Starting phenix.real_space_refine (version: dev) on Mon Apr 4 20:58:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/04_2022/7ew4_31347_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/04_2022/7ew4_31347.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/04_2022/7ew4_31347_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/04_2022/7ew4_31347_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/04_2022/7ew4_31347_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/04_2022/7ew4_31347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/04_2022/7ew4_31347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/04_2022/7ew4_31347_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew4_31347/04_2022/7ew4_31347_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 9, 'TRANS': 221, 'PCIS': 1} 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: 5.49, per 1000 atoms: 0.61 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: 3.57 Conformation dependent library (CDL) restraints added in 1.5 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: 0.79 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: 2.41 Time building geometry restraints manager: 3.75 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=" C8 JF9 R 401 " pdb=" N7 JF9 R 401 " ideal model delta sigma weight residual 1.482 1.516 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C19 JF9 R 401 " pdb=" O18 JF9 R 401 " ideal model delta sigma weight residual 1.347 1.318 0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 PLM R 402 " pdb=" C2 PLM R 402 " ideal model delta sigma weight residual 1.542 1.570 -0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" C1 PLM R 403 " pdb=" C2 PLM R 403 " ideal model delta sigma weight residual 1.542 1.570 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" N17 JF9 R 401 " pdb=" O18 JF9 R 401 " ideal model delta sigma weight residual 1.390 1.367 0.023 2.00e-02 2.50e+03 1.37e+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=" 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=" C19 JF9 R 401 " pdb=" C21 JF9 R 401 " pdb=" C23 JF9 R 401 " ideal model delta sigma weight residual 131.19 124.71 6.48 3.00e+00 1.11e-01 4.67e+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 angle pdb=" CA LEU R 55 " pdb=" CB LEU R 55 " pdb=" CG LEU R 55 " ideal model delta sigma weight residual 116.30 123.68 -7.38 3.50e+00 8.16e-02 4.45e+00 angle pdb=" CA LEU B 14 " pdb=" CB LEU B 14 " pdb=" CG LEU B 14 " ideal model delta sigma weight residual 116.30 123.05 -6.75 3.50e+00 8.16e-02 3.72e+00 ... (remaining 12319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 5042 21.72 - 43.43: 339 43.43 - 65.15: 26 65.15 - 86.87: 9 86.87 - 108.58: 4 Dihedral angle restraints: 5420 sinusoidal: 2098 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=" C1 JF9 R 401 " pdb=" C5 JF9 R 401 " pdb=" C6 JF9 R 401 " pdb=" C4 JF9 R 401 " ideal model delta sinusoidal sigma weight residual -52.94 55.64 -108.58 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C11 JF9 R 401 " pdb=" C10 JF9 R 401 " pdb=" C9 JF9 R 401 " pdb=" C8 JF9 R 401 " ideal model delta sinusoidal sigma weight residual -52.94 54.15 -107.09 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 5417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.990: 1411 0.990 - 1.979: 0 1.979 - 2.969: 0 2.969 - 3.958: 0 3.958 - 4.948: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C4 JF9 R 401 " pdb=" C3 JF9 R 401 " pdb=" C5 JF9 R 401 " pdb=" N7 JF9 R 401 " both_signs ideal model delta sigma weight residual False 2.64 -2.31 4.95 2.00e-01 2.50e+01 6.12e+02 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 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.80e-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 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. 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 4.450 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.080 Process input model: 26.090 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9106 Z= 0.142 Angle : 0.498 8.302 12324 Z= 0.274 Chirality : 0.137 4.948 1412 Planarity : 0.004 0.096 1550 Dihedral : 13.996 108.582 3265 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 % 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 *********************** 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 : 1.089 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2288 time to fit residues: 41.9619 Evaluate side-chains 100 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3359 ------------------------------------------------------------------------------- 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: 0.7980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 9106 Z= 0.236 Angle : 0.539 11.913 12324 Z= 0.280 Chirality : 0.043 0.410 1412 Planarity : 0.005 0.089 1550 Dihedral : 5.041 64.563 1272 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.83 % 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: 0.86 (0.25), residues: 1129 helix: 2.57 (0.26), residues: 403 sheet: 0.44 (0.32), residues: 276 loop : -1.26 (0.27), residues: 450 *********************** 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 119 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.223 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 116 average time/residue: 0.2459 time to fit residues: 38.1864 Evaluate side-chains 103 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0822 time to fit residues: 2.1784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.0470 chunk 100 optimal weight: 3.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 294 ASN ** 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: 0.7613 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 9106 Z= 0.183 Angle : 0.507 12.157 12324 Z= 0.262 Chirality : 0.041 0.332 1412 Planarity : 0.004 0.065 1550 Dihedral : 4.925 70.155 1272 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.83 % 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: 0.87 (0.25), residues: 1129 helix: 2.55 (0.26), residues: 404 sheet: 0.45 (0.31), residues: 275 loop : -1.25 (0.27), residues: 450 *********************** 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 112 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.066 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 110 average time/residue: 0.2541 time to fit residues: 37.7013 Evaluate side-chains 99 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0964 time to fit residues: 2.2162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0070 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.0010 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN R 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9106 Z= 0.122 Angle : 0.471 13.170 12324 Z= 0.242 Chirality : 0.040 0.328 1412 Planarity : 0.004 0.057 1550 Dihedral : 4.679 69.299 1272 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.83 % 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: 0.90 (0.25), residues: 1129 helix: 2.57 (0.26), residues: 405 sheet: 0.48 (0.31), residues: 278 loop : -1.26 (0.27), residues: 446 *********************** 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 113 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.061 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 109 average time/residue: 0.2621 time to fit residues: 38.0229 Evaluate side-chains 100 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0820 time to fit residues: 1.9226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 125 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.124 9106 Z= 0.352 Angle : 0.615 12.703 12324 Z= 0.320 Chirality : 0.044 0.342 1412 Planarity : 0.005 0.052 1550 Dihedral : 5.418 74.718 1272 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 1.25 % 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: 2.22 (0.26), residues: 404 sheet: 0.19 (0.31), residues: 278 loop : -1.40 (0.26), residues: 447 *********************** 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 117 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.230 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 112 average time/residue: 0.2524 time to fit residues: 38.0613 Evaluate side-chains 96 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0795 time to fit residues: 1.8398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 125 ASN B 237 ASN B 239 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.125 9106 Z= 0.222 Angle : 0.547 13.756 12324 Z= 0.292 Chirality : 0.041 0.328 1412 Planarity : 0.004 0.072 1550 Dihedral : 4.972 70.306 1272 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.73 % 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: 0.64 (0.25), residues: 1129 helix: 2.45 (0.26), residues: 398 sheet: 0.35 (0.31), residues: 271 loop : -1.41 (0.26), residues: 460 *********************** 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 110 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 1.078 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 107 average time/residue: 0.2530 time to fit residues: 36.3571 Evaluate side-chains 100 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0800 time to fit residues: 1.6801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 0.0060 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN S 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.110 9106 Z= 0.198 Angle : 0.521 13.022 12324 Z= 0.274 Chirality : 0.041 0.328 1412 Planarity : 0.005 0.089 1550 Dihedral : 4.827 69.155 1272 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.94 % 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: 0.68 (0.25), residues: 1129 helix: 2.47 (0.26), residues: 399 sheet: 0.33 (0.31), residues: 276 loop : -1.37 (0.26), residues: 454 *********************** 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 113 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.099 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 109 average time/residue: 0.2717 time to fit residues: 39.2939 Evaluate side-chains 101 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0820 time to fit residues: 1.9045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7642 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.304 9106 Z= 0.324 Angle : 0.561 17.245 12324 Z= 0.311 Chirality : 0.042 0.328 1412 Planarity : 0.005 0.091 1550 Dihedral : 4.776 68.601 1272 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.42 % 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: 0.66 (0.25), residues: 1129 helix: 2.46 (0.26), residues: 399 sheet: 0.33 (0.31), residues: 274 loop : -1.41 (0.26), residues: 456 *********************** 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 109 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.094 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 109 average time/residue: 0.2760 time to fit residues: 39.9552 Evaluate side-chains 103 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3199 time to fit residues: 2.2486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 103 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.7628 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.105 9106 Z= 0.198 Angle : 0.537 13.268 12324 Z= 0.283 Chirality : 0.042 0.328 1412 Planarity : 0.005 0.112 1550 Dihedral : 4.705 68.174 1272 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.73 % 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: 0.68 (0.25), residues: 1129 helix: 2.48 (0.27), residues: 399 sheet: 0.35 (0.31), residues: 272 loop : -1.38 (0.26), residues: 458 *********************** 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 112 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 1.025 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 110 average time/residue: 0.2702 time to fit residues: 39.2765 Evaluate side-chains 103 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0942 time to fit residues: 1.9323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 chunk 54 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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: 0.7611 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.136 9106 Z= 0.202 Angle : 0.546 13.377 12324 Z= 0.286 Chirality : 0.042 0.328 1412 Planarity : 0.005 0.096 1550 Dihedral : 4.633 67.708 1272 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.00 % 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: 0.68 (0.25), residues: 1129 helix: 2.46 (0.26), residues: 399 sheet: 0.36 (0.31), residues: 272 loop : -1.37 (0.26), residues: 458 ********************** 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 108 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.932 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2790 time to fit residues: 40.4425 Evaluate side-chains 103 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.0670 chunk 13 optimal weight: 0.4980 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.186120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.146168 restraints weight = 11211.263| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.31 r_work: 0.3712 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work: 0.3672 rms_B_bonded: 2.16 restraints_weight: 0.1250 r_work: 0.3649 rms_B_bonded: 2.37 restraints_weight: 0.0625 r_work: 0.3622 rms_B_bonded: 2.68 restraints_weight: 0.0312 r_work: 0.3589 rms_B_bonded: 3.14 restraints_weight: 0.0156 r_work: 0.3548 rms_B_bonded: 3.77 restraints_weight: 0.0078 r_work: 0.3494 rms_B_bonded: 4.66 restraints_weight: 0.0039 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.841 9106 Z= 0.885 Angle : 1.181 105.400 12324 Z= 0.565 Chirality : 0.048 0.643 1412 Planarity : 0.005 0.093 1550 Dihedral : 4.631 67.705 1272 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.09 % 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: 0.67 (0.25), residues: 1129 helix: 2.44 (0.26), residues: 399 sheet: 0.36 (0.31), residues: 272 loop : -1.37 (0.26), residues: 458 =============================================================================== Job complete usr+sys time: 1815.82 seconds wall clock time: 33 minutes 49.10 seconds (2029.10 seconds total)