006 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9162 (mptt) cc_final: 0.8834 (tptt) REVERT: E 406 GLU cc_start: 0.9442 (mt-10) cc_final: 0.8666 (mp0) REVERT: E 465 GLU cc_start: 0.7117 (tt0) cc_final: 0.6760 (tt0) REVERT: E 471 GLU cc_start: 0.8911 (tp30) cc_final: 0.8522 (tm-30) REVERT: E 515 PHE cc_start: 0.9465 (m-80) cc_final: 0.9175 (m-80) REVERT: D 4 MET cc_start: 0.7833 (tpp) cc_final: 0.7395 (mmm) REVERT: D 93 ASN cc_start: 0.8764 (m-40) cc_final: 0.8273 (t0) REVERT: D 105 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8094 (pt0) REVERT: D 142 ARG cc_start: 0.9013 (tmt170) cc_final: 0.8524 (ttp80) REVERT: D 187 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8907 (mm-30) REVERT: B 100 ARG cc_start: 0.8208 (mtt180) cc_final: 0.7771 (mtt180) REVERT: B 161 TRP cc_start: 0.8145 (m100) cc_final: 0.7891 (m100) REVERT: B 199 GLN cc_start: 0.8325 (mt0) cc_final: 0.8048 (tp40) REVERT: B 216 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8679 (ttpp) REVERT: C 4 LEU cc_start: 0.8251 (mt) cc_final: 0.8036 (mt) REVERT: C 87 ARG cc_start: 0.8843 (mtm-85) cc_final: 0.8097 (mtm180) REVERT: A 49 MET cc_start: 0.8308 (mmm) cc_final: 0.7815 (mmm) outliers start: 17 outliers final: 9 residues processed: 118 average time/residue: 0.2837 time to fit residues: 42.1942 Evaluate side-chains 95 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 87 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 0.0770 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 101 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 overall best weight: 2.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 189 HIS B 82 GLN B 178 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8199 Z= 0.241 Angle : 0.670 9.021 11171 Z= 0.341 Chirality : 0.044 0.146 1262 Planarity : 0.004 0.046 1425 Dihedral : 7.730 72.426 1210 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.94 % Favored : 90.86 % Rotamer: Outliers : 2.36 % Allowed : 16.16 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.80 (0.25), residues: 1030 helix: -2.44 (0.54), residues: 55 sheet: -1.36 (0.27), residues: 376 loop : -2.18 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 110 HIS 0.004 0.001 HIS A 201 PHE 0.012 0.001 PHE E 400 TYR 0.014 0.001 TYR E 365 ARG 0.006 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9134 (mptt) cc_final: 0.8837 (tptt) REVERT: E 406 GLU cc_start: 0.9449 (mt-10) cc_final: 0.8673 (mp0) REVERT: E 432 CYS cc_start: 0.7459 (m) cc_final: 0.7186 (m) REVERT: E 465 GLU cc_start: 0.7092 (tt0) cc_final: 0.6228 (tt0) REVERT: E 515 PHE cc_start: 0.9439 (m-80) cc_final: 0.8551 (m-80) REVERT: D 4 MET cc_start: 0.7806 (tpp) cc_final: 0.7357 (mmm) REVERT: D 93 ASN cc_start: 0.8804 (m-40) cc_final: 0.8326 (t0) REVERT: D 105 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8088 (pt0) REVERT: D 142 ARG cc_start: 0.8978 (tmt170) cc_final: 0.8512 (ttp80) REVERT: D 187 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8879 (mm-30) REVERT: B 161 TRP cc_start: 0.8337 (m100) cc_final: 0.8073 (m100) REVERT: B 199 GLN cc_start: 0.8406 (mt0) cc_final: 0.8127 (tp40) REVERT: B 216 LYS cc_start: 0.9095 (ttmm) cc_final: 0.8583 (ttpp) REVERT: C 4 LEU cc_start: 0.8260 (mt) cc_final: 0.8056 (mt) REVERT: A 49 MET cc_start: 0.8333 (mmm) cc_final: 0.7812 (mmm) outliers start: 21 outliers final: 15 residues processed: 115 average time/residue: 0.2660 time to fit residues: 39.1230 Evaluate side-chains 95 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 87 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8199 Z= 0.249 Angle : 0.665 12.014 11171 Z= 0.337 Chirality : 0.044 0.152 1262 Planarity : 0.005 0.069 1425 Dihedral : 7.037 59.064 1210 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.14 % Favored : 90.67 % Rotamer: Outliers : 2.92 % Allowed : 16.95 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % 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: -2.53 (0.25), residues: 1030 helix: -2.14 (0.56), residues: 55 sheet: -1.18 (0.27), residues: 382 loop : -2.01 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 110 HIS 0.003 0.001 HIS A 201 PHE 0.022 0.002 PHE E 497 TYR 0.026 0.002 TYR E 495 ARG 0.002 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9099 (mptt) cc_final: 0.8782 (tptt) REVERT: E 406 GLU cc_start: 0.9457 (mt-10) cc_final: 0.8654 (mp0) REVERT: E 515 PHE cc_start: 0.9321 (m-80) cc_final: 0.8521 (m-80) REVERT: D 4 MET cc_start: 0.7785 (tpp) cc_final: 0.7428 (mmm) REVERT: D 93 ASN cc_start: 0.8794 (m-40) cc_final: 0.8279 (t0) REVERT: D 105 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8058 (pt0) REVERT: D 142 ARG cc_start: 0.8874 (tmt170) cc_final: 0.8313 (ttp80) REVERT: D 187 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8835 (mm-30) REVERT: B 34 MET cc_start: 0.8292 (mmm) cc_final: 0.8061 (mmt) REVERT: B 62 ASP cc_start: 0.8615 (t0) cc_final: 0.8361 (t0) REVERT: B 161 TRP cc_start: 0.8364 (m100) cc_final: 0.8069 (m100) REVERT: B 206 ASN cc_start: 0.7194 (t0) cc_final: 0.6879 (t0) REVERT: B 216 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8597 (ttpp) REVERT: C 87 ARG cc_start: 0.8654 (mtm-85) cc_final: 0.8285 (mtm180) REVERT: A 38 TYR cc_start: 0.8043 (m-80) cc_final: 0.7797 (m-10) REVERT: A 49 MET cc_start: 0.8288 (mmm) cc_final: 0.7821 (mmm) outliers start: 26 outliers final: 22 residues processed: 109 average time/residue: 0.2642 time to fit residues: 37.4698 Evaluate side-chains 101 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.0670 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8199 Z= 0.289 Angle : 0.671 9.282 11171 Z= 0.344 Chirality : 0.044 0.146 1262 Planarity : 0.005 0.049 1425 Dihedral : 6.514 44.793 1210 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.62 % Favored : 90.09 % Rotamer: Outliers : 3.70 % Allowed : 18.52 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % 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: -2.40 (0.26), residues: 1030 helix: -1.86 (0.59), residues: 54 sheet: -0.93 (0.27), residues: 367 loop : -2.05 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 110 HIS 0.004 0.001 HIS A 201 PHE 0.030 0.002 PHE E 497 TYR 0.030 0.002 TYR E 495 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.9097 (mptt) cc_final: 0.8796 (tptt) REVERT: E 406 GLU cc_start: 0.9450 (mt-10) cc_final: 0.8691 (mp0) REVERT: E 471 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8304 (tm-30) REVERT: E 515 PHE cc_start: 0.9351 (m-80) cc_final: 0.8951 (m-80) REVERT: D 4 MET cc_start: 0.7718 (tpp) cc_final: 0.7425 (mmm) REVERT: D 93 ASN cc_start: 0.8824 (m-40) cc_final: 0.8318 (t0) REVERT: D 105 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8049 (pt0) REVERT: D 142 ARG cc_start: 0.8826 (tmt170) cc_final: 0.8306 (ttp80) REVERT: D 187 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8865 (mm-30) REVERT: B 34 MET cc_start: 0.8324 (mmm) cc_final: 0.8105 (mmt) REVERT: B 62 ASP cc_start: 0.8642 (t0) cc_final: 0.8411 (t0) REVERT: B 161 TRP cc_start: 0.8403 (m100) cc_final: 0.8018 (m100) REVERT: B 206 ASN cc_start: 0.7301 (t0) cc_final: 0.6980 (t0) REVERT: B 216 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8556 (ttpp) REVERT: C 35 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.7127 (m-80) REVERT: C 147 CYS cc_start: 0.7814 (p) cc_final: 0.6753 (m) REVERT: A 38 TYR cc_start: 0.8222 (m-80) cc_final: 0.7958 (m-10) REVERT: A 49 MET cc_start: 0.8297 (mmm) cc_final: 0.7836 (mmm) outliers start: 33 outliers final: 28 residues processed: 111 average time/residue: 0.2362 time to fit residues: 34.5746 Evaluate side-chains 106 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 77 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 165 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 82 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8199 Z= 0.160 Angle : 0.632 8.485 11171 Z= 0.318 Chirality : 0.044 0.162 1262 Planarity : 0.005 0.073 1425 Dihedral : 5.849 52.296 1210 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.58 % Favored : 92.23 % Rotamer: Outliers : 3.25 % Allowed : 18.74 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % 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: -2.03 (0.26), residues: 1030 helix: -1.60 (0.63), residues: 54 sheet: -0.75 (0.28), residues: 364 loop : -1.75 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 353 HIS 0.004 0.001 HIS A 201 PHE 0.019 0.001 PHE E 497 TYR 0.019 0.001 TYR E 495 ARG 0.002 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.9395 (mt-10) cc_final: 0.8736 (mp0) REVERT: E 465 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7053 (tt0) REVERT: E 468 ILE cc_start: 0.9287 (pt) cc_final: 0.9021 (tp) REVERT: E 471 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8303 (tm-30) REVERT: E 515 PHE cc_start: 0.9316 (m-80) cc_final: 0.8955 (m-80) REVERT: D 4 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7391 (mmm) REVERT: D 42 LYS cc_start: 0.9202 (mttt) cc_final: 0.8932 (ttmm) REVERT: D 93 ASN cc_start: 0.8675 (m-40) cc_final: 0.8170 (t0) REVERT: D 105 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8040 (pt0) REVERT: D 142 ARG cc_start: 0.8726 (tmt170) cc_final: 0.8205 (ttp80) REVERT: D 187 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8820 (mm-30) REVERT: B 13 LYS cc_start: 0.9150 (mmmm) cc_final: 0.8536 (tptp) REVERT: B 34 MET cc_start: 0.8201 (mmm) cc_final: 0.7853 (mmm) REVERT: B 213 LYS cc_start: 0.9291 (mtpt) cc_final: 0.8849 (tptt) REVERT: B 216 LYS cc_start: 0.9013 (ttmm) cc_final: 0.8476 (ttpp) REVERT: C 129 PHE cc_start: 0.8224 (m-10) cc_final: 0.7971 (m-10) REVERT: C 147 CYS cc_start: 0.7691 (p) cc_final: 0.6614 (m) REVERT: A 38 TYR cc_start: 0.8129 (m-80) cc_final: 0.7900 (m-80) REVERT: A 49 MET cc_start: 0.8308 (mmm) cc_final: 0.7791 (mmm) outliers start: 29 outliers final: 21 residues processed: 114 average time/residue: 0.2440 time to fit residues: 36.0940 Evaluate side-chains 112 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 83 optimal weight: 0.0170 chunk 55 optimal weight: 0.0670 chunk 99 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8199 Z= 0.234 Angle : 0.644 8.771 11171 Z= 0.324 Chirality : 0.043 0.156 1262 Planarity : 0.004 0.049 1425 Dihedral : 5.750 59.935 1210 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.55 % Favored : 91.25 % Rotamer: Outliers : 3.25 % Allowed : 20.20 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.94 (0.26), residues: 1030 helix: -1.56 (0.58), residues: 61 sheet: -0.71 (0.27), residues: 367 loop : -1.66 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 161 HIS 0.003 0.001 HIS A 201 PHE 0.027 0.002 PHE E 497 TYR 0.019 0.002 TYR E 495 ARG 0.007 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.9500 (mt-10) cc_final: 0.8727 (mp0) REVERT: E 465 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7638 (tm-30) REVERT: E 468 ILE cc_start: 0.9287 (pt) cc_final: 0.9036 (tp) REVERT: E 515 PHE cc_start: 0.9365 (m-80) cc_final: 0.8998 (m-80) REVERT: D 4 MET cc_start: 0.7751 (tpp) cc_final: 0.7395 (mmm) REVERT: D 42 LYS cc_start: 0.9271 (mttt) cc_final: 0.9001 (ttmm) REVERT: D 93 ASN cc_start: 0.8729 (m-40) cc_final: 0.8206 (t0) REVERT: D 105 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8017 (pt0) REVERT: D 142 ARG cc_start: 0.8751 (tmt170) cc_final: 0.8206 (ttp80) REVERT: D 187 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8847 (mm-30) REVERT: B 34 MET cc_start: 0.8301 (mmm) cc_final: 0.7931 (mmm) REVERT: B 216 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8505 (ttpp) REVERT: C 129 PHE cc_start: 0.8237 (m-10) cc_final: 0.7962 (m-10) REVERT: C 147 CYS cc_start: 0.7776 (p) cc_final: 0.6813 (m) REVERT: A 38 TYR cc_start: 0.8233 (m-80) cc_final: 0.8009 (m-80) REVERT: A 49 MET cc_start: 0.8304 (mmm) cc_final: 0.7826 (mmm) outliers start: 29 outliers final: 24 residues processed: 112 average time/residue: 0.2473 time to fit residues: 36.2881 Evaluate side-chains 102 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 165 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8199 Z= 0.255 Angle : 0.679 9.937 11171 Z= 0.341 Chirality : 0.043 0.156 1262 Planarity : 0.005 0.093 1425 Dihedral : 5.649 55.574 1210 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.75 % Favored : 90.96 % Rotamer: Outliers : 3.37 % Allowed : 20.20 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % 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: -1.89 (0.26), residues: 1030 helix: -1.51 (0.57), residues: 61 sheet: -0.69 (0.27), residues: 376 loop : -1.62 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 110 HIS 0.003 0.001 HIS A 201 PHE 0.025 0.002 PHE E 497 TYR 0.019 0.002 TYR A 34 ARG 0.009 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.9491 (mt-10) cc_final: 0.8736 (mp0) REVERT: E 465 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7744 (tm-30) REVERT: E 468 ILE cc_start: 0.9326 (pt) cc_final: 0.9117 (tp) REVERT: E 515 PHE cc_start: 0.9361 (m-80) cc_final: 0.9031 (m-80) REVERT: D 4 MET cc_start: 0.7690 (tpp) cc_final: 0.7411 (mmm) REVERT: D 42 LYS cc_start: 0.9275 (mttt) cc_final: 0.8998 (ttmm) REVERT: D 93 ASN cc_start: 0.8708 (m-40) cc_final: 0.8219 (t0) REVERT: D 105 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8045 (pt0) REVERT: D 142 ARG cc_start: 0.8683 (tmt170) cc_final: 0.8091 (ttp80) REVERT: D 187 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8836 (mm-30) REVERT: B 34 MET cc_start: 0.8260 (mmm) cc_final: 0.7983 (mmm) REVERT: B 213 LYS cc_start: 0.9298 (mtpt) cc_final: 0.8811 (tptt) REVERT: B 216 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8503 (ttpp) REVERT: C 129 PHE cc_start: 0.8201 (m-10) cc_final: 0.7924 (m-10) REVERT: C 147 CYS cc_start: 0.7738 (p) cc_final: 0.6841 (m) REVERT: A 49 MET cc_start: 0.8273 (mmm) cc_final: 0.7796 (mmm) outliers start: 30 outliers final: 26 residues processed: 108 average time/residue: 0.2451 time to fit residues: 35.7899 Evaluate side-chains 107 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 4.9990 chunk 92 optimal weight: 0.0970 chunk 95 optimal weight: 40.0000 chunk 55 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 83 optimal weight: 0.0270 chunk 87 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8199 Z= 0.214 Angle : 0.657 9.465 11171 Z= 0.329 Chirality : 0.043 0.158 1262 Planarity : 0.004 0.052 1425 Dihedral : 5.598 56.737 1210 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.16 % Favored : 91.64 % Rotamer: Outliers : 3.03 % Allowed : 20.99 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % 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: -1.71 (0.26), residues: 1030 helix: -1.44 (0.57), residues: 61 sheet: -0.50 (0.28), residues: 363 loop : -1.53 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 161 HIS 0.004 0.001 HIS A 201 PHE 0.022 0.002 PHE E 497 TYR 0.018 0.001 TYR B 32 ARG 0.002 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.9475 (mt-10) cc_final: 0.8723 (mp0) REVERT: E 465 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7798 (tm-30) REVERT: E 468 ILE cc_start: 0.9332 (pt) cc_final: 0.9130 (tp) REVERT: D 4 MET cc_start: 0.7737 (tpp) cc_final: 0.7460 (mmm) REVERT: D 42 LYS cc_start: 0.9277 (mttt) cc_final: 0.9000 (ttmm) REVERT: D 93 ASN cc_start: 0.8733 (m-40) cc_final: 0.8247 (t0) REVERT: D 105 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8043 (pt0) REVERT: D 142 ARG cc_start: 0.8652 (tmt170) cc_final: 0.8063 (ttp80) REVERT: D 187 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8840 (mm-30) REVERT: B 33 TYR cc_start: 0.6108 (m-80) cc_final: 0.5883 (m-80) REVERT: B 34 MET cc_start: 0.8238 (mmm) cc_final: 0.7932 (mmm) REVERT: B 213 LYS cc_start: 0.9294 (mtpt) cc_final: 0.8813 (tptt) REVERT: B 216 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8511 (ttpp) REVERT: C 129 PHE cc_start: 0.8214 (m-10) cc_final: 0.7903 (m-10) REVERT: C 147 CYS cc_start: 0.7716 (p) cc_final: 0.6845 (m) REVERT: A 49 MET cc_start: 0.8280 (mmm) cc_final: 0.7787 (mmm) outliers start: 27 outliers final: 25 residues processed: 112 average time/residue: 0.2432 time to fit residues: 36.1239 Evaluate side-chains 109 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 ASN ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8199 Z= 0.239 Angle : 0.677 9.181 11171 Z= 0.343 Chirality : 0.043 0.169 1262 Planarity : 0.005 0.078 1425 Dihedral : 5.670 57.148 1210 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.04 % Favored : 90.77 % Rotamer: Outliers : 3.14 % Allowed : 21.21 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % 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: -1.71 (0.27), residues: 1030 helix: -1.38 (0.58), residues: 61 sheet: -0.58 (0.27), residues: 380 loop : -1.50 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 161 HIS 0.003 0.001 HIS A 201 PHE 0.023 0.002 PHE E 497 TYR 0.019 0.001 TYR B 32 ARG 0.007 0.001 ARG E 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 406 GLU cc_start: 0.9482 (mt-10) cc_final: 0.8729 (mp0) REVERT: E 465 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7902 (tm-30) REVERT: D 4 MET cc_start: 0.7720 (tpp) cc_final: 0.7464 (mmm) REVERT: D 42 LYS cc_start: 0.9280 (mttt) cc_final: 0.8998 (ttmm) REVERT: D 93 ASN cc_start: 0.8754 (m-40) cc_final: 0.8268 (t0) REVERT: D 105 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7988 (pt0) REVERT: D 142 ARG cc_start: 0.8658 (tmt170) cc_final: 0.8064 (ttp80) REVERT: D 187 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8823 (mm-30) REVERT: B 34 MET cc_start: 0.8288 (mmm) cc_final: 0.8000 (mmm) REVERT: B 213 LYS cc_start: 0.9287 (mtpt) cc_final: 0.8790 (tptt) REVERT: B 216 LYS cc_start: 0.9053 (ttmm) cc_final: 0.8515 (ttpp) REVERT: C 129 PHE cc_start: 0.8224 (m-10) cc_final: 0.7918 (m-10) REVERT: C 147 CYS cc_start: 0.7698 (p) cc_final: 0.6855 (m) REVERT: A 49 MET cc_start: 0.8268 (mmm) cc_final: 0.7789 (mmm) outliers start: 28 outliers final: 25 residues processed: 104 average time/residue: 0.2222 time to fit residues: 31.2193 Evaluate side-chains 106 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 34 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 0.0060 chunk 15 optimal weight: 0.0470 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.4294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.082629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.055111 restraints weight = 56443.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058380 restraints weight = 21149.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060349 restraints weight = 11798.763| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8199 Z= 0.168 Angle : 0.663 9.285 11171 Z= 0.330 Chirality : 0.044 0.186 1262 Planarity : 0.005 0.051 1425 Dihedral : 5.505 58.593 1210 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.90 % Favored : 92.91 % Rotamer: Outliers : 2.58 % Allowed : 21.77 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.55 (0.27), residues: 1030 helix: -1.30 (0.60), residues: 61 sheet: -0.52 (0.28), residues: 362 loop : -1.32 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 161 HIS 0.004 0.001 HIS A 201 PHE 0.017 0.001 PHE E 497 TYR 0.013 0.001 TYR A 34 ARG 0.008 0.001 ARG E 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.68 seconds wall clock time: 37 minutes 22.82 seconds (2242.82 seconds total)