Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 16:40:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w56_32315/04_2023/7w56_32315.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w56_32315/04_2023/7w56_32315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w56_32315/04_2023/7w56_32315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w56_32315/04_2023/7w56_32315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w56_32315/04_2023/7w56_32315.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w56_32315/04_2023/7w56_32315.pdb" } resolution = 2.9 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 C 5706 2.51 5 N 1568 2.21 5 O 1649 1.98 5 H 8894 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 284": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 234": "OE1" <-> "OE2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 257": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 17881 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3759 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 5136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 5136 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "C" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 156 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3504 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 4441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4441 Classifications: {'peptide': 276} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 262} Chain breaks: 2 Time building chain proxies: 7.88, per 1000 atoms: 0.44 Number of scatterers: 17881 At special positions: 0 Unit cell: (118.8, 130.68, 110.16, 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 64 16.00 O 1649 8.00 N 1568 7.00 C 5706 6.00 H 8894 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 219 " 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: 14.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 39.5% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.935A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 210 through 218 removed outlier: 4.263A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 218 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.753A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.757A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.735A 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 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'G' and resid 44 through 47 removed outlier: 3.512A pdb=" N ASP G 47 " --> pdb=" O ALA G 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 44 through 47' Processing helix chain 'R' and resid 60 through 88 removed outlier: 3.520A pdb=" N HIS R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 92 removed outlier: 3.758A pdb=" N ARG R 92 " --> pdb=" O LYS R 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 89 through 92' Processing helix chain 'R' and resid 93 through 123 removed outlier: 3.672A pdb=" N TYR R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR R 98 " --> pdb=" O PRO R 94 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU R 99 " --> pdb=" O THR R 95 " (cutoff:3.500A) Proline residue: R 115 - end of helix Processing helix chain 'R' and resid 129 through 160 Processing helix chain 'R' and resid 161 through 163 No H-bonds generated for 'chain 'R' and resid 161 through 163' Processing helix chain 'R' and resid 164 through 165 No H-bonds generated for 'chain 'R' and resid 164 through 165' Processing helix chain 'R' and resid 166 through 172 Processing helix chain 'R' and resid 174 through 198 removed outlier: 3.820A pdb=" N VAL R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Proline residue: R 195 - end of helix Processing helix chain 'R' and resid 224 through 240 Processing helix chain 'R' and resid 240 through 260 Processing helix chain 'R' and resid 293 through 323 removed outlier: 3.899A pdb=" N PHE R 300 " --> pdb=" O THR R 296 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 330 through 357 removed outlier: 3.872A pdb=" N PHE R 334 " --> pdb=" O LEU R 330 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL R 339 " --> pdb=" O GLN R 335 " (cutoff:3.500A) Proline residue: R 353 - end of helix Processing helix chain 'R' and resid 360 through 365 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.159A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.885A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 333 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 323 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY B 335 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.865A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.383A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.654A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.015A 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 removed outlier: 3.674A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.691A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 283 removed outlier: 3.705A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS B 299 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL B 312 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 301 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.536A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.179A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.501A 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: 6.179A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.050A 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 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.722A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG E 191 " --> pdb=" O ASN E 194 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1266 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: 6.24 Time building geometry restraints manager: 14.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8864 1.02 - 1.22: 38 1.22 - 1.41: 3812 1.41 - 1.61: 5260 1.61 - 1.81: 96 Bond restraints: 18070 Sorted by residual: bond pdb=" SG CYS B 322 " pdb=" HG CYS B 322 " ideal model delta sigma weight residual 1.200 1.338 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" SG CYS B 238 " pdb=" HG CYS B 238 " ideal model delta sigma weight residual 1.200 1.336 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" NE ARG A 323 " pdb=" HE ARG A 323 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" CA GLU E 234 " pdb=" C GLU E 234 " ideal model delta sigma weight residual 1.522 1.459 0.063 1.21e-02 6.83e+03 2.69e+01 bond pdb=" CA LEU B 151 " pdb=" C LEU B 151 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.01e+01 ... (remaining 18065 not shown) Histogram of bond angle deviations from ideal: 98.70 - 106.68: 296 106.68 - 114.67: 21898 114.67 - 122.66: 7970 122.66 - 130.65: 2283 130.65 - 138.64: 46 Bond angle restraints: 32493 Sorted by residual: angle pdb=" N ASP B 251 " pdb=" CA ASP B 251 " pdb=" C ASP B 251 " ideal model delta sigma weight residual 111.28 102.85 8.43 1.09e+00 8.42e-01 5.98e+01 angle pdb=" N PHE B 240 " pdb=" CA PHE B 240 " pdb=" C PHE B 240 " ideal model delta sigma weight residual 110.39 99.49 10.90 1.50e+00 4.44e-01 5.28e+01 angle pdb=" N GLY E 113 " pdb=" CA GLY E 113 " pdb=" C GLY E 113 " ideal model delta sigma weight residual 111.95 118.81 -6.86 9.50e-01 1.11e+00 5.21e+01 angle pdb=" N TYR B 294 " pdb=" CA TYR B 294 " pdb=" C TYR B 294 " ideal model delta sigma weight residual 114.39 124.49 -10.10 1.45e+00 4.76e-01 4.85e+01 angle pdb=" C TYR E 235 " pdb=" N PRO E 236 " pdb=" CA PRO E 236 " ideal model delta sigma weight residual 119.84 111.51 8.33 1.25e+00 6.40e-01 4.44e+01 ... (remaining 32488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.54: 6915 19.54 - 39.07: 279 39.07 - 58.61: 86 58.61 - 78.14: 27 78.14 - 97.68: 5 Dihedral angle restraints: 7312 sinusoidal: 3367 harmonic: 3945 Sorted by residual: dihedral pdb=" CA ASP B 296 " pdb=" C ASP B 296 " pdb=" N PHE B 297 " pdb=" CA PHE B 297 " ideal model delta harmonic sigma weight residual 180.00 82.32 97.68 0 5.00e+00 4.00e-02 3.82e+02 dihedral pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " ideal model delta harmonic sigma weight residual 122.80 145.00 -22.20 0 2.50e+00 1.60e-01 7.88e+01 dihedral pdb=" C TYR E 235 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " ideal model delta harmonic sigma weight residual -122.60 -144.34 21.74 0 2.50e+00 1.60e-01 7.57e+01 ... (remaining 7309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 1398 0.213 - 0.425: 4 0.425 - 0.638: 0 0.638 - 0.850: 0 0.850 - 1.063: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CA TYR B 294 " pdb=" N TYR B 294 " pdb=" C TYR B 294 " pdb=" CB TYR B 294 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA TYR R 125 " pdb=" N TYR R 125 " pdb=" C TYR R 125 " pdb=" CB TYR R 125 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1400 not shown) Planarity restraints: 2677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 233 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C LEU E 233 " 0.066 2.00e-02 2.50e+03 pdb=" O LEU E 233 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU E 234 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 297 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.88e+00 pdb=" N ASN B 298 " -0.054 2.00e-02 2.50e+03 pdb=" CA ASN B 298 " 0.014 2.00e-02 2.50e+03 pdb=" H ASN B 298 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 240 " 0.045 5.00e-02 4.00e+02 6.73e-02 7.26e+00 pdb=" N PRO B 241 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.038 5.00e-02 4.00e+02 ... (remaining 2674 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 413 2.10 - 2.73: 31740 2.73 - 3.35: 52701 3.35 - 3.98: 67220 3.98 - 4.60: 105606 Nonbonded interactions: 257680 Sorted by model distance: nonbonded pdb="HH12 ARG A 15 " pdb=" O VAL B 95 " model vdw 1.480 1.850 nonbonded pdb=" OE2 GLU A 8 " pdb=" HH TYR E 175 " model vdw 1.533 1.850 nonbonded pdb=" OD1 ASP A 298 " pdb=" H ARG A 300 " model vdw 1.568 1.850 nonbonded pdb=" OD1 ASP B 210 " pdb=" HG SER B 212 " model vdw 1.570 1.850 nonbonded pdb="HH22 ARG E 66 " pdb=" OD2 ASP E 89 " model vdw 1.574 1.850 ... (remaining 257675 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=0.00 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: 0.460 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: 0.260 Extract box with map and model: 3.270 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 54.920 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 : 0.006 0.074 9176 Z= 0.368 Angle : 0.719 11.648 12429 Z= 0.435 Chirality : 0.053 1.063 1403 Planarity : 0.004 0.067 1582 Dihedral : 11.515 97.681 3317 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1124 helix: 1.24 (0.26), residues: 393 sheet: 0.22 (0.29), residues: 302 loop : -0.30 (0.30), residues: 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 323 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 319 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 321 average time/residue: 2.1616 time to fit residues: 748.9466 Evaluate side-chains 274 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.4084 time to fit residues: 2.3331 ------------------------------------------------------------------------------- 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: 1.9990 chunk 84 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 259 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN R 124 ASN ** R 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 9176 Z= 0.267 Angle : 0.593 9.527 12429 Z= 0.317 Chirality : 0.042 0.209 1403 Planarity : 0.004 0.061 1582 Dihedral : 5.595 51.864 1252 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1124 helix: 1.50 (0.26), residues: 398 sheet: 0.05 (0.29), residues: 286 loop : -0.14 (0.31), residues: 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 294 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 276 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 286 average time/residue: 2.4040 time to fit residues: 737.6833 Evaluate side-chains 275 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 265 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.2699 time to fit residues: 3.0449 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN A 259 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN R 124 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 9176 Z= 0.298 Angle : 0.565 6.272 12429 Z= 0.303 Chirality : 0.042 0.189 1403 Planarity : 0.004 0.066 1582 Dihedral : 5.390 52.193 1252 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1124 helix: 1.75 (0.26), residues: 392 sheet: -0.14 (0.29), residues: 286 loop : -0.23 (0.30), residues: 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 308 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 281 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 291 average time/residue: 2.3662 time to fit residues: 738.6665 Evaluate side-chains 280 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 266 time to evaluate : 1.381 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 6 average time/residue: 0.5028 time to fit residues: 5.8335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0770 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN A 259 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9176 Z= 0.285 Angle : 0.557 5.955 12429 Z= 0.295 Chirality : 0.042 0.211 1403 Planarity : 0.004 0.042 1582 Dihedral : 5.214 47.434 1252 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.73 (0.25), residues: 1124 helix: 1.88 (0.26), residues: 392 sheet: -0.17 (0.28), residues: 285 loop : -0.21 (0.30), residues: 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 278 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 286 average time/residue: 2.4668 time to fit residues: 757.0034 Evaluate side-chains 282 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 271 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.1873 time to fit residues: 3.2653 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN A 259 ASN A 324 HIS ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 9176 Z= 0.285 Angle : 0.555 5.507 12429 Z= 0.293 Chirality : 0.042 0.191 1403 Planarity : 0.004 0.079 1582 Dihedral : 5.095 44.226 1252 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1124 helix: 1.94 (0.26), residues: 392 sheet: -0.32 (0.29), residues: 279 loop : -0.29 (0.30), residues: 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 302 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 276 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 290 average time/residue: 2.2907 time to fit residues: 715.0601 Evaluate side-chains 290 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 272 time to evaluate : 1.433 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 7 average time/residue: 0.7675 time to fit residues: 8.7084 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 259 ASN A 324 HIS ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 9176 Z= 0.389 Angle : 0.580 5.627 12429 Z= 0.310 Chirality : 0.043 0.210 1403 Planarity : 0.004 0.080 1582 Dihedral : 5.167 42.845 1252 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.57 (0.25), residues: 1124 helix: 1.84 (0.26), residues: 392 sheet: -0.39 (0.29), residues: 267 loop : -0.33 (0.29), residues: 465 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 266 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 278 average time/residue: 2.4136 time to fit residues: 720.2266 Evaluate side-chains 276 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 258 time to evaluate : 1.273 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 8 average time/residue: 0.5491 time to fit residues: 7.4193 ------------------------------------------------------------------------------- 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: 0.8980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 245 ASN A 259 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9176 Z= 0.200 Angle : 0.534 6.254 12429 Z= 0.281 Chirality : 0.041 0.160 1403 Planarity : 0.004 0.085 1582 Dihedral : 4.913 40.066 1252 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.77 (0.25), residues: 1124 helix: 2.07 (0.26), residues: 392 sheet: -0.35 (0.29), residues: 267 loop : -0.22 (0.30), residues: 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 258 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 267 average time/residue: 2.3161 time to fit residues: 664.4970 Evaluate side-chains 267 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 252 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 7 average time/residue: 0.7709 time to fit residues: 8.3937 ------------------------------------------------------------------------------- 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: 2.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 259 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS B 244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 9176 Z= 0.267 Angle : 0.539 5.664 12429 Z= 0.285 Chirality : 0.041 0.171 1403 Planarity : 0.004 0.045 1582 Dihedral : 4.867 38.639 1252 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.73 (0.25), residues: 1124 helix: 2.07 (0.26), residues: 392 sheet: -0.45 (0.29), residues: 281 loop : -0.21 (0.30), residues: 451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 257 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 270 average time/residue: 2.4558 time to fit residues: 713.0198 Evaluate side-chains 265 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 253 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 3 average time/residue: 0.2975 time to fit residues: 3.3718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.0270 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 259 ASN A 324 HIS ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS B 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9176 Z= 0.176 Angle : 0.521 6.874 12429 Z= 0.272 Chirality : 0.040 0.161 1403 Planarity : 0.004 0.048 1582 Dihedral : 4.653 36.038 1252 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1124 helix: 2.19 (0.26), residues: 393 sheet: -0.41 (0.29), residues: 281 loop : -0.10 (0.31), residues: 450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 269 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 280 average time/residue: 2.4065 time to fit residues: 723.5338 Evaluate side-chains 272 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 258 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 6 average time/residue: 0.5934 time to fit residues: 6.4086 ------------------------------------------------------------------------------- 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: 0.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 259 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9176 Z= 0.226 Angle : 0.550 7.039 12429 Z= 0.287 Chirality : 0.041 0.156 1403 Planarity : 0.005 0.077 1582 Dihedral : 4.683 35.602 1252 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1124 helix: 2.24 (0.26), residues: 393 sheet: -0.42 (0.29), residues: 281 loop : -0.09 (0.31), residues: 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 264 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 273 average time/residue: 2.3360 time to fit residues: 685.0402 Evaluate side-chains 273 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 261 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 4 average time/residue: 0.6500 time to fit residues: 5.1080 ------------------------------------------------------------------------------- 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: 0.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115941 restraints weight = 37862.620| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.09 r_work: 0.3444 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 9176 Z= 0.316 Angle : 0.577 7.288 12429 Z= 0.303 Chirality : 0.042 0.165 1403 Planarity : 0.005 0.081 1582 Dihedral : 4.806 35.032 1252 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.80 (0.25), residues: 1124 helix: 2.10 (0.26), residues: 392 sheet: -0.41 (0.30), residues: 261 loop : -0.16 (0.30), residues: 471 =============================================================================== Job complete usr+sys time: 10563.28 seconds wall clock time: 184 minutes 41.38 seconds (11081.38 seconds total)