Starting phenix.real_space_refine on Fri Dec 8 11:10:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/12_2023/6s8h_10122_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/12_2023/6s8h_10122.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/12_2023/6s8h_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_10122/12_2023/6s8h_10122_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/12_2023/6s8h_10122_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/12_2023/6s8h_10122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/12_2023/6s8h_10122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/12_2023/6s8h_10122_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/12_2023/6s8h_10122_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 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. 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-1.21rc1-5172/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: {'DCQ': 1, 'JSG': 1, 'LMN': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 21 Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {'DCQ': 1, 'LMN': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 25 Time building chain proxies: 4.78, per 1000 atoms: 0.61 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 1.6 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: 1.31 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: 1.78 Time building geometry restraints manager: 3.42 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 1.621 1.340 0.281 2.00e-02 2.50e+03 1.97e+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=" CAN JSG F 402 " pdb=" CAP JSG F 402 " ideal model delta sigma weight residual 1.419 1.565 -0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" C2 DCQ F 403 " pdb=" C3 DCQ F 403 " ideal model delta sigma weight residual 1.485 1.375 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" CEE JSG F 402 " pdb=" OAQ JSG F 402 " ideal model delta sigma weight residual 1.469 1.360 0.109 2.00e-02 2.50e+03 2.98e+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=" 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=" CBJ LMN F 401 " pdb=" CBL LMN F 401 " pdb=" CBR LMN F 401 " ideal model delta sigma weight residual 112.20 135.02 -22.82 3.00e+00 1.11e-01 5.78e+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 angle pdb=" C3 DCQ F 403 " pdb=" O3 DCQ F 403 " pdb=" C3M DCQ F 403 " ideal model delta sigma weight residual 115.29 137.13 -21.84 3.00e+00 1.11e-01 5.30e+01 ... (remaining 10743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 4540 25.74 - 51.47: 281 51.47 - 77.21: 35 77.21 - 102.94: 16 102.94 - 128.68: 4 Dihedral angle restraints: 4876 sinusoidal: 2125 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 4873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.000: 1277 1.000 - 2.001: 2 2.001 - 3.001: 0 3.001 - 4.001: 0 4.001 - 5.002: 1 Chirality restraints: 1280 Sorted by residual: 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 2.42 -2.59 5.00 2.00e-01 2.50e+01 6.25e+02 chirality pdb=" CBG JSG F 402 " pdb=" CBE JSG F 402 " pdb=" CBI JSG F 402 " pdb=" OBH JSG F 402 " both_signs ideal model delta sigma weight residual False -2.55 -1.20 -1.35 2.00e-01 2.50e+01 4.53e+01 chirality pdb=" CEW JSG F 402 " pdb=" C8 JSG F 402 " pdb=" CEX JSG F 402 " pdb=" OFJ JSG F 402 " both_signs ideal model delta sigma weight residual False -2.61 -1.58 -1.03 2.00e-01 2.50e+01 2.65e+01 ... (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 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.670 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.600 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 29.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 0.281 7953 Z= 0.696 Angle : 1.653 24.381 10748 Z= 0.726 Chirality : 0.164 5.002 1280 Planarity : 0.008 0.080 1303 Dihedral : 17.584 128.679 3102 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 % Allowed : 10.29 % Favored : 89.59 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 119 HIS 0.007 0.002 HIS F 89 PHE 0.026 0.002 PHE G 280 TYR 0.019 0.002 TYR A 234 ARG 0.006 0.000 ARG A 150 *********************** 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 : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 300 average time/residue: 0.2424 time to fit residues: 92.6115 Evaluate side-chains 199 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0642 time to fit residues: 1.2421 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.0770 chunk 84 optimal weight: 9.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8179 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7953 Z= 0.183 Angle : 0.832 11.904 10748 Z= 0.387 Chirality : 0.045 0.311 1280 Planarity : 0.006 0.062 1303 Dihedral : 14.554 135.821 1333 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.83 % Favored : 91.96 % Rotamer: Outliers : 3.72 % Allowed : 19.21 % Favored : 77.08 % 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: -4.87 (0.22), residues: 945 helix: -3.07 (0.18), residues: 478 sheet: -3.04 (0.56), residues: 69 loop : -3.33 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 119 HIS 0.003 0.001 HIS B 218 PHE 0.014 0.001 PHE G 348 TYR 0.015 0.001 TYR G 135 ARG 0.006 0.000 ARG B 178 *********************** 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 255 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 225 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 21 residues processed: 243 average time/residue: 0.2079 time to fit residues: 66.7209 Evaluate side-chains 224 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0820 time to fit residues: 4.2939 ------------------------------------------------------------------------------- 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: 0.8980 chunk 26 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 83 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8179 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7953 Z= 0.167 Angle : 0.711 9.167 10748 Z= 0.339 Chirality : 0.044 0.294 1280 Planarity : 0.005 0.061 1303 Dihedral : 13.378 134.094 1333 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.83 % Favored : 92.06 % Rotamer: Outliers : 2.97 % Allowed : 23.42 % Favored : 73.61 % 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: -3.95 (0.24), residues: 945 helix: -2.15 (0.22), residues: 471 sheet: -2.82 (0.53), residues: 79 loop : -3.06 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 276 HIS 0.004 0.001 HIS F 89 PHE 0.010 0.001 PHE G 280 TYR 0.011 0.001 TYR B 96 ARG 0.006 0.000 ARG F 33 *********************** 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 238 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 214 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 229 average time/residue: 0.2184 time to fit residues: 66.3805 Evaluate side-chains 206 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0751 time to fit residues: 2.3093 ------------------------------------------------------------------------------- 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: 7.9990 chunk 63 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 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: 0.8331 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 7953 Z= 0.469 Angle : 0.856 10.090 10748 Z= 0.416 Chirality : 0.051 0.292 1280 Planarity : 0.005 0.059 1303 Dihedral : 13.828 107.092 1333 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.79 % Favored : 89.10 % Rotamer: Outliers : 5.45 % Allowed : 24.29 % Favored : 70.26 % 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: -3.68 (0.25), residues: 945 helix: -1.95 (0.21), residues: 505 sheet: -2.82 (0.57), residues: 69 loop : -2.92 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 119 HIS 0.006 0.001 HIS F 89 PHE 0.024 0.002 PHE G 280 TYR 0.013 0.002 TYR B 82 ARG 0.006 0.001 ARG F 33 *********************** 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 242 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 0.919 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 29 residues processed: 221 average time/residue: 0.2205 time to fit residues: 64.4002 Evaluate side-chains 218 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1002 time to fit residues: 5.8696 ------------------------------------------------------------------------------- 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: 0.7980 chunk 51 optimal weight: 7.9990 chunk 1 optimal weight: 0.0070 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 136 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: 0.8213 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7953 Z= 0.156 Angle : 0.698 9.384 10748 Z= 0.336 Chirality : 0.043 0.253 1280 Planarity : 0.005 0.055 1303 Dihedral : 13.208 96.330 1333 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.62 % Favored : 92.28 % Rotamer: Outliers : 2.23 % Allowed : 26.52 % Favored : 71.25 % 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: -3.01 (0.26), residues: 945 helix: -1.32 (0.23), residues: 472 sheet: -2.57 (0.58), residues: 69 loop : -2.65 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 255 HIS 0.002 0.001 HIS F 89 PHE 0.012 0.001 PHE G 280 TYR 0.017 0.001 TYR B 234 ARG 0.005 0.000 ARG F 33 *********************** 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: 18 poor density : 209 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 219 average time/residue: 0.2367 time to fit residues: 68.8526 Evaluate side-chains 205 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 197 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1044 time to fit residues: 2.8709 ------------------------------------------------------------------------------- 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: 5.9990 chunk 80 optimal weight: 0.4980 chunk 17 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7953 Z= 0.189 Angle : 0.703 10.157 10748 Z= 0.336 Chirality : 0.044 0.237 1280 Planarity : 0.005 0.054 1303 Dihedral : 13.070 86.725 1333 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.47 % Favored : 91.43 % Rotamer: Outliers : 2.23 % Allowed : 27.88 % Favored : 69.89 % 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: -2.78 (0.26), residues: 945 helix: -1.05 (0.23), residues: 480 sheet: -2.52 (0.54), residues: 79 loop : -2.66 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 276 HIS 0.004 0.001 HIS F 89 PHE 0.018 0.001 PHE G 280 TYR 0.011 0.001 TYR B 96 ARG 0.004 0.000 ARG F 33 *********************** 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 225 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 207 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 219 average time/residue: 0.2154 time to fit residues: 62.3967 Evaluate side-chains 208 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0829 time to fit residues: 2.4192 ------------------------------------------------------------------------------- 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: 4.9990 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 0.0870 overall best weight: 1.2562 ------------------------------------------------------------------------------- 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 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: 0.8220 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7953 Z= 0.184 Angle : 0.688 9.126 10748 Z= 0.330 Chirality : 0.044 0.240 1280 Planarity : 0.004 0.054 1303 Dihedral : 12.803 83.392 1333 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.72 % Favored : 92.17 % Rotamer: Outliers : 1.36 % Allowed : 29.24 % Favored : 69.39 % 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: -2.40 (0.27), residues: 945 helix: -0.72 (0.24), residues: 474 sheet: -2.21 (0.59), residues: 69 loop : -2.53 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 255 HIS 0.004 0.001 HIS F 89 PHE 0.008 0.001 PHE G 280 TYR 0.012 0.001 TYR A 96 ARG 0.004 0.000 ARG F 33 *********************** 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 219 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 213 average time/residue: 0.2168 time to fit residues: 60.9421 Evaluate side-chains 204 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 200 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0773 time to fit residues: 1.7557 ------------------------------------------------------------------------------- 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: 7.9990 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** 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: 0.8201 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7953 Z= 0.162 Angle : 0.677 8.882 10748 Z= 0.322 Chirality : 0.043 0.239 1280 Planarity : 0.004 0.053 1303 Dihedral : 12.307 81.528 1333 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.41 % Favored : 92.49 % Rotamer: Outliers : 1.24 % Allowed : 29.37 % Favored : 69.39 % 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: -2.25 (0.27), residues: 945 helix: -0.63 (0.24), residues: 481 sheet: -2.10 (0.56), residues: 79 loop : -2.43 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 276 HIS 0.003 0.001 HIS F 89 PHE 0.020 0.001 PHE G 280 TYR 0.013 0.001 TYR B 96 ARG 0.004 0.000 ARG F 33 *********************** 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 219 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 0.862 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 215 average time/residue: 0.2206 time to fit residues: 62.5524 Evaluate side-chains 207 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 202 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0768 time to fit residues: 1.8202 ------------------------------------------------------------------------------- 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: 4.9990 chunk 83 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 ** 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: 0.8250 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7953 Z= 0.256 Angle : 0.738 14.210 10748 Z= 0.347 Chirality : 0.045 0.245 1280 Planarity : 0.005 0.052 1303 Dihedral : 12.228 81.137 1333 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.25 % Favored : 91.64 % Rotamer: Outliers : 1.36 % Allowed : 31.10 % Favored : 67.53 % 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 (0.28), residues: 945 helix: -0.53 (0.24), residues: 481 sheet: -1.82 (0.62), residues: 69 loop : -2.40 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 255 HIS 0.005 0.001 HIS F 89 PHE 0.012 0.001 PHE A 90 TYR 0.014 0.001 TYR A 96 ARG 0.004 0.000 ARG G 86 *********************** 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 218 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 207 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 214 average time/residue: 0.2175 time to fit residues: 61.4924 Evaluate side-chains 206 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 200 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0757 time to fit residues: 1.8785 ------------------------------------------------------------------------------- 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: 0.6980 chunk 41 optimal weight: 0.0010 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 58 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7953 Z= 0.152 Angle : 0.692 12.146 10748 Z= 0.324 Chirality : 0.042 0.239 1280 Planarity : 0.004 0.052 1303 Dihedral : 11.723 78.989 1333 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.30 % Favored : 92.59 % Rotamer: Outliers : 0.37 % Allowed : 32.22 % Favored : 67.41 % 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: -1.89 (0.28), residues: 945 helix: -0.29 (0.24), residues: 475 sheet: -1.75 (0.58), residues: 79 loop : -2.32 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 255 HIS 0.002 0.001 HIS F 89 PHE 0.008 0.001 PHE B 239 TYR 0.008 0.001 TYR A 96 ARG 0.005 0.000 ARG F 33 ********************** 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: 3 poor density : 210 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 212 average time/residue: 0.2288 time to fit residues: 64.2347 Evaluate side-chains 201 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 198 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1081 time to fit residues: 1.6399 ------------------------------------------------------------------------------- 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: 3.9990 chunk 68 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104544 restraints weight = 12610.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108042 restraints weight = 6894.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110367 restraints weight = 4601.792| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7953 Z= 0.164 Angle : 0.711 11.784 10748 Z= 0.332 Chirality : 0.043 0.266 1280 Planarity : 0.004 0.052 1303 Dihedral : 11.487 79.352 1333 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.51 % Favored : 92.38 % Rotamer: Outliers : 0.25 % Allowed : 32.71 % Favored : 67.04 % 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: -1.84 (0.28), residues: 945 helix: -0.23 (0.24), residues: 485 sheet: -1.64 (0.59), residues: 79 loop : -2.40 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 255 HIS 0.003 0.000 HIS F 89 PHE 0.009 0.001 PHE F 310 TYR 0.016 0.001 TYR A 96 ARG 0.005 0.000 ARG A 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1928.36 seconds wall clock time: 35 minutes 45.48 seconds (2145.48 seconds total)