Starting phenix.real_space_refine (version: dev) on Tue Apr 5 04:49:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew7_31349/04_2022/7ew7_31349_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew7_31349/04_2022/7ew7_31349.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew7_31349/04_2022/7ew7_31349_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew7_31349/04_2022/7ew7_31349_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew7_31349/04_2022/7ew7_31349_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew7_31349/04_2022/7ew7_31349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew7_31349/04_2022/7ew7_31349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew7_31349/04_2022/7ew7_31349_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew7_31349/04_2022/7ew7_31349_updated.pdb" } resolution = 3.27 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= 0.003 sd= 0.082 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 238": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 9004 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1838 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2297 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 6, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'JEX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.58, per 1000 atoms: 0.62 Number of scatterers: 9004 At special positions: 0 Unit cell: (96.05, 119.85, 133.45, 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 65 16.00 F 6 9.00 O 1670 8.00 N 1520 7.00 C 5743 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 287 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.5 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 14 sheets defined 32.7% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 9 through 27 removed outlier: 3.600A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 210 through 215 removed outlier: 4.349A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.872A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 removed outlier: 4.008A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 350 Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 22 Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.694A pdb=" N ALA C 45 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 32 removed outlier: 3.703A pdb=" N ARG D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 72 removed outlier: 3.854A pdb=" N VAL D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 104 removed outlier: 4.201A pdb=" N ILE D 84 " --> pdb=" O TYR D 81 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 104 " --> pdb=" O ASN D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 110 removed outlier: 4.272A pdb=" N TYR D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 110' Processing helix chain 'D' and resid 114 through 147 removed outlier: 4.101A pdb=" N MET D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 180 removed outlier: 3.956A pdb=" N LEU D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 200 through 234 removed outlier: 3.647A pdb=" N LEU D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 208 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 209 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 281 removed outlier: 3.514A pdb=" N ALA D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Proline residue: D 271 - end of helix Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 298 through 312 Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 316 through 324 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.006A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.618A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.385A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.679A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.978A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.594A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.732A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.734A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.528A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.782A pdb=" N THR E 118 " --> pdb=" O VAL E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 92 through 99 removed outlier: 3.562A pdb=" N TRP E 36 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 7.013A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.620A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 225 through 231 removed outlier: 5.904A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1727 1.33 - 1.45: 2319 1.45 - 1.57: 5046 1.57 - 1.69: 0 1.69 - 1.82: 93 Bond restraints: 9185 Sorted by residual: bond pdb=" C06 JEX D 401 " pdb=" C07 JEX D 401 " ideal model delta sigma weight residual 1.596 1.391 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C05 JEX D 401 " pdb=" S04 JEX D 401 " ideal model delta sigma weight residual 1.555 1.708 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C17 JEX D 401 " pdb=" C19 JEX D 401 " ideal model delta sigma weight residual 1.528 1.377 0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" C03 JEX D 401 " pdb=" S04 JEX D 401 " ideal model delta sigma weight residual 1.555 1.705 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" C07 JEX D 401 " pdb=" C08 JEX D 401 " ideal model delta sigma weight residual 1.527 1.383 0.144 2.00e-02 2.50e+03 5.19e+01 ... (remaining 9180 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.03: 110 105.03 - 112.28: 4721 112.28 - 119.52: 2836 119.52 - 126.76: 4638 126.76 - 134.00: 127 Bond angle restraints: 12432 Sorted by residual: angle pdb=" N LYS D 150 " pdb=" CA LYS D 150 " pdb=" C LYS D 150 " ideal model delta sigma weight residual 111.36 119.73 -8.37 1.09e+00 8.42e-01 5.89e+01 angle pdb=" N ASN D 153 " pdb=" CA ASN D 153 " pdb=" C ASN D 153 " ideal model delta sigma weight residual 111.28 119.24 -7.96 1.09e+00 8.42e-01 5.33e+01 angle pdb=" N LEU D 147 " pdb=" CA LEU D 147 " pdb=" C LEU D 147 " ideal model delta sigma weight residual 111.07 116.80 -5.73 1.07e+00 8.73e-01 2.87e+01 angle pdb=" N HIS D 152 " pdb=" CA HIS D 152 " pdb=" C HIS D 152 " ideal model delta sigma weight residual 108.75 117.66 -8.91 1.71e+00 3.42e-01 2.71e+01 angle pdb=" N SER D 49 " pdb=" CA SER D 49 " pdb=" C SER D 49 " ideal model delta sigma weight residual 111.11 116.18 -5.07 1.20e+00 6.94e-01 1.79e+01 ... (remaining 12427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4934 17.84 - 35.68: 421 35.68 - 53.52: 74 53.52 - 71.36: 13 71.36 - 89.20: 7 Dihedral angle restraints: 5449 sinusoidal: 2129 harmonic: 3320 Sorted by residual: dihedral pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " pdb=" SG CYS D 191 " pdb=" CB CYS D 191 " ideal model delta sinusoidal sigma weight residual -86.00 -126.75 40.75 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" C HIS D 152 " pdb=" N HIS D 152 " pdb=" CA HIS D 152 " pdb=" CB HIS D 152 " ideal model delta harmonic sigma weight residual -122.60 -131.63 9.03 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" N HIS D 152 " pdb=" C HIS D 152 " pdb=" CA HIS D 152 " pdb=" CB HIS D 152 " ideal model delta harmonic sigma weight residual 122.80 131.74 -8.94 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 5446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1322 0.079 - 0.157: 92 0.157 - 0.236: 3 0.236 - 0.314: 2 0.314 - 0.393: 3 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA HIS D 152 " pdb=" N HIS D 152 " pdb=" C HIS D 152 " pdb=" CB HIS D 152 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA LYS D 150 " pdb=" N LYS D 150 " pdb=" C LYS D 150 " pdb=" CB LYS D 150 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA ASN D 153 " pdb=" N ASN D 153 " pdb=" C ASN D 153 " pdb=" CB ASN D 153 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 1419 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 JEX D 401 " -0.010 2.00e-02 2.50e+03 1.79e-02 6.44e+00 pdb=" C03 JEX D 401 " -0.003 2.00e-02 2.50e+03 pdb=" C05 JEX D 401 " 0.033 2.00e-02 2.50e+03 pdb=" C06 JEX D 401 " 0.008 2.00e-02 2.50e+03 pdb=" C07 JEX D 401 " 0.004 2.00e-02 2.50e+03 pdb=" C08 JEX D 401 " -0.008 2.00e-02 2.50e+03 pdb=" C14 JEX D 401 " -0.034 2.00e-02 2.50e+03 pdb=" S04 JEX D 401 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 JEX D 401 " -0.025 2.00e-02 2.50e+03 1.81e-02 5.71e+00 pdb=" C14 JEX D 401 " 0.039 2.00e-02 2.50e+03 pdb=" C17 JEX D 401 " -0.003 2.00e-02 2.50e+03 pdb=" C19 JEX D 401 " -0.005 2.00e-02 2.50e+03 pdb=" N16 JEX D 401 " -0.005 2.00e-02 2.50e+03 pdb=" N18 JEX D 401 " 0.003 2.00e-02 2.50e+03 pdb=" O15 JEX D 401 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 150 " 0.010 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C LYS D 150 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS D 150 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU D 151 " 0.013 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 70 2.59 - 3.17: 7257 3.17 - 3.75: 13119 3.75 - 4.32: 17306 4.32 - 4.90: 30221 Nonbonded interactions: 67973 Sorted by model distance: nonbonded pdb=" O SER D 232 " pdb=" OG1 THR D 236 " model vdw 2.016 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.218 2.440 nonbonded pdb=" OG SER E 17 " pdb=" O MET E 83 " model vdw 2.222 2.440 nonbonded pdb=" O LEU D 278 " pdb=" N CYS D 282 " model vdw 2.256 2.520 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.275 2.440 ... (remaining 67968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 65 5.16 5 C 5743 2.51 5 N 1520 2.21 5 O 1670 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 4.410 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 27.770 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 : 0.005 0.205 9185 Z= 0.302 Angle : 0.578 9.777 12432 Z= 0.340 Chirality : 0.044 0.393 1422 Planarity : 0.003 0.050 1553 Dihedral : 13.569 89.196 3298 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.71 % 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: -2.17 (0.23), residues: 1126 helix: 0.10 (0.25), residues: 380 sheet: -1.53 (0.31), residues: 265 loop : -2.66 (0.22), residues: 481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 1.100 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 176 average time/residue: 0.2521 time to fit residues: 58.6470 Evaluate side-chains 131 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0887 time to fit residues: 2.2838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.0050 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 241 ASN A 294 ASN A 333 GLN B 75 GLN B 220 GLN B 239 ASN C 11 GLN D 116 GLN D 183 ASN D 303 ASN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 9185 Z= 0.154 Angle : 0.515 13.702 12432 Z= 0.264 Chirality : 0.040 0.150 1422 Planarity : 0.005 0.096 1553 Dihedral : 3.628 47.609 1240 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.73 % 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: -1.19 (0.24), residues: 1126 helix: 1.29 (0.27), residues: 376 sheet: -1.16 (0.33), residues: 240 loop : -2.26 (0.23), residues: 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 139 average time/residue: 0.2033 time to fit residues: 40.3722 Evaluate side-chains 129 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0883 time to fit residues: 3.4732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 9185 Z= 0.279 Angle : 0.557 9.938 12432 Z= 0.293 Chirality : 0.043 0.209 1422 Planarity : 0.005 0.068 1553 Dihedral : 4.018 47.423 1240 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 2.13 % 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: -1.05 (0.24), residues: 1126 helix: 1.49 (0.27), residues: 368 sheet: -1.04 (0.33), residues: 254 loop : -2.25 (0.23), residues: 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 19 residues processed: 132 average time/residue: 0.2073 time to fit residues: 38.5117 Evaluate side-chains 134 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0850 time to fit residues: 4.4385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 0.0470 chunk 102 optimal weight: 30.0000 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 295 ASN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 9185 Z= 0.167 Angle : 0.496 9.221 12432 Z= 0.258 Chirality : 0.040 0.181 1422 Planarity : 0.004 0.057 1553 Dihedral : 3.834 46.677 1240 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 1.22 % 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: -0.76 (0.25), residues: 1126 helix: 1.83 (0.28), residues: 368 sheet: -0.84 (0.33), residues: 251 loop : -2.17 (0.23), residues: 507 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 127 average time/residue: 0.2275 time to fit residues: 40.2853 Evaluate side-chains 115 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0871 time to fit residues: 2.8177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 9185 Z= 0.313 Angle : 0.568 7.478 12432 Z= 0.300 Chirality : 0.043 0.217 1422 Planarity : 0.004 0.054 1553 Dihedral : 4.190 47.542 1240 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 1.42 % 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: -0.85 (0.25), residues: 1126 helix: 1.81 (0.28), residues: 365 sheet: -1.02 (0.33), residues: 258 loop : -2.18 (0.24), residues: 503 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.110 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 132 average time/residue: 0.2096 time to fit residues: 38.8980 Evaluate side-chains 118 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0799 time to fit residues: 2.5636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 16 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9185 Z= 0.135 Angle : 0.501 8.379 12432 Z= 0.258 Chirality : 0.040 0.160 1422 Planarity : 0.004 0.050 1553 Dihedral : 3.889 46.935 1240 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 1.42 % 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: -0.53 (0.25), residues: 1126 helix: 2.01 (0.28), residues: 372 sheet: -0.72 (0.33), residues: 263 loop : -2.08 (0.24), residues: 491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.074 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 124 average time/residue: 0.2042 time to fit residues: 36.0785 Evaluate side-chains 118 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0979 time to fit residues: 3.0159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.0670 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 16 ASN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9185 Z= 0.226 Angle : 0.533 7.971 12432 Z= 0.278 Chirality : 0.041 0.168 1422 Planarity : 0.004 0.056 1553 Dihedral : 3.967 47.264 1240 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 1.52 % 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: -0.56 (0.25), residues: 1126 helix: 2.14 (0.28), residues: 362 sheet: -0.81 (0.33), residues: 265 loop : -2.11 (0.24), residues: 499 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.218 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 126 average time/residue: 0.2026 time to fit residues: 36.4329 Evaluate side-chains 121 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0844 time to fit residues: 2.9292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.0030 chunk 73 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9185 Z= 0.152 Angle : 0.510 9.162 12432 Z= 0.263 Chirality : 0.040 0.194 1422 Planarity : 0.004 0.050 1553 Dihedral : 3.879 46.668 1240 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.81 % 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: -0.47 (0.25), residues: 1126 helix: 2.09 (0.28), residues: 372 sheet: -0.74 (0.33), residues: 265 loop : -2.04 (0.25), residues: 489 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.171 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 118 average time/residue: 0.2004 time to fit residues: 33.4840 Evaluate side-chains 110 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0675 time to fit residues: 1.5247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.0020 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9185 Z= 0.149 Angle : 0.532 14.886 12432 Z= 0.264 Chirality : 0.040 0.196 1422 Planarity : 0.004 0.054 1553 Dihedral : 3.794 46.279 1240 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.20 % 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: -0.42 (0.25), residues: 1126 helix: 2.15 (0.28), residues: 369 sheet: -0.72 (0.32), residues: 267 loop : -2.00 (0.25), residues: 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 1.092 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 112 average time/residue: 0.2047 time to fit residues: 32.7597 Evaluate side-chains 110 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0902 time to fit residues: 1.6491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.121 9185 Z= 0.227 Angle : 0.565 15.079 12432 Z= 0.289 Chirality : 0.041 0.220 1422 Planarity : 0.005 0.122 1553 Dihedral : 3.934 46.229 1240 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.30 % 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: -0.49 (0.25), residues: 1126 helix: 2.07 (0.28), residues: 372 sheet: -0.76 (0.32), residues: 266 loop : -2.05 (0.25), residues: 488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 1.198 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 112 average time/residue: 0.2005 time to fit residues: 32.2872 Evaluate side-chains 112 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0823 time to fit residues: 1.8791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 37 optimal weight: 0.0000 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.0020 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 259 GLN ** 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 = 0.4391 r_free = 0.4391 target = 0.191320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.140618 restraints weight = 10381.610| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 3.25 r_work: 0.3851 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work: 0.3810 rms_B_bonded: 2.97 restraints_weight: 0.1250 r_work: 0.3790 rms_B_bonded: 3.05 restraints_weight: 0.0625 r_work: 0.3770 rms_B_bonded: 3.18 restraints_weight: 0.0312 r_work: 0.3748 rms_B_bonded: 3.34 restraints_weight: 0.0156 r_work: 0.3726 rms_B_bonded: 3.55 restraints_weight: 0.0078 r_work: 0.3701 rms_B_bonded: 3.81 restraints_weight: 0.0039 r_work: 0.3676 rms_B_bonded: 4.11 restraints_weight: 0.0020 r_work: 0.3648 rms_B_bonded: 4.47 restraints_weight: 0.0010 r_work: 0.3618 rms_B_bonded: 4.89 restraints_weight: 0.0005 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.113 9185 Z= 0.181 Angle : 0.539 14.591 12432 Z= 0.272 Chirality : 0.040 0.202 1422 Planarity : 0.004 0.103 1553 Dihedral : 3.812 45.561 1240 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.61 % 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: -0.44 (0.25), residues: 1126 helix: 2.07 (0.28), residues: 375 sheet: -0.74 (0.33), residues: 260 loop : -1.99 (0.25), residues: 491 =============================================================================== Job complete usr+sys time: 1941.17 seconds wall clock time: 35 minutes 58.47 seconds (2158.47 seconds total)