Starting phenix.real_space_refine on Wed Feb 14 06:54:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/02_2024/8gus_34278_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/02_2024/8gus_34278.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/02_2024/8gus_34278_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/02_2024/8gus_34278_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/02_2024/8gus_34278_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/02_2024/8gus_34278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/02_2024/8gus_34278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/02_2024/8gus_34278_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/02_2024/8gus_34278_neut_updated.pdb" } resolution = 2.97 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5618 2.51 5 N 1495 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" 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: 8805 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1733 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2250 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'KO3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.07, per 1000 atoms: 0.58 Number of scatterers: 8805 At special positions: 0 Unit cell: (89.44, 117.52, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1626 8.00 N 1495 7.00 C 5618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.9 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 12 sheets defined 34.9% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 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 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 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'R' and resid 31 through 61 Processing helix chain 'R' and resid 68 through 94 removed outlier: 3.887A pdb=" N PHE R 72 " --> pdb=" O PRO R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.698A pdb=" N LEU R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 170 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 188 through 226 removed outlier: 3.523A pdb=" N GLY R 210 " --> pdb=" O ILE R 206 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS R 226 " --> pdb=" O SER R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 270 Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 276 through 299 removed outlier: 3.976A pdb=" N SER R 285 " --> pdb=" O ALA R 282 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 304 through 318 Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.580A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.793A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.135A 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: 6.609A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.204A 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: 6.626A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.037A 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: 6.846A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.182A 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: 6.678A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.934A 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: 6.446A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.534A 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 49 removed outlier: 3.633A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.618A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.816A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.506A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 143 through 148 removed outlier: 3.624A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1170 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: 2.73 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1414 1.32 - 1.44: 2484 1.44 - 1.57: 4997 1.57 - 1.69: 2 1.69 - 1.82: 95 Bond restraints: 8992 Sorted by residual: bond pdb=" C18 KO3 R 401 " pdb=" C19 KO3 R 401 " ideal model delta sigma weight residual 1.718 1.324 0.394 2.00e-02 2.50e+03 3.88e+02 bond pdb=" C22 KO3 R 401 " pdb=" C23 KO3 R 401 " ideal model delta sigma weight residual 1.242 1.549 -0.307 2.00e-02 2.50e+03 2.35e+02 bond pdb=" C20 KO3 R 401 " pdb=" C23 KO3 R 401 " ideal model delta sigma weight residual 1.334 1.571 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C17 KO3 R 401 " pdb=" C18 KO3 R 401 " ideal model delta sigma weight residual 1.694 1.508 0.186 2.00e-02 2.50e+03 8.62e+01 bond pdb=" CG PRO R 184 " pdb=" CD PRO R 184 " ideal model delta sigma weight residual 1.503 1.194 0.309 3.40e-02 8.65e+02 8.26e+01 ... (remaining 8987 not shown) Histogram of bond angle deviations from ideal: 84.78 - 94.62: 7 94.62 - 104.47: 104 104.47 - 114.31: 5396 114.31 - 124.16: 6467 124.16 - 134.00: 211 Bond angle restraints: 12185 Sorted by residual: angle pdb=" CA PRO R 184 " pdb=" N PRO R 184 " pdb=" CD PRO R 184 " ideal model delta sigma weight residual 112.00 93.91 18.09 1.40e+00 5.10e-01 1.67e+02 angle pdb=" N PRO R 184 " pdb=" CD PRO R 184 " pdb=" CG PRO R 184 " ideal model delta sigma weight residual 103.20 85.39 17.81 1.50e+00 4.44e-01 1.41e+02 angle pdb=" C13 KO3 R 401 " pdb=" C14 KO3 R 401 " pdb=" O1 KO3 R 401 " ideal model delta sigma weight residual 143.09 114.76 28.33 3.00e+00 1.11e-01 8.92e+01 angle pdb=" C15 KO3 R 401 " pdb=" C14 KO3 R 401 " pdb=" O1 KO3 R 401 " ideal model delta sigma weight residual 96.61 124.65 -28.04 3.00e+00 1.11e-01 8.74e+01 angle pdb=" C20 KO3 R 401 " pdb=" C23 KO3 R 401 " pdb=" C22 KO3 R 401 " ideal model delta sigma weight residual 109.69 84.78 24.91 3.00e+00 1.11e-01 6.90e+01 ... (remaining 12180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.72: 4943 23.72 - 47.45: 355 47.45 - 71.17: 31 71.17 - 94.89: 1 94.89 - 118.61: 2 Dihedral angle restraints: 5332 sinusoidal: 2048 harmonic: 3284 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 180.00 141.50 38.50 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CB CYS R 174 " pdb=" SG CYS R 174 " pdb=" SG CYS R 179 " pdb=" CB CYS R 179 " ideal model delta sinusoidal sigma weight residual -86.00 -150.83 64.83 1 1.00e+01 1.00e-02 5.52e+01 dihedral pdb=" C18 KO3 R 401 " pdb=" C19 KO3 R 401 " pdb=" C26 KO3 R 401 " pdb=" O2 KO3 R 401 " ideal model delta sinusoidal sigma weight residual -88.71 29.90 -118.61 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 5329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.053: 1390 1.053 - 2.105: 0 2.105 - 3.158: 0 3.158 - 4.210: 0 4.210 - 5.263: 1 Chirality restraints: 1391 Sorted by residual: chirality pdb=" C17 KO3 R 401 " pdb=" C13 KO3 R 401 " pdb=" C18 KO3 R 401 " pdb=" C22 KO3 R 401 " both_signs ideal model delta sigma weight residual False 2.82 -2.45 5.26 2.00e-01 2.50e+01 6.92e+02 chirality pdb=" C20 KO3 R 401 " pdb=" C19 KO3 R 401 " pdb=" C21 KO3 R 401 " pdb=" C23 KO3 R 401 " both_signs ideal model delta sigma weight residual False -2.74 -3.28 0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" C22 KO3 R 401 " pdb=" C17 KO3 R 401 " pdb=" C21 KO3 R 401 " pdb=" C23 KO3 R 401 " both_signs ideal model delta sigma weight residual False 2.66 3.17 -0.51 2.00e-01 2.50e+01 6.43e+00 ... (remaining 1388 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 183 " 0.112 5.00e-02 4.00e+02 1.51e-01 3.65e+01 pdb=" N PRO R 184 " -0.260 5.00e-02 4.00e+02 pdb=" CA PRO R 184 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO R 184 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 194 " 0.035 2.00e-02 2.50e+03 3.22e-02 2.59e+01 pdb=" CG TRP R 194 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP R 194 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP R 194 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 194 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP R 194 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP R 194 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 194 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 194 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP R 194 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.077 5.00e-02 4.00e+02 1.11e-01 1.99e+01 pdb=" N PRO R 168 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.062 5.00e-02 4.00e+02 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1150 2.75 - 3.28: 8870 3.28 - 3.82: 15266 3.82 - 4.36: 18182 4.36 - 4.90: 31319 Nonbonded interactions: 74787 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.207 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.225 2.440 nonbonded pdb=" OG SER A 6 " pdb=" OD2 ASP A 9 " model vdw 2.236 2.440 nonbonded pdb=" OG SER B 161 " pdb=" O THR B 165 " model vdw 2.266 2.440 nonbonded pdb=" O LYS B 280 " pdb=" OG SER B 281 " model vdw 2.310 2.440 ... (remaining 74782 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: 0.780 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: 3.810 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 28.510 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 0.009 0.394 8992 Z= 0.627 Angle : 0.878 28.335 12185 Z= 0.417 Chirality : 0.149 5.263 1391 Planarity : 0.007 0.151 1525 Dihedral : 14.941 118.614 3202 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 23.21 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1117 helix: 1.67 (0.26), residues: 412 sheet: 0.03 (0.32), residues: 290 loop : -0.87 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.003 TRP R 194 HIS 0.004 0.001 HIS S 220 PHE 0.041 0.002 PHE R 281 TYR 0.013 0.001 TYR S 50 ARG 0.009 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 277 LYS cc_start: 0.7554 (ttmm) cc_final: 0.7061 (tppp) REVERT: B 197 ARG cc_start: 0.7340 (ttm110) cc_final: 0.6980 (ttm110) REVERT: B 277 SER cc_start: 0.8413 (t) cc_final: 0.8005 (p) REVERT: B 304 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.8034 (ttp-110) REVERT: S 59 TYR cc_start: 0.8077 (m-10) cc_final: 0.7854 (m-10) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 1.1014 time to fit residues: 250.0003 Evaluate side-chains 215 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 62 HIS B 110 ASN B 220 GLN B 340 ASN R 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8992 Z= 0.288 Angle : 0.642 13.425 12185 Z= 0.307 Chirality : 0.045 0.608 1391 Planarity : 0.005 0.068 1525 Dihedral : 6.223 83.615 1236 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.80 % Allowed : 20.46 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1117 helix: 1.59 (0.25), residues: 412 sheet: -0.01 (0.31), residues: 289 loop : -0.87 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 194 HIS 0.005 0.001 HIS B 62 PHE 0.016 0.001 PHE R 183 TYR 0.015 0.001 TYR S 50 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 212 time to evaluate : 1.027 Fit side-chains REVERT: A 32 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.7113 (mtm-85) REVERT: A 251 ASP cc_start: 0.7787 (m-30) cc_final: 0.7526 (m-30) REVERT: A 277 LYS cc_start: 0.7646 (ttmm) cc_final: 0.7189 (tppp) REVERT: B 170 ASP cc_start: 0.7900 (t70) cc_final: 0.7395 (t0) REVERT: B 197 ARG cc_start: 0.7375 (ttm110) cc_final: 0.6948 (ttm110) REVERT: S 60 TYR cc_start: 0.8676 (m-80) cc_final: 0.8090 (m-80) REVERT: S 183 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8511 (mt) REVERT: S 223 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.8024 (t80) outliers start: 36 outliers final: 15 residues processed: 226 average time/residue: 1.0490 time to fit residues: 254.7690 Evaluate side-chains 210 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 89 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 62 HIS B 176 GLN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8992 Z= 0.215 Angle : 0.592 13.004 12185 Z= 0.283 Chirality : 0.044 0.649 1391 Planarity : 0.004 0.049 1525 Dihedral : 6.218 69.768 1236 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.22 % Allowed : 21.52 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1117 helix: 1.64 (0.26), residues: 412 sheet: 0.01 (0.30), residues: 291 loop : -0.83 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.018 0.001 PHE R 183 TYR 0.014 0.001 TYR S 50 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 208 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.7137 (mtm-85) REVERT: A 251 ASP cc_start: 0.7753 (m-30) cc_final: 0.7485 (m-30) REVERT: A 270 LYS cc_start: 0.8261 (mttp) cc_final: 0.8033 (mttp) REVERT: A 277 LYS cc_start: 0.7704 (ttmm) cc_final: 0.7180 (tppp) REVERT: B 170 ASP cc_start: 0.7893 (t70) cc_final: 0.7389 (t0) REVERT: B 197 ARG cc_start: 0.7352 (ttm110) cc_final: 0.6963 (ttm110) REVERT: B 336 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8486 (tp) REVERT: R 115 MET cc_start: 0.7388 (tmm) cc_final: 0.7143 (tmm) REVERT: S 60 TYR cc_start: 0.8684 (m-80) cc_final: 0.8111 (m-80) REVERT: S 223 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.8029 (t80) outliers start: 40 outliers final: 20 residues processed: 224 average time/residue: 1.0295 time to fit residues: 248.4743 Evaluate side-chains 219 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 197 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 237 MET Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 110 ASN B 176 GLN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8992 Z= 0.246 Angle : 0.605 13.026 12185 Z= 0.287 Chirality : 0.044 0.663 1391 Planarity : 0.004 0.050 1525 Dihedral : 5.933 70.665 1236 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.43 % Allowed : 22.57 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1117 helix: 1.60 (0.26), residues: 414 sheet: 0.06 (0.30), residues: 293 loop : -0.76 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.031 0.001 PHE R 94 TYR 0.016 0.001 TYR S 50 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7745 (m-30) cc_final: 0.7462 (m-30) REVERT: A 270 LYS cc_start: 0.8271 (mttp) cc_final: 0.7954 (mttp) REVERT: A 276 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6866 (pp20) REVERT: A 277 LYS cc_start: 0.7725 (ttmm) cc_final: 0.7116 (tppp) REVERT: A 317 LYS cc_start: 0.8185 (ptmt) cc_final: 0.7967 (ptpt) REVERT: B 170 ASP cc_start: 0.7868 (t70) cc_final: 0.7360 (t0) REVERT: B 197 ARG cc_start: 0.7504 (ttm110) cc_final: 0.7072 (ttm110) REVERT: B 289 TYR cc_start: 0.8482 (m-80) cc_final: 0.8196 (m-80) REVERT: R 115 MET cc_start: 0.7416 (tmm) cc_final: 0.7011 (tmm) REVERT: S 223 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.7983 (t80) outliers start: 42 outliers final: 26 residues processed: 227 average time/residue: 1.0089 time to fit residues: 246.6330 Evaluate side-chains 229 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 35 ASN B 62 HIS B 176 GLN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8992 Z= 0.229 Angle : 0.606 12.681 12185 Z= 0.285 Chirality : 0.044 0.654 1391 Planarity : 0.003 0.051 1525 Dihedral : 5.871 74.803 1236 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.64 % Allowed : 22.26 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1117 helix: 1.63 (0.26), residues: 414 sheet: 0.08 (0.30), residues: 291 loop : -0.74 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.035 0.001 PHE R 94 TYR 0.016 0.001 TYR S 50 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 203 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7716 (m-30) cc_final: 0.7428 (m-30) REVERT: A 270 LYS cc_start: 0.8256 (mttp) cc_final: 0.7902 (mttp) REVERT: A 276 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6939 (pp20) REVERT: A 277 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7249 (tppp) REVERT: A 317 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7903 (ptpt) REVERT: B 86 THR cc_start: 0.8547 (p) cc_final: 0.8344 (p) REVERT: B 134 ARG cc_start: 0.7567 (ptt90) cc_final: 0.7366 (ptt90) REVERT: B 170 ASP cc_start: 0.7864 (t70) cc_final: 0.7365 (t0) REVERT: R 115 MET cc_start: 0.7448 (tmm) cc_final: 0.6922 (tmm) REVERT: S 166 LEU cc_start: 0.8789 (tt) cc_final: 0.8581 (tp) REVERT: S 223 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7911 (t80) outliers start: 44 outliers final: 27 residues processed: 227 average time/residue: 0.9753 time to fit residues: 239.2931 Evaluate side-chains 234 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 205 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 110 ASN B 176 GLN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8992 Z= 0.250 Angle : 0.609 12.672 12185 Z= 0.289 Chirality : 0.044 0.647 1391 Planarity : 0.004 0.051 1525 Dihedral : 5.877 77.961 1236 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.64 % Allowed : 22.68 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1117 helix: 1.59 (0.26), residues: 413 sheet: 0.08 (0.31), residues: 286 loop : -0.74 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.037 0.001 PHE R 94 TYR 0.018 0.001 TYR S 50 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 205 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7743 (m-30) cc_final: 0.7483 (m-30) REVERT: A 270 LYS cc_start: 0.8230 (mttp) cc_final: 0.7874 (mttp) REVERT: A 276 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6903 (pp20) REVERT: A 277 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7254 (tppp) REVERT: B 133 VAL cc_start: 0.7930 (t) cc_final: 0.7524 (p) REVERT: B 170 ASP cc_start: 0.8029 (t70) cc_final: 0.7458 (t0) REVERT: B 172 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7347 (mm-30) REVERT: B 289 TYR cc_start: 0.8469 (m-80) cc_final: 0.8220 (m-80) REVERT: B 290 ASP cc_start: 0.7050 (m-30) cc_final: 0.6737 (m-30) REVERT: R 115 MET cc_start: 0.7461 (tmm) cc_final: 0.6990 (tmm) REVERT: R 253 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8579 (t) REVERT: S 223 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7851 (t80) outliers start: 44 outliers final: 29 residues processed: 226 average time/residue: 1.0479 time to fit residues: 254.7796 Evaluate side-chains 237 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.0470 chunk 32 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 176 GLN B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8992 Z= 0.219 Angle : 0.601 12.472 12185 Z= 0.284 Chirality : 0.044 0.647 1391 Planarity : 0.003 0.051 1525 Dihedral : 5.856 79.275 1236 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.64 % Allowed : 23.63 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1117 helix: 1.65 (0.26), residues: 412 sheet: 0.07 (0.30), residues: 286 loop : -0.76 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.038 0.001 PHE R 94 TYR 0.019 0.001 TYR S 50 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 205 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7740 (m-30) cc_final: 0.7482 (m-30) REVERT: A 270 LYS cc_start: 0.8296 (mttp) cc_final: 0.7976 (mttp) REVERT: A 276 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6870 (pp20) REVERT: A 277 LYS cc_start: 0.7804 (ttmm) cc_final: 0.7235 (tppp) REVERT: B 7 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7355 (mp) REVERT: B 133 VAL cc_start: 0.7920 (t) cc_final: 0.7508 (p) REVERT: B 170 ASP cc_start: 0.8005 (t70) cc_final: 0.7465 (t0) REVERT: B 172 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7297 (mm-30) REVERT: B 290 ASP cc_start: 0.7048 (m-30) cc_final: 0.6729 (m-30) REVERT: C 50 LEU cc_start: 0.8958 (mm) cc_final: 0.8582 (mt) REVERT: R 253 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8570 (t) REVERT: S 223 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.7784 (t80) outliers start: 44 outliers final: 31 residues processed: 224 average time/residue: 1.0570 time to fit residues: 254.6325 Evaluate side-chains 239 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 204 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 237 MET Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.0670 chunk 99 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 110 ASN B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8992 Z= 0.215 Angle : 0.603 12.329 12185 Z= 0.285 Chirality : 0.043 0.643 1391 Planarity : 0.003 0.052 1525 Dihedral : 5.863 80.342 1236 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.64 % Allowed : 23.95 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1117 helix: 1.69 (0.26), residues: 411 sheet: -0.00 (0.30), residues: 293 loop : -0.76 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.040 0.001 PHE R 94 TYR 0.020 0.001 TYR S 50 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 208 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7741 (m-30) cc_final: 0.7447 (m-30) REVERT: A 270 LYS cc_start: 0.8306 (mttp) cc_final: 0.7958 (mttp) REVERT: A 276 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6878 (pp20) REVERT: A 277 LYS cc_start: 0.7766 (ttmm) cc_final: 0.7154 (tppp) REVERT: A 310 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8199 (mt) REVERT: B 7 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7353 (mp) REVERT: B 133 VAL cc_start: 0.7931 (t) cc_final: 0.7506 (p) REVERT: B 170 ASP cc_start: 0.7944 (t70) cc_final: 0.7410 (t0) REVERT: B 172 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7293 (mm-30) REVERT: B 289 TYR cc_start: 0.8459 (m-80) cc_final: 0.8225 (m-80) REVERT: B 290 ASP cc_start: 0.7046 (m-30) cc_final: 0.6711 (m-30) REVERT: C 50 LEU cc_start: 0.8946 (mm) cc_final: 0.8633 (mt) REVERT: R 115 MET cc_start: 0.7967 (tmm) cc_final: 0.7118 (tmm) REVERT: R 253 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8563 (t) REVERT: S 223 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7801 (t80) outliers start: 44 outliers final: 25 residues processed: 227 average time/residue: 1.0699 time to fit residues: 262.1015 Evaluate side-chains 237 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 207 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 62 HIS B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8992 Z= 0.274 Angle : 0.628 12.625 12185 Z= 0.299 Chirality : 0.045 0.643 1391 Planarity : 0.004 0.052 1525 Dihedral : 5.969 82.144 1236 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.48 % Allowed : 25.84 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1117 helix: 1.58 (0.26), residues: 412 sheet: 0.01 (0.30), residues: 286 loop : -0.78 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.040 0.002 PHE R 94 TYR 0.020 0.001 TYR S 50 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 207 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7769 (m-30) cc_final: 0.7498 (m-30) REVERT: A 270 LYS cc_start: 0.8323 (mttp) cc_final: 0.7901 (mttp) REVERT: A 273 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7723 (mt) REVERT: A 276 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6887 (pp20) REVERT: A 277 LYS cc_start: 0.7736 (ttmm) cc_final: 0.7144 (tppp) REVERT: A 310 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8225 (mt) REVERT: B 7 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7348 (mp) REVERT: B 133 VAL cc_start: 0.7983 (t) cc_final: 0.7575 (p) REVERT: B 170 ASP cc_start: 0.7967 (t70) cc_final: 0.7446 (t0) REVERT: B 289 TYR cc_start: 0.8494 (m-80) cc_final: 0.8258 (m-80) REVERT: B 290 ASP cc_start: 0.7100 (m-30) cc_final: 0.6746 (m-30) REVERT: R 115 MET cc_start: 0.7950 (tmm) cc_final: 0.7010 (tmm) REVERT: R 253 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8628 (t) REVERT: S 223 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7850 (t80) outliers start: 33 outliers final: 25 residues processed: 223 average time/residue: 1.0038 time to fit residues: 240.9212 Evaluate side-chains 237 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 0.0770 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 110 ASN B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8992 Z= 0.186 Angle : 0.602 12.198 12185 Z= 0.283 Chirality : 0.043 0.637 1391 Planarity : 0.003 0.051 1525 Dihedral : 5.909 83.532 1236 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.27 % Allowed : 25.84 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1117 helix: 1.73 (0.26), residues: 412 sheet: -0.03 (0.30), residues: 287 loop : -0.77 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.039 0.001 PHE R 94 TYR 0.020 0.001 TYR S 50 ARG 0.009 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7715 (m-30) cc_final: 0.7427 (m-30) REVERT: A 270 LYS cc_start: 0.8317 (mttp) cc_final: 0.7973 (mttp) REVERT: A 276 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6890 (pp20) REVERT: A 277 LYS cc_start: 0.7711 (ttmm) cc_final: 0.7091 (tppp) REVERT: B 7 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7355 (mp) REVERT: B 170 ASP cc_start: 0.7950 (t70) cc_final: 0.7414 (t0) REVERT: B 277 SER cc_start: 0.8465 (t) cc_final: 0.8068 (p) REVERT: B 289 TYR cc_start: 0.8450 (m-80) cc_final: 0.8218 (m-80) REVERT: B 290 ASP cc_start: 0.7029 (m-30) cc_final: 0.6703 (m-30) REVERT: C 50 LEU cc_start: 0.8914 (mm) cc_final: 0.8634 (mt) REVERT: R 115 MET cc_start: 0.7948 (tmm) cc_final: 0.7004 (tmm) REVERT: R 253 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8513 (t) REVERT: S 223 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7740 (t80) outliers start: 31 outliers final: 24 residues processed: 222 average time/residue: 1.0382 time to fit residues: 247.6471 Evaluate side-chains 232 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 62 HIS B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120598 restraints weight = 13252.485| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.14 r_work: 0.3484 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8992 Z= 0.209 Angle : 0.622 13.087 12185 Z= 0.291 Chirality : 0.044 0.639 1391 Planarity : 0.003 0.052 1525 Dihedral : 5.933 85.635 1236 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.16 % Allowed : 25.95 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1117 helix: 1.75 (0.26), residues: 412 sheet: 0.04 (0.30), residues: 293 loop : -0.74 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.040 0.002 PHE R 94 TYR 0.026 0.001 TYR S 50 ARG 0.009 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4245.94 seconds wall clock time: 76 minutes 2.63 seconds (4562.63 seconds total)