Starting phenix.real_space_refine (version: dev) on Thu May 12 22:50:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/05_2022/6s8h_10122_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/05_2022/6s8h_10122.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/05_2022/6s8h_10122_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/05_2022/6s8h_10122_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/05_2022/6s8h_10122_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/05_2022/6s8h_10122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/05_2022/6s8h_10122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/05_2022/6s8h_10122_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/05_2022/6s8h_10122_updated.pdb" } resolution = 3.7 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= -0.000 sd= 0.005 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 GLU 86": "OE1" <-> "OE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B ASP 64": "OD1" <-> "OD2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B ASP 227": "OD1" <-> "OD2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F ASP 40": "OD1" <-> "OD2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ARG 295": "NH1" <-> "NH2" Residue "F TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 8": "OD1" <-> "OD2" Residue "G ASP 37": "OD1" <-> "OD2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 7818 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1868 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 8, 'TRANS': 230} Chain: "B" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1857 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "F" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1864 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 9, 'TRANS': 229} Chain breaks: 1 Chain: "G" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1876 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Chain breaks: 2 Chain: "F" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 281 Unusual residues: {'JSG': 1, 'LMT': 1, 'LMN': 1, 'DCQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 21 Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {'LMT': 1, 'LMN': 1, 'DCQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 25 Time building chain proxies: 5.16, per 1000 atoms: 0.66 Number of scatterers: 7818 At special positions: 0 Unit cell: (114.582, 77.064, 95.316, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 4 15.00 O 1418 8.00 N 1285 7.00 C 5068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.5 seconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 6 sheets defined 40.9% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.723A pdb=" N VAL A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.963A pdb=" N LEU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 230 through 233 No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'B' and resid 40 through 49 removed outlier: 3.865A pdb=" N THR B 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 45 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 49 " --> pdb=" O PHE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 75 No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 95 through 103 removed outlier: 4.067A pdb=" N VAL B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.649A pdb=" N ALA B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.710A pdb=" N ASP B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 203 removed outlier: 3.958A pdb=" N LEU B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'F' and resid 3 through 15 removed outlier: 3.821A pdb=" N LYS F 13 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 36 removed outlier: 3.521A pdb=" N ARG F 33 " --> pdb=" O GLN F 29 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY F 36 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 removed outlier: 3.843A pdb=" N LEU F 52 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.392A pdb=" N GLN F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Proline residue: F 65 - end of helix removed outlier: 3.887A pdb=" N LEU F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 99 No H-bonds generated for 'chain 'F' and resid 96 through 99' Processing helix chain 'F' and resid 104 through 117 removed outlier: 3.991A pdb=" N PHE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 115 " --> pdb=" O ILE F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 271 through 279 removed outlier: 4.312A pdb=" N VAL F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 315 removed outlier: 3.524A pdb=" N LEU F 300 " --> pdb=" O LEU F 297 " (cutoff:3.500A) Proline residue: F 301 - end of helix removed outlier: 4.232A pdb=" N LEU F 304 " --> pdb=" O PRO F 301 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU F 308 " --> pdb=" O LEU F 305 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE F 310 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU F 311 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN F 313 " --> pdb=" O PHE F 310 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR F 314 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 344 removed outlier: 3.751A pdb=" N ALA F 342 " --> pdb=" O TYR F 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 35 removed outlier: 3.689A pdb=" N PHE G 24 " --> pdb=" O MET G 20 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU G 29 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 63 No H-bonds generated for 'chain 'G' and resid 60 through 63' Processing helix chain 'G' and resid 72 through 78 removed outlier: 3.719A pdb=" N ALA G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 85 Processing helix chain 'G' and resid 90 through 95 Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.642A pdb=" N THR G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE G 111 " --> pdb=" O MET G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix Processing helix chain 'G' and resid 125 through 137 removed outlier: 3.770A pdb=" N MET G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN G 134 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG G 136 " --> pdb=" O ALA G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 258 No H-bonds generated for 'chain 'G' and resid 256 through 258' Processing helix chain 'G' and resid 272 through 279 removed outlier: 4.081A pdb=" N LYS G 278 " --> pdb=" O ASN G 274 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE G 279 " --> pdb=" O MET G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 296 removed outlier: 3.625A pdb=" N MET G 288 " --> pdb=" O SER G 284 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE G 296 " --> pdb=" O ALA G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 324 removed outlier: 3.844A pdb=" N PHE G 315 " --> pdb=" O THR G 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY G 316 " --> pdb=" O GLY G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 333 removed outlier: 3.761A pdb=" N TYR G 333 " --> pdb=" O LEU G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 340 No H-bonds generated for 'chain 'G' and resid 337 through 340' Processing helix chain 'G' and resid 343 through 356 removed outlier: 4.060A pdb=" N PHE G 348 " --> pdb=" O PRO G 344 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE G 351 " --> pdb=" O SER G 347 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER G 352 " --> pdb=" O PHE G 348 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 24 through 26 Processing sheet with id= B, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.482A pdb=" N VAL A 190 " --> pdb=" O VAL A 32 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 9 through 11 removed outlier: 3.719A pdb=" N VAL A 22 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LYS A 11 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLU A 20 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 59 through 62 removed outlier: 5.840A pdb=" N VAL B 22 " --> pdb=" O ASN B 8 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 32 through 35 removed outlier: 7.062A pdb=" N ARG B 206 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LEU B 35 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR B 208 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 217 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.693A pdb=" N LYS B 11 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 19 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TYR B 13 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ARG B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 189 hydrogen bonds defined for protein. 522 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: 1.80 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2410 1.34 - 1.46: 1355 1.46 - 1.57: 4099 1.57 - 1.69: 7 1.69 - 1.81: 82 Bond restraints: 7953 Sorted by residual: bond pdb=" C7 JSG F 402 " pdb=" N2 JSG F 402 " ideal model delta sigma weight residual 1.551 1.340 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CDO JSG F 402 " pdb=" NAO JSG F 402 " ideal model delta sigma weight residual 1.505 1.329 0.176 2.00e-02 2.50e+03 7.72e+01 bond pdb=" CFK JSG F 402 " pdb=" O3 JSG F 402 " ideal model delta sigma weight residual 1.509 1.355 0.154 2.00e-02 2.50e+03 5.91e+01 bond pdb=" CAN JSG F 402 " pdb=" CAP JSG F 402 " ideal model delta sigma weight residual 1.431 1.565 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" OCK JSG F 402 " pdb=" PHO JSG F 402 " ideal model delta sigma weight residual 1.705 1.590 0.115 2.00e-02 2.50e+03 3.30e+01 ... (remaining 7948 not shown) Histogram of bond angle deviations from ideal: 96.61 - 105.22: 190 105.22 - 113.84: 4679 113.84 - 122.45: 4887 122.45 - 131.06: 947 131.06 - 139.67: 45 Bond angle restraints: 10748 Sorted by residual: angle pdb=" CBJ LMN F 401 " pdb=" CBL LMN F 401 " pdb=" CBR LMN F 401 " ideal model delta sigma weight residual 109.52 135.02 -25.50 3.00e+00 1.11e-01 7.22e+01 angle pdb=" C3 DCQ G 403 " pdb=" O3 DCQ G 403 " pdb=" C3M DCQ G 403 " ideal model delta sigma weight residual 115.29 139.67 -24.38 3.00e+00 1.11e-01 6.60e+01 angle pdb=" C4 DCQ G 403 " pdb=" O4 DCQ G 403 " pdb=" C4M DCQ G 403 " ideal model delta sigma weight residual 115.20 138.59 -23.39 3.00e+00 1.11e-01 6.08e+01 angle pdb=" CBF LMN F 401 " pdb=" CBH LMN F 401 " pdb=" CBJ LMN F 401 " ideal model delta sigma weight residual 109.55 132.28 -22.73 3.00e+00 1.11e-01 5.74e+01 angle pdb=" C4 DCQ F 403 " pdb=" O4 DCQ F 403 " pdb=" C4M DCQ F 403 " ideal model delta sigma weight residual 115.20 137.60 -22.40 3.00e+00 1.11e-01 5.57e+01 ... (remaining 10743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.23: 4451 28.23 - 56.45: 245 56.45 - 84.68: 25 84.68 - 112.90: 4 112.90 - 141.13: 4 Dihedral angle restraints: 4729 sinusoidal: 1978 harmonic: 2751 Sorted by residual: dihedral pdb=" CA GLY B 39 " pdb=" C GLY B 39 " pdb=" N ALA B 40 " pdb=" CA ALA B 40 " ideal model delta harmonic sigma weight residual -180.00 -139.27 -40.73 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA ALA B 40 " pdb=" C ALA B 40 " pdb=" N GLY B 41 " pdb=" CA GLY B 41 " ideal model delta harmonic sigma weight residual 180.00 146.96 33.04 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA TYR A 234 " pdb=" C TYR A 234 " pdb=" N LEU A 235 " pdb=" CA LEU A 235 " ideal model delta harmonic sigma weight residual -180.00 -148.85 -31.15 0 5.00e+00 4.00e-02 3.88e+01 ... (remaining 4726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.057: 1276 1.057 - 2.114: 1 2.114 - 3.171: 0 3.171 - 4.228: 0 4.228 - 5.284: 3 Chirality restraints: 1280 Sorted by residual: chirality pdb=" CBP JSG F 402 " pdb=" CBM JSG F 402 " pdb=" CBQ JSG F 402 " pdb=" OBW JSG F 402 " both_signs ideal model delta sigma weight residual False 2.51 -2.77 5.28 2.00e-01 2.50e+01 6.98e+02 chirality pdb=" CBA JSG F 402 " pdb=" CAX JSG F 402 " pdb=" CBB JSG F 402 " pdb=" OBH JSG F 402 " both_signs ideal model delta sigma weight residual False 2.57 -2.58 5.16 2.00e-01 2.50e+01 6.64e+02 chirality pdb=" CCB JSG F 402 " pdb=" CCC JSG F 402 " pdb=" OBF JSG F 402 " pdb=" OCL JSG F 402 " both_signs ideal model delta sigma weight residual False 2.44 -2.59 5.02 2.00e-01 2.50e+01 6.31e+02 ... (remaining 1277 not shown) Planarity restraints: 1303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CGB JSG F 402 " 0.060 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" CGC JSG F 402 " -0.016 2.00e-02 2.50e+03 pdb=" OFJ JSG F 402 " -0.020 2.00e-02 2.50e+03 pdb=" OGA JSG F 402 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DCQ G 403 " 0.002 2.00e-02 2.50e+03 1.99e-02 1.19e+01 pdb=" C1M DCQ G 403 " 0.040 2.00e-02 2.50e+03 pdb=" C2 DCQ G 403 " -0.005 2.00e-02 2.50e+03 pdb=" C3 DCQ G 403 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DCQ G 403 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DCQ G 403 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DCQ G 403 " 0.015 2.00e-02 2.50e+03 pdb=" C7 DCQ G 403 " -0.029 2.00e-02 2.50e+03 pdb=" O2 DCQ G 403 " -0.042 2.00e-02 2.50e+03 pdb=" O3 DCQ G 403 " 0.011 2.00e-02 2.50e+03 pdb=" O4 DCQ G 403 " 0.006 2.00e-02 2.50e+03 pdb=" O5 DCQ G 403 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CFK JSG F 402 " -0.057 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" CFL JSG F 402 " 0.016 2.00e-02 2.50e+03 pdb=" O3 JSG F 402 " 0.017 2.00e-02 2.50e+03 pdb=" OFY JSG F 402 " 0.023 2.00e-02 2.50e+03 ... (remaining 1300 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2283 2.82 - 3.34: 6837 3.34 - 3.86: 12228 3.86 - 4.38: 14287 4.38 - 4.90: 24081 Nonbonded interactions: 59716 Sorted by model distance: nonbonded pdb=" O1B LMT F 404 " pdb=" O6' LMT F 404 " model vdw 2.300 2.440 nonbonded pdb=" O SER G 277 " pdb=" OG SER G 277 " model vdw 2.308 2.440 nonbonded pdb=" O SER F 315 " pdb=" OG SER F 315 " model vdw 2.315 2.440 nonbonded pdb=" O SER A 137 " pdb=" OG SER A 137 " model vdw 2.322 2.440 nonbonded pdb=" O SER B 172 " pdb=" OG SER B 172 " model vdw 2.329 2.440 ... (remaining 59711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 239) selection = chain 'B' } 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 43 5.16 5 C 5068 2.51 5 N 1285 2.21 5 O 1418 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.940 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.060 Process input model: 24.690 Find NCS groups from input model: 0.370 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.011 0.211 7953 Z= 0.671 Angle : 1.652 25.495 10748 Z= 0.726 Chirality : 0.263 5.284 1280 Planarity : 0.008 0.080 1303 Dihedral : 17.603 141.126 2955 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.95 % Favored : 89.84 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -6.48 (0.18), residues: 945 helix: -4.56 (0.10), residues: 507 sheet: -3.41 (0.54), residues: 69 loop : -3.82 (0.26), residues: 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 300 average time/residue: 0.2325 time to fit residues: 89.0063 Evaluate side-chains 199 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0681 time to fit residues: 1.3523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 212 GLN F 127 HIS ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN F 346 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7953 Z= 0.185 Angle : 1.023 24.890 10748 Z= 0.437 Chirality : 0.093 2.176 1280 Planarity : 0.006 0.062 1303 Dihedral : 13.764 96.000 1186 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.83 % Favored : 91.96 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.22), residues: 945 helix: -3.06 (0.18), residues: 478 sheet: -3.05 (0.56), residues: 69 loop : -3.33 (0.27), residues: 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 222 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 238 average time/residue: 0.1957 time to fit residues: 61.7334 Evaluate side-chains 219 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 199 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0724 time to fit residues: 3.7084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN A 195 HIS A 214 HIS B 85 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN F 46 ASN F 116 ASN F 335 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 7953 Z= 0.194 Angle : 0.932 25.575 10748 Z= 0.399 Chirality : 0.092 2.159 1280 Planarity : 0.005 0.063 1303 Dihedral : 13.204 98.626 1186 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.25 % Favored : 91.64 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.24), residues: 945 helix: -2.19 (0.21), residues: 471 sheet: -2.88 (0.57), residues: 69 loop : -3.13 (0.27), residues: 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 231 average time/residue: 0.2038 time to fit residues: 62.3016 Evaluate side-chains 207 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0740 time to fit residues: 2.4919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 7953 Z= 0.313 Angle : 0.966 25.415 10748 Z= 0.421 Chirality : 0.093 2.150 1280 Planarity : 0.005 0.058 1303 Dihedral : 13.136 106.371 1186 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.10 % Favored : 90.79 % Rotamer Outliers : 4.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.25), residues: 945 helix: -1.73 (0.22), residues: 477 sheet: -2.72 (0.57), residues: 69 loop : -2.87 (0.29), residues: 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 205 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 223 average time/residue: 0.2072 time to fit residues: 61.9041 Evaluate side-chains 217 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 193 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1055 time to fit residues: 5.1696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.0470 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.110 7953 Z= 0.177 Angle : 0.905 25.558 10748 Z= 0.387 Chirality : 0.091 2.146 1280 Planarity : 0.005 0.077 1303 Dihedral : 12.830 96.141 1186 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.04 % Favored : 91.85 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.26), residues: 945 helix: -1.33 (0.23), residues: 463 sheet: -2.62 (0.54), residues: 79 loop : -2.75 (0.29), residues: 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 211 time to evaluate : 0.969 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 220 average time/residue: 0.2071 time to fit residues: 60.8582 Evaluate side-chains 203 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0871 time to fit residues: 2.3635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 9.9990 chunk 80 optimal weight: 0.0010 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 89 optimal weight: 0.4980 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.117 7953 Z= 0.232 Angle : 0.909 25.402 10748 Z= 0.389 Chirality : 0.092 2.147 1280 Planarity : 0.005 0.059 1303 Dihedral : 12.563 93.418 1186 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.78 % Favored : 91.11 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.26), residues: 945 helix: -1.09 (0.23), residues: 487 sheet: -2.44 (0.58), residues: 69 loop : -2.77 (0.30), residues: 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 217 average time/residue: 0.2101 time to fit residues: 60.3098 Evaluate side-chains 209 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 199 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0706 time to fit residues: 2.4474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 136 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.136 7953 Z= 0.196 Angle : 0.911 25.432 10748 Z= 0.389 Chirality : 0.092 2.147 1280 Planarity : 0.005 0.063 1303 Dihedral : 12.279 87.937 1186 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.51 % Favored : 92.38 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.27), residues: 945 helix: -0.78 (0.24), residues: 475 sheet: -2.39 (0.54), residues: 79 loop : -2.58 (0.31), residues: 391 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 212 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 218 average time/residue: 0.1992 time to fit residues: 57.6474 Evaluate side-chains 204 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 199 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0813 time to fit residues: 1.9489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 85 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.156 7953 Z= 0.210 Angle : 0.914 25.373 10748 Z= 0.390 Chirality : 0.092 2.148 1280 Planarity : 0.005 0.065 1303 Dihedral : 12.074 89.049 1186 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.25 % Favored : 91.64 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.27), residues: 945 helix: -0.61 (0.24), residues: 475 sheet: -2.20 (0.55), residues: 79 loop : -2.57 (0.30), residues: 391 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 210 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 217 average time/residue: 0.2043 time to fit residues: 59.3109 Evaluate side-chains 210 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 202 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0773 time to fit residues: 2.2067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 36 optimal weight: 0.0270 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 0.0000 chunk 88 optimal weight: 0.8980 overall best weight: 1.1846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 85 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.177 7953 Z= 0.215 Angle : 0.918 25.451 10748 Z= 0.393 Chirality : 0.092 2.148 1280 Planarity : 0.005 0.080 1303 Dihedral : 11.961 89.455 1186 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.83 % Favored : 92.06 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.27), residues: 945 helix: -0.57 (0.24), residues: 481 sheet: -2.09 (0.56), residues: 79 loop : -2.55 (0.31), residues: 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 205 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 207 average time/residue: 0.2052 time to fit residues: 56.4994 Evaluate side-chains 202 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 200 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0675 time to fit residues: 1.4379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.141 7953 Z= 0.191 Angle : 0.917 25.387 10748 Z= 0.388 Chirality : 0.091 2.147 1280 Planarity : 0.005 0.067 1303 Dihedral : 11.780 88.502 1186 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.83 % Favored : 92.06 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.27), residues: 945 helix: -0.50 (0.24), residues: 480 sheet: -1.91 (0.58), residues: 79 loop : -2.55 (0.31), residues: 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 207 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 210 average time/residue: 0.1980 time to fit residues: 55.6020 Evaluate side-chains 197 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0844 time to fit residues: 1.8112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.106269 restraints weight = 12423.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109819 restraints weight = 6827.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112156 restraints weight = 4558.884| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.123 7953 Z= 0.185 Angle : 0.927 25.448 10748 Z= 0.396 Chirality : 0.092 2.147 1280 Planarity : 0.005 0.105 1303 Dihedral : 11.473 87.151 1186 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.30 % Favored : 92.59 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.27), residues: 945 helix: -0.48 (0.24), residues: 488 sheet: -1.63 (0.60), residues: 79 loop : -2.57 (0.31), residues: 378 =============================================================================== Job complete usr+sys time: 1810.88 seconds wall clock time: 33 minutes 22.63 seconds (2002.63 seconds total)