Starting phenix.real_space_refine on Wed Feb 14 07:20:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrb_37771/02_2024/8wrb_37771_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrb_37771/02_2024/8wrb_37771.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrb_37771/02_2024/8wrb_37771_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrb_37771/02_2024/8wrb_37771_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrb_37771/02_2024/8wrb_37771_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrb_37771/02_2024/8wrb_37771.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrb_37771/02_2024/8wrb_37771.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrb_37771/02_2024/8wrb_37771_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrb_37771/02_2024/8wrb_37771_updated.pdb" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.078 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 1 5.49 5 S 65 5.16 5 C 5646 2.51 5 N 1484 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 228": "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: 8842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1747 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2195 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 4, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'CLR': 1, 'UBL': 1} Inner-chain residues flagged as termini: ['pdbres="SER R 602 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.33, per 1000 atoms: 0.60 Number of scatterers: 8842 At special positions: 0 Unit cell: (89.88, 116.63, 125.19, 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 65 16.00 P 1 15.00 O 1646 8.00 N 1484 7.00 C 5646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 204 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.8 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 35.6% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.516A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.502A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.500A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'R' and resid 51 through 80 removed outlier: 3.649A pdb=" N THR R 55 " --> pdb=" O LYS R 51 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 115 removed outlier: 3.526A pdb=" N LEU R 107 " --> pdb=" O LEU R 103 " (cutoff:3.500A) Proline residue: R 108 - end of helix Processing helix chain 'R' and resid 124 through 156 removed outlier: 3.613A pdb=" N TYR R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 196 removed outlier: 4.086A pdb=" N LYS R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 251 removed outlier: 3.788A pdb=" N LYS R 240 " --> pdb=" O LEU R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 294 removed outlier: 3.510A pdb=" N PHE R 269 " --> pdb=" O ALA R 265 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 4.051A pdb=" N PHE R 287 " --> pdb=" O HIS R 283 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 330 removed outlier: 4.041A pdb=" N ASN R 319 " --> pdb=" O LEU R 315 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N CYS R 321 " --> pdb=" O SER R 317 " (cutoff:3.500A) Proline residue: R 324 - end of helix removed outlier: 3.568A pdb=" N TYR R 327 " --> pdb=" O ASP R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.542A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.791A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.930A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.698A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.859A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.562A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.508A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.566A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.960A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.581A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.131A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1212 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: 2.56 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1421 1.31 - 1.44: 2500 1.44 - 1.56: 5005 1.56 - 1.69: 1 1.69 - 1.82: 95 Bond restraints: 9022 Sorted by residual: bond pdb=" CAM UBL R 603 " pdb=" CAN UBL R 603 " ideal model delta sigma weight residual 1.599 1.555 0.044 2.00e-02 2.50e+03 4.79e+00 bond pdb=" CBA UBL R 603 " pdb=" CBB UBL R 603 " ideal model delta sigma weight residual 1.583 1.549 0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" CAG UBL R 603 " pdb=" CAH UBL R 603 " ideal model delta sigma weight residual 1.521 1.554 -0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" CAN UBL R 603 " pdb=" CAO UBL R 603 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C SER R 602 " pdb=" OXT SER R 602 " ideal model delta sigma weight residual 1.231 1.264 -0.033 2.00e-02 2.50e+03 2.70e+00 ... (remaining 9017 not shown) Histogram of bond angle deviations from ideal: 99.85 - 110.19: 1592 110.19 - 120.53: 7149 120.53 - 130.86: 3439 130.86 - 141.20: 42 141.20 - 151.54: 1 Bond angle restraints: 12223 Sorted by residual: angle pdb=" CAR UBL R 603 " pdb=" CAS UBL R 603 " pdb=" CAT UBL R 603 " ideal model delta sigma weight residual 119.99 151.54 -31.55 3.00e+00 1.11e-01 1.11e+02 angle pdb=" CAS UBL R 603 " pdb=" CAT UBL R 603 " pdb=" CAU UBL R 603 " ideal model delta sigma weight residual 120.00 111.16 8.84 3.00e+00 1.11e-01 8.69e+00 angle pdb=" C13 CLR R 601 " pdb=" C17 CLR R 601 " pdb=" C20 CLR R 601 " ideal model delta sigma weight residual 119.60 112.88 6.72 3.00e+00 1.11e-01 5.02e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.32 -3.78 1.91e+00 2.74e-01 3.92e+00 angle pdb=" C23 CLR R 601 " pdb=" C24 CLR R 601 " pdb=" C25 CLR R 601 " ideal model delta sigma weight residual 115.14 109.67 5.47 3.00e+00 1.11e-01 3.32e+00 ... (remaining 12218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.18: 5299 26.18 - 52.35: 68 52.35 - 78.53: 10 78.53 - 104.70: 1 104.70 - 130.88: 1 Dihedral angle restraints: 5379 sinusoidal: 2087 harmonic: 3292 Sorted by residual: dihedral pdb=" CAI UBL R 603 " pdb=" CAG UBL R 603 " pdb=" CAH UBL R 603 " pdb=" OAF UBL R 603 " ideal model delta sinusoidal sigma weight residual 137.75 -91.37 -130.88 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1327 0.089 - 0.178: 73 0.178 - 0.266: 0 0.266 - 0.355: 2 0.355 - 0.444: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" C10 CLR R 601 " pdb=" C1 CLR R 601 " pdb=" C5 CLR R 601 " pdb=" C9 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.51 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C17 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C16 CLR R 601 " pdb=" C20 CLR R 601 " both_signs ideal model delta sigma weight residual False 2.55 2.82 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1400 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO B 236 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 323 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO R 324 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO R 324 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 324 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 255 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO R 256 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO R 256 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 256 " -0.018 5.00e-02 4.00e+02 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1075 2.75 - 3.29: 8496 3.29 - 3.83: 14804 3.83 - 4.36: 18285 4.36 - 4.90: 31686 Nonbonded interactions: 74346 Sorted by model distance: nonbonded pdb=" OD1 ASP A 341 " pdb=" OH TYR R 261 " model vdw 2.218 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.220 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.269 2.440 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.287 2.520 nonbonded pdb=" OH TYR A 230 " pdb=" O SER A 281 " model vdw 2.296 2.440 ... (remaining 74341 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 2.050 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.610 Find NCS groups from input model: 0.260 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:13.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.002 0.044 9022 Z= 0.131 Angle : 0.490 31.547 12223 Z= 0.221 Chirality : 0.042 0.444 1403 Planarity : 0.003 0.039 1532 Dihedral : 9.420 130.876 3248 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.06 % Allowed : 1.90 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.02 (0.24), residues: 1118 helix: 1.36 (0.25), residues: 411 sheet: 0.72 (0.29), residues: 293 loop : 0.09 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.007 0.001 PHE A 189 TYR 0.009 0.001 TYR E 190 ARG 0.002 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 188 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8030 (tp30) cc_final: 0.6952 (tt0) REVERT: A 208 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7181 (ttp80) REVERT: A 251 ASP cc_start: 0.8388 (t70) cc_final: 0.8004 (t0) REVERT: A 275 GLU cc_start: 0.8175 (tt0) cc_final: 0.7890 (mt-10) REVERT: A 308 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7777 (mt-10) REVERT: A 330 LYS cc_start: 0.7731 (mttt) cc_final: 0.7440 (mttm) REVERT: A 354 PHE cc_start: 0.8219 (t80) cc_final: 0.7423 (t80) REVERT: B 23 LYS cc_start: 0.8342 (ttmm) cc_final: 0.7828 (tptm) REVERT: B 42 ARG cc_start: 0.7909 (ttt90) cc_final: 0.7677 (ttm-80) REVERT: B 46 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7572 (mtp-110) REVERT: B 219 ARG cc_start: 0.7561 (mtp85) cc_final: 0.7268 (mmm160) REVERT: B 226 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 259 GLN cc_start: 0.8534 (pt0) cc_final: 0.8101 (pt0) REVERT: E 83 MET cc_start: 0.8868 (mtm) cc_final: 0.8572 (mtp) REVERT: E 160 ARG cc_start: 0.7265 (mtp-110) cc_final: 0.6687 (mtp85) REVERT: E 213 THR cc_start: 0.7949 (m) cc_final: 0.7605 (p) REVERT: E 218 ARG cc_start: 0.7236 (mpp-170) cc_final: 0.6913 (mtt90) REVERT: R 64 ILE cc_start: 0.7775 (mt) cc_final: 0.7550 (mp) REVERT: R 180 MET cc_start: 0.7656 (mmm) cc_final: 0.7098 (mpt) REVERT: R 288 ILE cc_start: 0.8408 (mt) cc_final: 0.8199 (mp) REVERT: R 326 MET cc_start: 0.7663 (ttp) cc_final: 0.7346 (ttm) outliers start: 10 outliers final: 9 residues processed: 197 average time/residue: 1.0493 time to fit residues: 222.2370 Evaluate side-chains 145 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 602 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 322 HIS B 220 GLN B 259 GLN E 113 GLN E 183 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 199 HIS R 293 GLN R 295 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 9022 Z= 0.393 Angle : 0.566 5.525 12223 Z= 0.307 Chirality : 0.045 0.156 1403 Planarity : 0.005 0.042 1532 Dihedral : 7.183 101.066 1323 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.38 % Allowed : 9.82 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.52 (0.25), residues: 1118 helix: 2.31 (0.25), residues: 408 sheet: 0.83 (0.30), residues: 298 loop : -0.14 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.024 0.002 PHE B 151 TYR 0.025 0.002 TYR R 92 ARG 0.008 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 207 GLU cc_start: 0.8053 (tp30) cc_final: 0.7009 (tt0) REVERT: A 208 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7418 (ttp80) REVERT: A 277 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7368 (mtpt) REVERT: A 330 LYS cc_start: 0.7677 (mttt) cc_final: 0.7352 (mttm) REVERT: B 23 LYS cc_start: 0.8313 (ttmm) cc_final: 0.7839 (tptm) REVERT: B 46 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7278 (mtp-110) REVERT: B 170 ASP cc_start: 0.7756 (t70) cc_final: 0.7309 (t70) REVERT: B 198 LEU cc_start: 0.8586 (mt) cc_final: 0.8353 (mt) REVERT: B 219 ARG cc_start: 0.7621 (mtp85) cc_final: 0.7208 (mmm160) REVERT: B 226 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8151 (mt-10) REVERT: B 234 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: C 47 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7572 (mt-10) REVERT: E 160 ARG cc_start: 0.7337 (mtp-110) cc_final: 0.6741 (mtp85) REVERT: E 218 ARG cc_start: 0.7281 (mpp-170) cc_final: 0.6915 (mtt90) REVERT: E 234 GLU cc_start: 0.8707 (pt0) cc_final: 0.8496 (pt0) REVERT: R 63 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8064 (p) REVERT: R 326 MET cc_start: 0.7533 (ttp) cc_final: 0.7278 (ttm) outliers start: 32 outliers final: 18 residues processed: 169 average time/residue: 1.2309 time to fit residues: 222.3882 Evaluate side-chains 146 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 602 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 88 ASN B 259 GLN E 113 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 199 HIS R 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9022 Z= 0.159 Angle : 0.442 7.153 12223 Z= 0.240 Chirality : 0.040 0.142 1403 Planarity : 0.003 0.041 1532 Dihedral : 6.493 81.609 1321 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.70 % Allowed : 11.62 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.81 (0.25), residues: 1118 helix: 2.89 (0.24), residues: 403 sheet: 0.74 (0.29), residues: 292 loop : -0.11 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE B 199 TYR 0.014 0.001 TYR R 92 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8307 (mt-10) REVERT: A 207 GLU cc_start: 0.7977 (tp30) cc_final: 0.6972 (tt0) REVERT: A 208 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7448 (ttp80) REVERT: A 247 MET cc_start: 0.7786 (mtt) cc_final: 0.7423 (mtp) REVERT: A 277 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7337 (mtpt) REVERT: A 330 LYS cc_start: 0.7658 (mttt) cc_final: 0.7332 (mttm) REVERT: A 349 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7773 (mtpp) REVERT: A 354 PHE cc_start: 0.8408 (t80) cc_final: 0.7639 (t80) REVERT: B 19 ARG cc_start: 0.7678 (mtp-110) cc_final: 0.7382 (mtp-110) REVERT: B 23 LYS cc_start: 0.8310 (ttmm) cc_final: 0.7846 (tptm) REVERT: B 46 ARG cc_start: 0.7616 (mtp-110) cc_final: 0.7209 (mtp-110) REVERT: B 138 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: B 170 ASP cc_start: 0.7614 (t70) cc_final: 0.7396 (t70) REVERT: B 198 LEU cc_start: 0.8592 (mt) cc_final: 0.8279 (mt) REVERT: B 219 ARG cc_start: 0.7596 (mtp85) cc_final: 0.7246 (mmm160) REVERT: B 226 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8205 (mt-10) REVERT: B 234 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8292 (m-80) REVERT: B 259 GLN cc_start: 0.8646 (pt0) cc_final: 0.8275 (pt0) REVERT: E 93 MET cc_start: 0.8308 (ttp) cc_final: 0.8081 (ttt) REVERT: E 160 ARG cc_start: 0.7310 (mtp-110) cc_final: 0.6731 (mtp85) REVERT: E 213 THR cc_start: 0.8229 (m) cc_final: 0.7853 (p) REVERT: E 218 ARG cc_start: 0.7288 (mpp-170) cc_final: 0.6894 (mtt90) REVERT: E 234 GLU cc_start: 0.8737 (pt0) cc_final: 0.8504 (pt0) REVERT: R 63 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8066 (p) REVERT: R 64 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7308 (mp) REVERT: R 149 SER cc_start: 0.8439 (m) cc_final: 0.8163 (p) REVERT: R 323 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7050 (m-30) REVERT: R 326 MET cc_start: 0.7531 (ttp) cc_final: 0.7249 (ttm) outliers start: 35 outliers final: 16 residues processed: 161 average time/residue: 1.2307 time to fit residues: 211.3695 Evaluate side-chains 158 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 320 SER Chi-restraints excluded: chain R residue 323 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 88 ASN B 259 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9022 Z= 0.342 Angle : 0.518 7.887 12223 Z= 0.278 Chirality : 0.044 0.140 1403 Planarity : 0.004 0.043 1532 Dihedral : 6.514 70.395 1320 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.12 % Allowed : 12.04 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.61 (0.25), residues: 1118 helix: 2.72 (0.24), residues: 403 sheet: 0.65 (0.29), residues: 293 loop : -0.22 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.021 0.002 PHE B 151 TYR 0.019 0.002 TYR R 92 ARG 0.003 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6502 (mpt) cc_final: 0.5990 (mmt) REVERT: A 186 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8290 (mt-10) REVERT: A 207 GLU cc_start: 0.8002 (tp30) cc_final: 0.6985 (tt0) REVERT: A 208 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7413 (ttp80) REVERT: A 247 MET cc_start: 0.7886 (mtt) cc_final: 0.7476 (mtm) REVERT: A 277 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7361 (mtpt) REVERT: A 308 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 330 LYS cc_start: 0.7648 (mttt) cc_final: 0.7346 (mttm) REVERT: B 19 ARG cc_start: 0.7715 (mtp-110) cc_final: 0.7433 (mtp-110) REVERT: B 23 LYS cc_start: 0.8429 (ttmm) cc_final: 0.7892 (tptm) REVERT: B 42 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6096 (ttm-80) REVERT: B 46 ARG cc_start: 0.7679 (mtp-110) cc_final: 0.7341 (mtp-110) REVERT: B 138 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: B 170 ASP cc_start: 0.7747 (t70) cc_final: 0.7487 (t70) REVERT: B 198 LEU cc_start: 0.8591 (mt) cc_final: 0.8358 (mt) REVERT: B 219 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7331 (mmm160) REVERT: B 226 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8187 (mt-10) REVERT: B 234 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: B 259 GLN cc_start: 0.8611 (pt0) cc_final: 0.8243 (pt0) REVERT: E 93 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8250 (ttt) REVERT: E 160 ARG cc_start: 0.7345 (mtp-110) cc_final: 0.6697 (mtp85) REVERT: E 218 ARG cc_start: 0.7198 (mpp-170) cc_final: 0.6802 (mtt90) REVERT: R 63 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8013 (p) REVERT: R 64 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7332 (mp) REVERT: R 149 SER cc_start: 0.8409 (m) cc_final: 0.8129 (p) REVERT: R 180 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6072 (mpp) REVERT: R 326 MET cc_start: 0.7489 (ttp) cc_final: 0.7206 (ttm) outliers start: 39 outliers final: 21 residues processed: 157 average time/residue: 1.3416 time to fit residues: 224.8274 Evaluate side-chains 163 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 259 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9022 Z= 0.170 Angle : 0.441 8.536 12223 Z= 0.237 Chirality : 0.041 0.139 1403 Planarity : 0.003 0.043 1532 Dihedral : 6.066 59.657 1320 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.59 % Allowed : 13.31 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.76 (0.25), residues: 1118 helix: 2.96 (0.24), residues: 404 sheet: 0.59 (0.29), residues: 292 loop : -0.16 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE B 199 TYR 0.013 0.001 TYR R 92 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6496 (mpt) cc_final: 0.5984 (mmt) REVERT: A 186 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8238 (mt-10) REVERT: A 207 GLU cc_start: 0.7976 (tp30) cc_final: 0.6993 (tt0) REVERT: A 208 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7400 (ttp80) REVERT: A 247 MET cc_start: 0.7857 (mtt) cc_final: 0.7468 (mtm) REVERT: A 330 LYS cc_start: 0.7664 (mttt) cc_final: 0.7390 (mttm) REVERT: B 19 ARG cc_start: 0.7717 (mtp-110) cc_final: 0.7448 (mtp-110) REVERT: B 23 LYS cc_start: 0.8418 (ttmm) cc_final: 0.7869 (tptm) REVERT: B 42 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.5803 (ttm-80) REVERT: B 46 ARG cc_start: 0.7658 (mtp-110) cc_final: 0.7265 (mtp-110) REVERT: B 219 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7337 (mmm160) REVERT: B 226 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8175 (mt-10) REVERT: B 234 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: B 259 GLN cc_start: 0.8642 (pt0) cc_final: 0.8289 (pt0) REVERT: B 322 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.8048 (m-30) REVERT: E 93 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8172 (ttt) REVERT: E 160 ARG cc_start: 0.7319 (mtp-110) cc_final: 0.6757 (mtp85) REVERT: R 63 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8080 (p) REVERT: R 149 SER cc_start: 0.8435 (m) cc_final: 0.8182 (p) REVERT: R 180 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.5940 (mpp) REVERT: R 326 MET cc_start: 0.7466 (ttp) cc_final: 0.7189 (ttm) outliers start: 34 outliers final: 20 residues processed: 159 average time/residue: 1.1880 time to fit residues: 202.2670 Evaluate side-chains 156 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 248 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 257 ASN Chi-restraints excluded: chain R residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 259 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 199 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9022 Z= 0.152 Angle : 0.433 8.527 12223 Z= 0.231 Chirality : 0.040 0.138 1403 Planarity : 0.003 0.042 1532 Dihedral : 5.661 57.346 1320 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.70 % Allowed : 13.83 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.88 (0.25), residues: 1118 helix: 3.11 (0.24), residues: 404 sheet: 0.61 (0.29), residues: 290 loop : -0.12 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE B 151 TYR 0.013 0.001 TYR R 92 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6301 (mpt) cc_final: 0.5822 (mmt) REVERT: A 186 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8259 (mt-10) REVERT: A 207 GLU cc_start: 0.7928 (tp30) cc_final: 0.7010 (tt0) REVERT: A 208 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7366 (ttp80) REVERT: A 247 MET cc_start: 0.7902 (mtt) cc_final: 0.7590 (mtm) REVERT: A 308 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7609 (mt-10) REVERT: A 318 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7885 (mt-10) REVERT: A 330 LYS cc_start: 0.7665 (mttt) cc_final: 0.7393 (mttm) REVERT: A 349 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8079 (mtpp) REVERT: B 23 LYS cc_start: 0.8434 (ttmm) cc_final: 0.7889 (tptm) REVERT: B 42 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6750 (tpp-160) REVERT: B 46 ARG cc_start: 0.7613 (mtp-110) cc_final: 0.7212 (mtp-110) REVERT: B 219 ARG cc_start: 0.7696 (mtp85) cc_final: 0.7296 (mmm160) REVERT: B 226 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8095 (mt-10) REVERT: B 234 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: B 259 GLN cc_start: 0.8513 (pt0) cc_final: 0.8177 (pt0) REVERT: E 93 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8156 (ttt) REVERT: E 160 ARG cc_start: 0.7338 (mtp-110) cc_final: 0.6766 (mtp85) REVERT: E 213 THR cc_start: 0.8127 (m) cc_final: 0.7792 (p) REVERT: R 63 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.8009 (p) REVERT: R 64 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7348 (mp) REVERT: R 149 SER cc_start: 0.8424 (m) cc_final: 0.8176 (p) REVERT: R 191 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7301 (pp) REVERT: R 326 MET cc_start: 0.7455 (ttp) cc_final: 0.7103 (ttm) outliers start: 35 outliers final: 23 residues processed: 156 average time/residue: 1.2336 time to fit residues: 205.0965 Evaluate side-chains 160 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 87 ASN Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 248 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 273 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 259 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9022 Z= 0.180 Angle : 0.451 8.672 12223 Z= 0.239 Chirality : 0.041 0.136 1403 Planarity : 0.003 0.046 1532 Dihedral : 5.570 56.247 1320 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.91 % Allowed : 13.73 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.89 (0.25), residues: 1118 helix: 3.16 (0.24), residues: 404 sheet: 0.57 (0.29), residues: 292 loop : -0.12 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE B 151 TYR 0.013 0.001 TYR R 92 ARG 0.013 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6359 (mpt) cc_final: 0.5905 (mmt) REVERT: A 186 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 207 GLU cc_start: 0.7910 (tp30) cc_final: 0.7006 (tt0) REVERT: A 208 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7363 (ttp80) REVERT: A 247 MET cc_start: 0.7955 (mtt) cc_final: 0.7617 (mtm) REVERT: A 308 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7631 (mt-10) REVERT: A 318 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7916 (mt-10) REVERT: A 330 LYS cc_start: 0.7665 (mttt) cc_final: 0.7393 (mttm) REVERT: A 349 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8098 (mtpp) REVERT: B 23 LYS cc_start: 0.8439 (ttmm) cc_final: 0.7886 (tptm) REVERT: B 42 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6755 (tpp-160) REVERT: B 46 ARG cc_start: 0.7620 (mtp-110) cc_final: 0.7219 (mtp-110) REVERT: B 219 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7272 (mmm160) REVERT: B 226 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8050 (mt-10) REVERT: B 234 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: B 259 GLN cc_start: 0.8655 (pt0) cc_final: 0.8255 (pt0) REVERT: E 93 MET cc_start: 0.8405 (ttp) cc_final: 0.8154 (ttt) REVERT: E 160 ARG cc_start: 0.7321 (mtp-110) cc_final: 0.6738 (mtp85) REVERT: E 213 THR cc_start: 0.8133 (m) cc_final: 0.7787 (p) REVERT: R 63 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8043 (p) REVERT: R 127 CYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7137 (t) REVERT: R 149 SER cc_start: 0.8426 (m) cc_final: 0.8189 (p) REVERT: R 180 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.5767 (mpp) REVERT: R 191 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7294 (pp) outliers start: 37 outliers final: 23 residues processed: 151 average time/residue: 1.2439 time to fit residues: 200.3513 Evaluate side-chains 158 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 87 ASN Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 248 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 257 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 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 88 ASN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9022 Z= 0.186 Angle : 0.453 8.908 12223 Z= 0.240 Chirality : 0.041 0.137 1403 Planarity : 0.003 0.055 1532 Dihedral : 5.539 55.704 1320 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.33 % Allowed : 13.73 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.88 (0.25), residues: 1118 helix: 3.16 (0.24), residues: 404 sheet: 0.55 (0.29), residues: 292 loop : -0.13 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE B 151 TYR 0.013 0.001 TYR R 92 ARG 0.014 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8285 (mt-10) REVERT: A 207 GLU cc_start: 0.7912 (tp30) cc_final: 0.7012 (tt0) REVERT: A 208 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7362 (ttp80) REVERT: A 247 MET cc_start: 0.7945 (mtt) cc_final: 0.7639 (mtm) REVERT: A 308 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 318 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7931 (mt-10) REVERT: A 330 LYS cc_start: 0.7660 (mttt) cc_final: 0.7390 (mttm) REVERT: A 349 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8101 (mtpp) REVERT: B 23 LYS cc_start: 0.8435 (ttmm) cc_final: 0.7877 (tptm) REVERT: B 42 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6812 (tpp-160) REVERT: B 46 ARG cc_start: 0.7603 (mtp-110) cc_final: 0.7207 (mtp-110) REVERT: B 138 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: B 219 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7227 (mmm160) REVERT: B 226 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8072 (mt-10) REVERT: B 234 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: B 259 GLN cc_start: 0.8631 (pt0) cc_final: 0.8299 (pt0) REVERT: E 93 MET cc_start: 0.8407 (ttp) cc_final: 0.8149 (ttt) REVERT: E 160 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.6748 (mtp85) REVERT: R 63 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8098 (p) REVERT: R 127 CYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7135 (t) REVERT: R 149 SER cc_start: 0.8427 (m) cc_final: 0.8191 (p) REVERT: R 180 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.5939 (mpp) REVERT: R 191 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7186 (pt) outliers start: 41 outliers final: 23 residues processed: 156 average time/residue: 1.3080 time to fit residues: 217.0755 Evaluate side-chains 158 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 87 ASN Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 248 ILE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9022 Z= 0.228 Angle : 0.479 9.101 12223 Z= 0.253 Chirality : 0.041 0.136 1403 Planarity : 0.004 0.060 1532 Dihedral : 5.637 55.256 1320 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.59 % Allowed : 14.36 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.80 (0.25), residues: 1118 helix: 3.06 (0.24), residues: 405 sheet: 0.52 (0.29), residues: 292 loop : -0.16 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.015 0.001 PHE B 151 TYR 0.014 0.001 TYR R 92 ARG 0.015 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8314 (mt-10) REVERT: A 207 GLU cc_start: 0.7881 (tp30) cc_final: 0.7126 (tt0) REVERT: A 208 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7350 (ttp80) REVERT: A 247 MET cc_start: 0.7960 (mtt) cc_final: 0.7607 (mtm) REVERT: A 308 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 330 LYS cc_start: 0.7647 (mttt) cc_final: 0.7373 (mttm) REVERT: A 349 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8172 (mtpp) REVERT: B 23 LYS cc_start: 0.8436 (ttmm) cc_final: 0.7877 (tptm) REVERT: B 42 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6775 (tpp-160) REVERT: B 46 ARG cc_start: 0.7623 (mtp-110) cc_final: 0.7218 (mtp-110) REVERT: B 138 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: B 219 ARG cc_start: 0.7668 (mtp85) cc_final: 0.7205 (mmm160) REVERT: B 226 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8074 (mt-10) REVERT: B 234 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: B 259 GLN cc_start: 0.8607 (pt0) cc_final: 0.8341 (pt0) REVERT: E 93 MET cc_start: 0.8414 (ttp) cc_final: 0.8143 (ttt) REVERT: E 160 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.6755 (mtp85) REVERT: R 63 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8071 (p) REVERT: R 149 SER cc_start: 0.8433 (m) cc_final: 0.8205 (p) REVERT: R 180 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.5946 (mpp) outliers start: 34 outliers final: 25 residues processed: 152 average time/residue: 1.3100 time to fit residues: 212.1026 Evaluate side-chains 159 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 87 ASN Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 248 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 259 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9022 Z= 0.182 Angle : 0.457 9.295 12223 Z= 0.242 Chirality : 0.041 0.137 1403 Planarity : 0.003 0.063 1532 Dihedral : 5.542 55.652 1320 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.27 % Allowed : 14.78 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.86 (0.25), residues: 1118 helix: 3.13 (0.24), residues: 405 sheet: 0.53 (0.29), residues: 292 loop : -0.13 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE B 151 TYR 0.012 0.001 TYR R 92 ARG 0.015 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8282 (mt-10) REVERT: A 207 GLU cc_start: 0.7913 (tp30) cc_final: 0.7013 (tt0) REVERT: A 208 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7350 (ttp80) REVERT: A 247 MET cc_start: 0.8041 (mtt) cc_final: 0.7778 (mtm) REVERT: A 330 LYS cc_start: 0.7649 (mttt) cc_final: 0.7376 (mttm) REVERT: A 349 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8160 (mtpp) REVERT: B 23 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8211 (ttpp) REVERT: B 42 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6790 (tpp-160) REVERT: B 46 ARG cc_start: 0.7600 (mtp-110) cc_final: 0.7204 (mtp-110) REVERT: B 138 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: B 219 ARG cc_start: 0.7670 (mtp85) cc_final: 0.7211 (mmm160) REVERT: B 226 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8083 (mt-10) REVERT: B 234 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: B 259 GLN cc_start: 0.8539 (pt0) cc_final: 0.8335 (pt0) REVERT: E 93 MET cc_start: 0.8410 (ttp) cc_final: 0.8146 (ttt) REVERT: E 160 ARG cc_start: 0.7329 (mtp-110) cc_final: 0.6684 (mtp85) REVERT: R 63 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8042 (p) REVERT: R 127 CYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7129 (t) REVERT: R 149 SER cc_start: 0.8429 (m) cc_final: 0.8192 (p) REVERT: R 180 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.5941 (mpp) outliers start: 31 outliers final: 22 residues processed: 147 average time/residue: 1.2987 time to fit residues: 203.1120 Evaluate side-chains 152 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 87 ASN Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 209 ASP Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 248 ILE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 259 GLN ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101293 restraints weight = 10304.638| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.09 r_work: 0.3018 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9022 Z= 0.204 Angle : 0.469 9.310 12223 Z= 0.248 Chirality : 0.041 0.136 1403 Planarity : 0.004 0.063 1532 Dihedral : 5.551 55.794 1320 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.48 % Allowed : 14.68 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.84 (0.25), residues: 1118 helix: 3.12 (0.24), residues: 405 sheet: 0.53 (0.29), residues: 292 loop : -0.14 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.013 0.001 PHE B 151 TYR 0.013 0.001 TYR R 92 ARG 0.015 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3801.64 seconds wall clock time: 68 minutes 23.47 seconds (4103.47 seconds total)