Starting phenix.real_space_refine on Fri Dec 8 17:08:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/12_2023/8gus_34278_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/12_2023/8gus_34278.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/12_2023/8gus_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_34278/12_2023/8gus_34278_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/12_2023/8gus_34278_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/12_2023/8gus_34278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/12_2023/8gus_34278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/12_2023/8gus_34278_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gus_34278/12_2023/8gus_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-1.21rc1-5172/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: 4.95, per 1000 atoms: 0.56 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: 3.48 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: 2.22 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: 2.49 Time building geometry restraints manager: 3.76 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: 0.850 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: 3.760 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 28.030 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 45.410 ------------------------------------------------------------------------------- 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 : 1.115 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 1.1360 time to fit residues: 257.6012 Evaluate side-chains 210 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4220 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.8180 ------------------------------------------------------------------------------- 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: 0.7491 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8992 Z= 0.293 Angle : 0.645 12.616 12185 Z= 0.308 Chirality : 0.045 0.644 1391 Planarity : 0.004 0.068 1525 Dihedral : 6.215 81.951 1236 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.90 % Allowed : 20.15 % Favored : 75.95 % 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: 0.34 (0.25), residues: 1117 helix: 1.58 (0.25), residues: 413 sheet: -0.04 (0.31), residues: 289 loop : -0.91 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.017 0.002 PHE R 183 TYR 0.016 0.001 TYR S 50 ARG 0.007 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 250 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 213 time to evaluate : 0.908 Fit side-chains outliers start: 37 outliers final: 17 residues processed: 227 average time/residue: 0.9569 time to fit residues: 235.1017 Evaluate side-chains 214 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 4 residues processed: 13 average time/residue: 0.4861 time to fit residues: 8.7594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 0.2980 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 89 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.7469 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8992 Z= 0.192 Angle : 0.587 12.863 12185 Z= 0.280 Chirality : 0.044 0.652 1391 Planarity : 0.004 0.049 1525 Dihedral : 6.144 70.533 1236 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.90 % Allowed : 21.94 % Favored : 74.16 % 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: 0.46 (0.25), residues: 1117 helix: 1.69 (0.26), residues: 413 sheet: -0.04 (0.30), residues: 292 loop : -0.80 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.010 0.001 PHE R 87 TYR 0.013 0.001 TYR S 50 ARG 0.005 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 243 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 206 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 14 residues processed: 222 average time/residue: 1.0263 time to fit residues: 245.0395 Evaluate side-chains 211 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 7 average time/residue: 0.5653 time to fit residues: 5.7580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 110 ASN B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 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: 0.7504 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8992 Z= 0.321 Angle : 0.632 13.099 12185 Z= 0.303 Chirality : 0.046 0.677 1391 Planarity : 0.004 0.050 1525 Dihedral : 6.081 77.141 1236 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.11 % Allowed : 22.78 % 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: 0.36 (0.25), residues: 1117 helix: 1.50 (0.26), residues: 415 sheet: 0.01 (0.30), residues: 288 loop : -0.82 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 194 HIS 0.005 0.001 HIS S 220 PHE 0.030 0.002 PHE R 94 TYR 0.016 0.001 TYR S 50 ARG 0.008 0.001 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 249 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 210 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 22 residues processed: 229 average time/residue: 0.9327 time to fit residues: 231.3686 Evaluate side-chains 225 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 203 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 10 residues processed: 12 average time/residue: 0.3425 time to fit residues: 6.2824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 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 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: 0.7498 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8992 Z= 0.278 Angle : 0.630 12.729 12185 Z= 0.298 Chirality : 0.045 0.665 1391 Planarity : 0.004 0.049 1525 Dihedral : 6.014 80.288 1236 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.43 % Allowed : 22.78 % Favored : 72.78 % 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: 1.62 (0.26), residues: 406 sheet: 0.08 (0.30), residues: 284 loop : -0.75 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 194 HIS 0.005 0.001 HIS B 62 PHE 0.034 0.002 PHE R 94 TYR 0.017 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 246 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 26 residues processed: 226 average time/residue: 0.9675 time to fit residues: 236.5415 Evaluate side-chains 230 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 13 residues processed: 13 average time/residue: 0.2993 time to fit residues: 6.2351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7496 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8992 Z= 0.266 Angle : 0.632 12.477 12185 Z= 0.298 Chirality : 0.045 0.661 1391 Planarity : 0.004 0.050 1525 Dihedral : 5.955 80.940 1236 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.80 % Allowed : 24.16 % Favored : 72.05 % 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: 0.48 (0.25), residues: 1117 helix: 1.67 (0.26), residues: 405 sheet: 0.03 (0.30), residues: 286 loop : -0.74 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.037 0.002 PHE R 94 TYR 0.016 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 241 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 205 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 22 residues processed: 225 average time/residue: 0.9810 time to fit residues: 238.6678 Evaluate side-chains 222 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 200 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 14 residues processed: 8 average time/residue: 0.2865 time to fit residues: 4.2661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 32 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8992 Z= 0.187 Angle : 0.609 11.960 12185 Z= 0.285 Chirality : 0.044 0.649 1391 Planarity : 0.003 0.050 1525 Dihedral : 5.865 82.240 1236 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.16 % Allowed : 25.21 % Favored : 71.62 % 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: 1.82 (0.26), residues: 405 sheet: 0.02 (0.30), residues: 293 loop : -0.75 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.039 0.001 PHE R 94 TYR 0.016 0.001 TYR S 50 ARG 0.004 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 235 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 223 average time/residue: 0.9688 time to fit residues: 233.4407 Evaluate side-chains 222 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 5 average time/residue: 0.1632 time to fit residues: 2.8099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7499 moved from start: 0.1729 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= 0.292 Angle : 0.646 12.282 12185 Z= 0.305 Chirality : 0.045 0.645 1391 Planarity : 0.004 0.051 1525 Dihedral : 5.971 82.827 1236 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.38 % Allowed : 25.11 % Favored : 71.52 % 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: 1.74 (0.26), residues: 401 sheet: 0.02 (0.30), residues: 286 loop : -0.75 (0.29), residues: 430 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 0.039 0.002 PHE R 94 TYR 0.025 0.001 TYR S 50 ARG 0.005 0.000 ARG B 52 *********************** 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 237 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 223 average time/residue: 1.0840 time to fit residues: 259.7084 Evaluate side-chains 222 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 13 residues processed: 8 average time/residue: 0.2552 time to fit residues: 3.9096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1796 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= 0.282 Angle : 0.656 12.489 12185 Z= 0.308 Chirality : 0.045 0.644 1391 Planarity : 0.004 0.050 1525 Dihedral : 6.086 84.683 1236 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.64 % Allowed : 26.37 % Favored : 70.99 % 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: 0.45 (0.25), residues: 1117 helix: 1.70 (0.26), residues: 400 sheet: -0.02 (0.30), residues: 286 loop : -0.77 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.015 0.002 PHE A 274 TYR 0.024 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 229 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 18 residues processed: 219 average time/residue: 0.9998 time to fit residues: 236.4321 Evaluate side-chains 220 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 202 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.4673 time to fit residues: 4.0515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.0370 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8992 Z= 0.187 Angle : 0.633 10.722 12185 Z= 0.293 Chirality : 0.044 0.666 1391 Planarity : 0.003 0.050 1525 Dihedral : 5.989 89.520 1236 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.22 % Allowed : 27.11 % 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: 0.48 (0.25), residues: 1117 helix: 1.78 (0.26), residues: 404 sheet: -0.08 (0.30), residues: 287 loop : -0.75 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.035 0.001 PHE R 94 TYR 0.022 0.001 TYR S 50 ARG 0.008 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 224 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 217 average time/residue: 0.9779 time to fit residues: 229.0138 Evaluate side-chains 218 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.4321 time to fit residues: 3.8350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.0770 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121400 restraints weight = 13164.550| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.12 r_work: 0.3490 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8992 Z= 0.193 Angle : 0.640 14.048 12185 Z= 0.294 Chirality : 0.044 0.640 1391 Planarity : 0.004 0.050 1525 Dihedral : 5.951 89.202 1236 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.11 % Allowed : 27.95 % Favored : 69.94 % 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: 0.52 (0.25), residues: 1117 helix: 1.82 (0.26), residues: 403 sheet: -0.06 (0.30), residues: 286 loop : -0.75 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 194 HIS 0.004 0.001 HIS B 62 PHE 0.040 0.002 PHE R 94 TYR 0.021 0.001 TYR S 50 ARG 0.008 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4208.75 seconds wall clock time: 75 minutes 17.38 seconds (4517.38 seconds total)