Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 04:38:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcq_34663/04_2023/8hcq_34663_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcq_34663/04_2023/8hcq_34663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcq_34663/04_2023/8hcq_34663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcq_34663/04_2023/8hcq_34663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcq_34663/04_2023/8hcq_34663_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcq_34663/04_2023/8hcq_34663_neut.pdb" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5725 2.51 5 N 1526 2.21 5 O 1673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "L PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 335": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8991 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1687 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 199} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2591 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1769 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 410 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "R" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2363 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Time building chain proxies: 5.24, per 1000 atoms: 0.58 Number of scatterers: 8991 At special positions: 0 Unit cell: (107.944, 112.888, 126.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1673 8.00 N 1526 7.00 C 5725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " 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: 3.47 Conformation dependent library (CDL) restraints added in 1.5 seconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 36.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.560A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.539A pdb=" N ALA A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 296 through 316 removed outlier: 3.989A pdb=" N THR A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 301 " --> pdb=" O PRO A 297 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 removed outlier: 3.558A pdb=" N LEU A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 355 " --> pdb=" O MET A 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 13 through 31 removed outlier: 3.521A pdb=" N GLU B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.997A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 7 through 25 removed outlier: 4.406A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.610A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 18 removed outlier: 3.726A pdb=" N VAL L 12 " --> pdb=" O ASP L 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 109 removed outlier: 3.529A pdb=" N TYR R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE R 86 " --> pdb=" O ILE R 82 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL R 96 " --> pdb=" O ILE R 92 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS R 109 " --> pdb=" O ILE R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 143 Proline residue: R 135 - end of helix removed outlier: 3.516A pdb=" N PHE R 139 " --> pdb=" O PRO R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 159 removed outlier: 3.806A pdb=" N VAL R 155 " --> pdb=" O ASN R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 189 Processing helix chain 'R' and resid 199 through 222 removed outlier: 3.678A pdb=" N VAL R 207 " --> pdb=" O ALA R 203 " (cutoff:3.500A) Proline residue: R 219 - end of helix removed outlier: 3.971A pdb=" N ILE R 222 " --> pdb=" O ILE R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 253 Processing helix chain 'R' and resid 254 through 264 Processing helix chain 'R' and resid 264 through 283 removed outlier: 3.836A pdb=" N VAL R 269 " --> pdb=" O CYS R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 330 Proline residue: R 321 - end of helix removed outlier: 3.783A pdb=" N ARG R 326 " --> pdb=" O LEU R 322 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS R 330 " --> pdb=" O ARG R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 373 removed outlier: 3.812A pdb=" N LEU R 343 " --> pdb=" O ASN R 339 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU R 344 " --> pdb=" O ARG R 340 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE R 346 " --> pdb=" O GLU R 342 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 3.792A pdb=" N LEU R 369 " --> pdb=" O ASN R 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 189 removed outlier: 4.525A pdb=" N PHE A 187 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ARG A 35 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ILE A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 37 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 222 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 39 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A 219 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A 255 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 221 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL A 252 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N HIS A 327 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU A 254 " --> pdb=" O HIS A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56 removed outlier: 6.717A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.930A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 93 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.924A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.970A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.776A pdb=" N ALA B 236 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 257 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 281 through 283 removed outlier: 3.579A pdb=" N ALA B 292 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.860A pdb=" N THR E 68 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.869A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR E 93 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.869A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR E 93 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 97 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.076A pdb=" N VAL E 147 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 230 through 231 removed outlier: 4.079A pdb=" N TYR R 231 " --> pdb=" O GLU R 234 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU R 234 " --> pdb=" O TYR R 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 402 hydrogen bonds defined for protein. 1140 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: 2.47 Time building geometry restraints manager: 3.74 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: 2904 1.34 - 1.46: 2087 1.46 - 1.58: 4095 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 9180 Sorted by residual: bond pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 1.457 1.506 -0.048 1.29e-02 6.01e+03 1.41e+01 bond pdb=" N LYS R 377 " pdb=" CA LYS R 377 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.22e-02 6.72e+03 6.33e+00 bond pdb=" C MET R 266 " pdb=" N PRO R 267 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.20e-02 6.94e+03 4.79e+00 bond pdb=" N MET E 92 " pdb=" CA MET E 92 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.29e-02 6.01e+03 3.22e+00 bond pdb=" C MET E 92 " pdb=" N TYR E 93 " ideal model delta sigma weight residual 1.330 1.310 0.019 1.32e-02 5.74e+03 2.17e+00 ... (remaining 9175 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.35: 192 106.35 - 113.26: 4901 113.26 - 120.18: 3184 120.18 - 127.09: 4079 127.09 - 134.01: 94 Bond angle restraints: 12450 Sorted by residual: angle pdb=" C ARG R 340 " pdb=" CA ARG R 340 " pdb=" CB ARG R 340 " ideal model delta sigma weight residual 116.34 110.69 5.65 1.40e+00 5.10e-01 1.63e+01 angle pdb=" C SER L 4 " pdb=" N SER L 5 " pdb=" CA SER L 5 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" CA MET R 266 " pdb=" CB MET R 266 " pdb=" CG MET R 266 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA LEU G 15 " pdb=" CB LEU G 15 " pdb=" CG LEU G 15 " ideal model delta sigma weight residual 116.30 129.15 -12.85 3.50e+00 8.16e-02 1.35e+01 angle pdb=" O ASP A 204 " pdb=" C ASP A 204 " pdb=" N GLU A 205 " ideal model delta sigma weight residual 123.29 119.66 3.63 1.00e+00 1.00e+00 1.32e+01 ... (remaining 12445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 4651 16.30 - 32.59: 554 32.59 - 48.89: 178 48.89 - 65.19: 37 65.19 - 81.49: 8 Dihedral angle restraints: 5428 sinusoidal: 2071 harmonic: 3357 Sorted by residual: dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 15 " pdb=" CB CYS L 15 " ideal model delta sinusoidal sigma weight residual -86.00 -127.39 41.39 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CG ARG A 230 " pdb=" CD ARG A 230 " pdb=" NE ARG A 230 " pdb=" CZ ARG A 230 " ideal model delta sinusoidal sigma weight residual 90.00 41.36 48.64 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CA GLN B 264 " pdb=" C GLN B 264 " pdb=" N GLU B 265 " pdb=" CA GLU B 265 " ideal model delta harmonic sigma weight residual 180.00 162.92 17.08 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 910 0.029 - 0.059: 324 0.059 - 0.088: 105 0.088 - 0.118: 66 0.118 - 0.147: 11 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA MET E 92 " pdb=" N MET E 92 " pdb=" C MET E 92 " pdb=" CB MET E 92 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ASN E 76 " pdb=" N ASN E 76 " pdb=" C ASN E 76 " pdb=" CB ASN E 76 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE R 196 " pdb=" N ILE R 196 " pdb=" C ILE R 196 " pdb=" CB ILE R 196 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1413 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN R 339 " -0.017 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ASN R 339 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN R 339 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG R 340 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 198 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.60e+00 pdb=" N PRO R 199 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO R 199 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 199 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 204 " -0.015 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C ASP A 204 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP A 204 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 205 " -0.016 2.00e-02 2.50e+03 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 10 2.27 - 2.93: 3874 2.93 - 3.58: 12956 3.58 - 4.24: 19861 4.24 - 4.90: 33518 Nonbonded interactions: 70219 Sorted by model distance: nonbonded pdb=" CE1 HIS A 195 " pdb=" CE1 PHE A 197 " model vdw 1.609 3.560 nonbonded pdb=" ND1 HIS A 195 " pdb=" CE1 PHE A 197 " model vdw 2.019 3.420 nonbonded pdb=" OD2 ASP B 32 " pdb=" OG SER G 31 " model vdw 2.191 2.440 nonbonded pdb=" OG SER B 336 " pdb=" OD1 ASP B 338 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR B 70 " pdb=" O PRO B 112 " model vdw 2.204 2.440 ... (remaining 70214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 4.270 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.220 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 9180 Z= 0.178 Angle : 0.662 12.855 12450 Z= 0.353 Chirality : 0.039 0.147 1416 Planarity : 0.005 0.077 1580 Dihedral : 16.120 81.487 3250 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.71 % Favored : 96.11 % Rotamer Outliers : 0.21 % 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: 0.43 (0.25), residues: 1131 helix: 1.42 (0.28), residues: 371 sheet: 0.87 (0.33), residues: 268 loop : -0.94 (0.27), residues: 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.108 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.2336 time to fit residues: 53.4443 Evaluate side-chains 151 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 342 ASN A 352 ASN B 93 ASN B 160 ASN B 181 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.051 9180 Z= 0.494 Angle : 0.786 13.770 12450 Z= 0.408 Chirality : 0.050 0.230 1416 Planarity : 0.006 0.075 1580 Dihedral : 5.049 20.377 1244 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.77 % Favored : 95.05 % Rotamer Outliers : 7.45 % 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: -0.05 (0.25), residues: 1131 helix: 0.75 (0.27), residues: 381 sheet: 0.46 (0.31), residues: 280 loop : -0.94 (0.27), residues: 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 207 time to evaluate : 0.979 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 44 residues processed: 251 average time/residue: 0.2456 time to fit residues: 81.5455 Evaluate side-chains 231 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.1168 time to fit residues: 9.6989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 93 ASN B 181 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 9180 Z= 0.253 Angle : 0.602 7.614 12450 Z= 0.310 Chirality : 0.043 0.190 1416 Planarity : 0.004 0.055 1580 Dihedral : 4.458 21.054 1244 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.80 % Favored : 96.02 % Rotamer Outliers : 3.10 % 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: 0.10 (0.25), residues: 1131 helix: 1.16 (0.27), residues: 379 sheet: 0.38 (0.31), residues: 279 loop : -1.00 (0.27), residues: 473 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 0.949 Fit side-chains outliers start: 30 outliers final: 18 residues processed: 212 average time/residue: 0.2462 time to fit residues: 69.2616 Evaluate side-chains 201 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1332 time to fit residues: 5.3141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 109 optimal weight: 0.0010 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 9180 Z= 0.302 Angle : 0.615 6.686 12450 Z= 0.318 Chirality : 0.044 0.229 1416 Planarity : 0.004 0.053 1580 Dihedral : 4.522 20.811 1244 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.33 % Favored : 95.49 % Rotamer Outliers : 3.00 % 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: 0.15 (0.25), residues: 1131 helix: 1.21 (0.27), residues: 377 sheet: 0.43 (0.32), residues: 267 loop : -0.96 (0.27), residues: 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 190 time to evaluate : 1.062 Fit side-chains outliers start: 29 outliers final: 13 residues processed: 205 average time/residue: 0.2759 time to fit residues: 73.8013 Evaluate side-chains 191 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 178 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0943 time to fit residues: 3.7139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 9180 Z= 0.238 Angle : 0.586 6.905 12450 Z= 0.303 Chirality : 0.043 0.206 1416 Planarity : 0.004 0.057 1580 Dihedral : 4.360 21.321 1244 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.07 % Favored : 95.76 % Rotamer Outliers : 2.48 % 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: 0.20 (0.25), residues: 1131 helix: 1.34 (0.27), residues: 378 sheet: 0.43 (0.32), residues: 265 loop : -0.99 (0.27), residues: 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 1.233 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 209 average time/residue: 0.2713 time to fit residues: 74.8669 Evaluate side-chains 204 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0926 time to fit residues: 3.3187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 109 optimal weight: 0.0010 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9180 Z= 0.195 Angle : 0.585 10.937 12450 Z= 0.298 Chirality : 0.042 0.192 1416 Planarity : 0.004 0.051 1580 Dihedral : 4.226 21.616 1244 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.16 % Favored : 95.67 % Rotamer Outliers : 2.28 % 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: 0.35 (0.25), residues: 1131 helix: 1.51 (0.27), residues: 376 sheet: 0.47 (0.32), residues: 263 loop : -0.90 (0.27), residues: 492 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 1.151 Fit side-chains outliers start: 22 outliers final: 7 residues processed: 207 average time/residue: 0.2689 time to fit residues: 72.8439 Evaluate side-chains 191 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1199 time to fit residues: 2.7796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 9180 Z= 0.267 Angle : 0.614 9.731 12450 Z= 0.314 Chirality : 0.044 0.209 1416 Planarity : 0.004 0.054 1580 Dihedral : 4.411 21.413 1244 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.23 % Rotamer Outliers : 1.76 % 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: 0.18 (0.25), residues: 1131 helix: 1.35 (0.27), residues: 382 sheet: 0.31 (0.32), residues: 260 loop : -0.96 (0.28), residues: 489 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 1.076 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 199 average time/residue: 0.2769 time to fit residues: 71.8822 Evaluate side-chains 193 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1040 time to fit residues: 2.7356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9180 Z= 0.204 Angle : 0.605 11.681 12450 Z= 0.306 Chirality : 0.043 0.194 1416 Planarity : 0.004 0.052 1580 Dihedral : 4.274 21.945 1244 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer Outliers : 1.24 % 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: 0.17 (0.25), residues: 1131 helix: 1.40 (0.27), residues: 383 sheet: 0.21 (0.31), residues: 260 loop : -0.96 (0.27), residues: 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 1.040 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 185 average time/residue: 0.2560 time to fit residues: 62.9193 Evaluate side-chains 187 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 181 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1426 time to fit residues: 2.8525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9180 Z= 0.227 Angle : 0.615 11.574 12450 Z= 0.312 Chirality : 0.043 0.196 1416 Planarity : 0.005 0.056 1580 Dihedral : 4.297 21.867 1244 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer Outliers : 0.93 % 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: 0.13 (0.25), residues: 1131 helix: 1.37 (0.27), residues: 382 sheet: 0.20 (0.31), residues: 260 loop : -0.99 (0.27), residues: 489 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 0.993 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 190 average time/residue: 0.2495 time to fit residues: 62.8264 Evaluate side-chains 187 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 181 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1004 time to fit residues: 2.5799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 chunk 54 optimal weight: 0.0030 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 0.0000 chunk 27 optimal weight: 1.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9180 Z= 0.172 Angle : 0.594 12.442 12450 Z= 0.301 Chirality : 0.042 0.173 1416 Planarity : 0.005 0.087 1580 Dihedral : 4.172 22.368 1244 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.76 % Rotamer Outliers : 0.00 % 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: 0.26 (0.25), residues: 1131 helix: 1.59 (0.27), residues: 376 sheet: 0.24 (0.31), residues: 259 loop : -0.96 (0.27), residues: 496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.132 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2769 time to fit residues: 67.1081 Evaluate side-chains 185 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 0.0070 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.144836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.128476 restraints weight = 12496.439| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.18 r_work: 0.3590 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9180 Z= 0.204 Angle : 0.605 12.104 12450 Z= 0.305 Chirality : 0.043 0.181 1416 Planarity : 0.005 0.090 1580 Dihedral : 4.168 22.110 1244 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.76 % Rotamer Outliers : 0.31 % 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: 0.21 (0.25), residues: 1131 helix: 1.49 (0.27), residues: 382 sheet: 0.19 (0.31), residues: 262 loop : -0.95 (0.27), residues: 487 =============================================================================== Job complete usr+sys time: 2531.78 seconds wall clock time: 46 minutes 24.35 seconds (2784.35 seconds total)