Starting phenix.real_space_refine on Wed Feb 14 09:15:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/02_2024/7ew4_31347_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/02_2024/7ew4_31347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/02_2024/7ew4_31347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/02_2024/7ew4_31347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/02_2024/7ew4_31347_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/02_2024/7ew4_31347_updated.pdb" } resolution = 3.2 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= 0.002 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 48 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5692 2.51 5 N 1508 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 114": "NH1" <-> "NH2" Residue "R ARG 144": "NH1" <-> "NH2" Residue "R ARG 217": "NH1" <-> "NH2" Residue "R ARG 237": "NH1" <-> "NH2" Residue "R ARG 270": "NH1" <-> "NH2" Residue "R GLU 304": "OE1" <-> "OE2" Residue "S GLU 153": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "S GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8929 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1820 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2211 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 57 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'JF9': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.92, per 1000 atoms: 0.55 Number of scatterers: 8929 At special positions: 0 Unit cell: (92.34, 122.265, 129.96, 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 65 16.00 O 1664 8.00 N 1508 7.00 C 5692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 178 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 269 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.8 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 35.2% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.449A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 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 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.815A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.601A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.806A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.008A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'R' and resid 17 through 24 Processing helix chain 'R' and resid 40 through 66 Processing helix chain 'R' and resid 73 through 101 Processing helix chain 'R' and resid 108 through 124 removed outlier: 3.602A pdb=" N PHE R 112 " --> pdb=" O PRO R 108 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET R 118 " --> pdb=" O ARG R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 141 Processing helix chain 'R' and resid 151 through 174 Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 194 through 227 Processing helix chain 'R' and resid 232 through 268 Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 277 through 300 removed outlier: 3.533A pdb=" N ALA R 280 " --> pdb=" O LEU R 277 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN R 281 " --> pdb=" O PHE R 278 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN R 290 " --> pdb=" O ALA R 287 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN R 294 " --> pdb=" O SER R 291 " (cutoff:3.500A) Proline residue: R 295 - end of helix removed outlier: 3.902A pdb=" N TYR R 298 " --> pdb=" O PRO R 295 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR R 299 " --> pdb=" O VAL R 296 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU R 300 " --> pdb=" O ILE R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 311 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 263 through 265 removed outlier: 3.687A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.075A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.028A 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: 7.123A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.536A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.913A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.235A 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: 6.731A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.090A 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: 6.680A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.529A 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 52 removed outlier: 6.853A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 5.072A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= L, first strand: chain 'S' and resid 229 through 231 removed outlier: 6.140A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 225 through 227 415 hydrogen bonds defined for protein. 1077 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: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1448 1.31 - 1.43: 2470 1.43 - 1.56: 5093 1.56 - 1.69: 2 1.69 - 1.82: 93 Bond restraints: 9106 Sorted by residual: bond pdb=" C14 JF9 R 401 " pdb=" N7 JF9 R 401 " ideal model delta sigma weight residual 1.338 1.497 -0.159 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C19 JF9 R 401 " pdb=" C21 JF9 R 401 " ideal model delta sigma weight residual 1.459 1.540 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C8 JF9 R 401 " pdb=" N7 JF9 R 401 " ideal model delta sigma weight residual 1.467 1.516 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C14 JF9 R 401 " pdb=" O15 JF9 R 401 " ideal model delta sigma weight residual 1.223 1.178 0.045 2.00e-02 2.50e+03 4.96e+00 bond pdb=" C14 JF9 R 401 " pdb=" C16 JF9 R 401 " ideal model delta sigma weight residual 1.500 1.542 -0.042 2.00e-02 2.50e+03 4.36e+00 ... (remaining 9101 not shown) Histogram of bond angle deviations from ideal: 59.72 - 74.57: 3 74.57 - 89.42: 0 89.42 - 104.27: 88 104.27 - 119.12: 7399 119.12 - 133.97: 4834 Bond angle restraints: 12324 Sorted by residual: angle pdb=" C19 JF9 R 401 " pdb=" C21 JF9 R 401 " pdb=" C22 JF9 R 401 " ideal model delta sigma weight residual 121.01 133.93 -12.92 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CA LEU R 97 " pdb=" CB LEU R 97 " pdb=" CG LEU R 97 " ideal model delta sigma weight residual 116.30 124.60 -8.30 3.50e+00 8.16e-02 5.63e+00 angle pdb=" C12 JF9 R 401 " pdb=" C13 JF9 R 401 " pdb=" C8 JF9 R 401 " ideal model delta sigma weight residual 109.43 116.39 -6.96 3.00e+00 1.11e-01 5.38e+00 angle pdb=" C14 JF9 R 401 " pdb=" C16 JF9 R 401 " pdb=" N17 JF9 R 401 " ideal model delta sigma weight residual 120.71 127.21 -6.50 3.00e+00 1.11e-01 4.69e+00 angle pdb=" C LYS A 54 " pdb=" N ILE A 55 " pdb=" CA ILE A 55 " ideal model delta sigma weight residual 121.70 125.54 -3.84 1.80e+00 3.09e-01 4.56e+00 ... (remaining 12319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 4891 16.98 - 33.95: 445 33.95 - 50.93: 89 50.93 - 67.91: 9 67.91 - 84.88: 8 Dihedral angle restraints: 5442 sinusoidal: 2120 harmonic: 3322 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 52.64 40.36 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CB CYS R 178 " pdb=" SG CYS R 178 " pdb=" SG CYS R 185 " pdb=" CB CYS R 185 " ideal model delta sinusoidal sigma weight residual -86.00 -114.71 28.71 1 1.00e+01 1.00e-02 1.18e+01 dihedral pdb=" CA ASP B 195 " pdb=" CB ASP B 195 " pdb=" CG ASP B 195 " pdb=" OD1 ASP B 195 " ideal model delta sinusoidal sigma weight residual -30.00 -87.19 57.19 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 5439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1161 0.050 - 0.100: 211 0.100 - 0.150: 36 0.150 - 0.200: 3 0.200 - 0.250: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C8 JF9 R 401 " pdb=" C13 JF9 R 401 " pdb=" C9 JF9 R 401 " pdb=" N7 JF9 R 401 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C21 JF9 R 401 " pdb=" C19 JF9 R 401 " pdb=" C22 JF9 R 401 " pdb=" C23 JF9 R 401 " both_signs ideal model delta sigma weight residual True 2.30 -2.10 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CB THR S 91 " pdb=" CA THR S 91 " pdb=" OG1 THR S 91 " pdb=" CG2 THR S 91 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 1409 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 182 " -0.062 5.00e-02 4.00e+02 9.57e-02 1.46e+01 pdb=" N PRO R 183 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO R 183 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO R 183 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO S 14 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 236 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.027 5.00e-02 4.00e+02 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1476 2.77 - 3.30: 8325 3.30 - 3.83: 14505 3.83 - 4.37: 16566 4.37 - 4.90: 29794 Nonbonded interactions: 70666 Sorted by model distance: nonbonded pdb=" OG SER R 186 " pdb=" O LEU R 189 " model vdw 2.237 2.440 nonbonded pdb=" O ILE S 138 " pdb=" OG1 THR S 238 " model vdw 2.238 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.254 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.282 2.440 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.291 2.520 ... (remaining 70661 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 4.700 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.850 Find NCS groups from input model: 0.270 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 0.003 0.159 9106 Z= 0.186 Angle : 0.515 12.917 12324 Z= 0.277 Chirality : 0.040 0.250 1412 Planarity : 0.004 0.096 1550 Dihedral : 13.407 84.884 3287 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1129 helix: 2.98 (0.26), residues: 399 sheet: 0.26 (0.31), residues: 288 loop : -1.21 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.003 0.001 HIS B 54 PHE 0.018 0.001 PHE R 52 TYR 0.019 0.001 TYR R 24 ARG 0.006 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.919 Fit side-chains REVERT: A 18 MET cc_start: 0.7675 (mtp) cc_final: 0.7467 (mtt) REVERT: R 106 LEU cc_start: 0.7822 (tp) cc_final: 0.7600 (tp) REVERT: R 257 SER cc_start: 0.7327 (m) cc_final: 0.7054 (m) REVERT: S 220 GLU cc_start: 0.7713 (mp0) cc_final: 0.7511 (mp0) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2380 time to fit residues: 43.2877 Evaluate side-chains 101 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 75 GLN B 125 ASN B 237 ASN B 239 ASN R 57 ASN ** R 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9106 Z= 0.361 Angle : 0.621 12.498 12324 Z= 0.327 Chirality : 0.044 0.222 1412 Planarity : 0.005 0.054 1550 Dihedral : 4.785 33.673 1294 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.04 % Allowed : 10.31 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1129 helix: 2.35 (0.26), residues: 399 sheet: 0.23 (0.31), residues: 276 loop : -1.34 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 36 HIS 0.009 0.002 HIS B 225 PHE 0.017 0.002 PHE B 199 TYR 0.019 0.002 TYR B 105 ARG 0.007 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.000 Fit side-chains REVERT: R 150 LYS cc_start: 0.7547 (mttt) cc_final: 0.7332 (mmtt) REVERT: R 195 LYS cc_start: 0.5618 (tmtt) cc_final: 0.5391 (mmmt) outliers start: 10 outliers final: 7 residues processed: 117 average time/residue: 0.2611 time to fit residues: 40.4911 Evaluate side-chains 104 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.0000 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 239 ASN R 67 ASN R 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9106 Z= 0.134 Angle : 0.465 12.415 12324 Z= 0.246 Chirality : 0.039 0.210 1412 Planarity : 0.004 0.047 1550 Dihedral : 4.174 32.287 1294 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.25 % Allowed : 12.60 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1129 helix: 2.59 (0.26), residues: 398 sheet: 0.41 (0.32), residues: 269 loop : -1.27 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.006 0.001 HIS B 225 PHE 0.015 0.001 PHE A 354 TYR 0.011 0.001 TYR R 219 ARG 0.005 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 1.034 Fit side-chains REVERT: S 230 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.5501 (tmm) outliers start: 12 outliers final: 5 residues processed: 114 average time/residue: 0.2602 time to fit residues: 39.5633 Evaluate side-chains 104 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9106 Z= 0.150 Angle : 0.466 12.365 12324 Z= 0.246 Chirality : 0.040 0.227 1412 Planarity : 0.004 0.048 1550 Dihedral : 4.060 32.153 1294 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.88 % Allowed : 12.40 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1129 helix: 2.58 (0.26), residues: 399 sheet: 0.39 (0.31), residues: 275 loop : -1.29 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.010 0.001 PHE A 354 TYR 0.012 0.001 TYR R 24 ARG 0.005 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: B 43 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8229 (pt) REVERT: S 230 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.5912 (tmm) outliers start: 18 outliers final: 12 residues processed: 116 average time/residue: 0.2688 time to fit residues: 41.1378 Evaluate side-chains 109 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9106 Z= 0.159 Angle : 0.473 12.657 12324 Z= 0.247 Chirality : 0.040 0.242 1412 Planarity : 0.004 0.048 1550 Dihedral : 4.042 32.510 1294 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.19 % Allowed : 12.60 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1129 helix: 2.49 (0.26), residues: 399 sheet: 0.41 (0.31), residues: 275 loop : -1.32 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS R 21 PHE 0.010 0.001 PHE A 189 TYR 0.013 0.001 TYR R 219 ARG 0.005 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: B 43 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8211 (pt) REVERT: B 338 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7907 (mp) REVERT: S 230 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.5953 (tmm) outliers start: 21 outliers final: 13 residues processed: 114 average time/residue: 0.2645 time to fit residues: 40.0172 Evaluate side-chains 111 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.0010 chunk 56 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9106 Z= 0.235 Angle : 0.524 13.402 12324 Z= 0.275 Chirality : 0.041 0.272 1412 Planarity : 0.004 0.049 1550 Dihedral : 4.338 34.829 1294 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.19 % Allowed : 12.50 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1129 helix: 2.29 (0.26), residues: 404 sheet: 0.34 (0.31), residues: 271 loop : -1.41 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 36 HIS 0.005 0.001 HIS R 21 PHE 0.012 0.002 PHE S 212 TYR 0.011 0.001 TYR R 219 ARG 0.006 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.751 Fit side-chains revert: symmetry clash REVERT: B 43 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8173 (pt) REVERT: B 338 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7988 (mp) REVERT: R 143 MET cc_start: 0.7513 (mmt) cc_final: 0.7195 (mmp) REVERT: S 230 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6113 (tmm) outliers start: 21 outliers final: 12 residues processed: 115 average time/residue: 0.3447 time to fit residues: 53.2696 Evaluate side-chains 107 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 0.0970 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9106 Z= 0.158 Angle : 0.481 13.317 12324 Z= 0.252 Chirality : 0.040 0.268 1412 Planarity : 0.004 0.048 1550 Dihedral : 4.081 33.415 1294 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.88 % Allowed : 14.38 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1129 helix: 2.33 (0.26), residues: 404 sheet: 0.36 (0.31), residues: 273 loop : -1.42 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS R 21 PHE 0.010 0.001 PHE A 189 TYR 0.015 0.001 TYR R 24 ARG 0.005 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: B 43 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8121 (pt) REVERT: B 338 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7863 (mp) REVERT: R 143 MET cc_start: 0.7480 (mmt) cc_final: 0.7128 (mmp) REVERT: S 83 MET cc_start: 0.6995 (mtm) cc_final: 0.6699 (mtp) REVERT: S 230 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.5889 (tmm) outliers start: 18 outliers final: 12 residues processed: 112 average time/residue: 0.2616 time to fit residues: 38.8522 Evaluate side-chains 110 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9106 Z= 0.192 Angle : 0.502 13.157 12324 Z= 0.263 Chirality : 0.041 0.288 1412 Planarity : 0.004 0.049 1550 Dihedral : 4.159 33.621 1294 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.98 % Allowed : 14.58 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1129 helix: 2.27 (0.26), residues: 404 sheet: 0.35 (0.31), residues: 271 loop : -1.43 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 36 HIS 0.005 0.001 HIS R 21 PHE 0.011 0.001 PHE S 212 TYR 0.013 0.001 TYR R 24 ARG 0.005 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: B 43 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8115 (pt) REVERT: B 338 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7915 (mp) REVERT: R 143 MET cc_start: 0.7512 (mmt) cc_final: 0.7188 (mmp) REVERT: S 230 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.5732 (tmm) outliers start: 19 outliers final: 13 residues processed: 112 average time/residue: 0.2656 time to fit residues: 39.6197 Evaluate side-chains 111 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 0.0470 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9106 Z= 0.228 Angle : 0.535 13.337 12324 Z= 0.278 Chirality : 0.042 0.304 1412 Planarity : 0.004 0.049 1550 Dihedral : 4.333 35.539 1294 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.08 % Allowed : 14.48 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1129 helix: 2.20 (0.26), residues: 404 sheet: 0.25 (0.31), residues: 271 loop : -1.48 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 36 HIS 0.005 0.001 HIS R 21 PHE 0.012 0.002 PHE B 199 TYR 0.014 0.001 TYR R 219 ARG 0.006 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: B 43 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8131 (pt) REVERT: B 234 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7491 (t80) REVERT: B 338 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7940 (mp) REVERT: R 143 MET cc_start: 0.7589 (mmt) cc_final: 0.7317 (mmp) REVERT: S 230 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6310 (tmm) REVERT: S 239 PHE cc_start: 0.5726 (m-10) cc_final: 0.4962 (m-80) outliers start: 20 outliers final: 13 residues processed: 117 average time/residue: 0.2606 time to fit residues: 40.6660 Evaluate side-chains 115 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 231 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.0670 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9106 Z= 0.180 Angle : 0.525 13.473 12324 Z= 0.270 Chirality : 0.041 0.304 1412 Planarity : 0.004 0.048 1550 Dihedral : 4.195 34.700 1294 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.77 % Allowed : 15.10 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1129 helix: 2.25 (0.26), residues: 404 sheet: 0.28 (0.31), residues: 269 loop : -1.46 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS R 21 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR R 219 ARG 0.006 0.000 ARG S 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: B 43 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8100 (pt) REVERT: B 234 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7519 (t80) REVERT: B 338 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7907 (mp) REVERT: R 143 MET cc_start: 0.7518 (mmt) cc_final: 0.7246 (mmp) REVERT: S 230 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.5694 (tmm) outliers start: 17 outliers final: 12 residues processed: 112 average time/residue: 0.2611 time to fit residues: 38.8156 Evaluate side-chains 114 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 161 CYS Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.183145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143061 restraints weight = 11204.735| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.16 r_work: 0.3458 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9106 Z= 0.150 Angle : 0.506 13.142 12324 Z= 0.260 Chirality : 0.041 0.301 1412 Planarity : 0.004 0.048 1550 Dihedral : 4.006 32.526 1294 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.67 % Allowed : 15.21 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1129 helix: 2.32 (0.26), residues: 405 sheet: 0.30 (0.31), residues: 271 loop : -1.42 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS R 21 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR R 24 ARG 0.005 0.000 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.45 seconds wall clock time: 40 minutes 36.49 seconds (2436.49 seconds total)