Starting phenix.real_space_refine on Wed Feb 14 08:23:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flr_29284/02_2024/8flr_29284.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flr_29284/02_2024/8flr_29284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flr_29284/02_2024/8flr_29284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flr_29284/02_2024/8flr_29284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flr_29284/02_2024/8flr_29284.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flr_29284/02_2024/8flr_29284.pdb" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.112 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 56 5.16 5 C 5688 2.51 5 N 1552 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "R GLU 431": "OE1" <-> "OE2" Residue "R GLU 465": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8928 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1897 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2563 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 403 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 957 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 272 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2826 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 3 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 5.38, per 1000 atoms: 0.60 Number of scatterers: 8928 At special positions: 0 Unit cell: (73.1, 94.35, 173.4, 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 56 16.00 O 1632 8.00 N 1552 7.00 C 5688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 43.2% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.542A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.535A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.757A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.492A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.639A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.590A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.537A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 54 Processing helix chain 'R' and resid 177 through 212 removed outlier: 4.336A pdb=" N ARG R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.660A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.676A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.987A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.524A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.293A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 479 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.811A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.758A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.520A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.151A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.984A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.937A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.535A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.670A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.529A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.705A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 499 hydrogen bonds defined for protein. 1440 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: 2.80 Time building geometry restraints manager: 3.53 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: 2905 1.34 - 1.46: 2048 1.46 - 1.58: 4089 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 9120 Sorted by residual: bond pdb=" N LEU R 321 " pdb=" CA LEU R 321 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.23e-02 6.61e+03 8.29e+00 bond pdb=" N VAL R 432 " pdb=" CA VAL R 432 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.03e+00 bond pdb=" N VAL R 171 " pdb=" CA VAL R 171 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.72e+00 bond pdb=" N ILE P 28 " pdb=" CA ILE P 28 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.36e+00 bond pdb=" N GLU R 317 " pdb=" CA GLU R 317 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.28e-02 6.10e+03 7.20e+00 ... (remaining 9115 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.87: 208 106.87 - 113.73: 5014 113.73 - 120.58: 3678 120.58 - 127.44: 3374 127.44 - 134.30: 105 Bond angle restraints: 12379 Sorted by residual: angle pdb=" CA CYS R 217 " pdb=" C CYS R 217 " pdb=" O CYS R 217 " ideal model delta sigma weight residual 121.40 116.94 4.46 1.13e+00 7.83e-01 1.56e+01 angle pdb=" N ILE P 31 " pdb=" CA ILE P 31 " pdb=" C ILE P 31 " ideal model delta sigma weight residual 112.80 108.57 4.23 1.15e+00 7.56e-01 1.35e+01 angle pdb=" C VAL R 334 " pdb=" N PHE R 335 " pdb=" CA PHE R 335 " ideal model delta sigma weight residual 121.14 114.94 6.20 1.75e+00 3.27e-01 1.25e+01 angle pdb=" CA TYR R 191 " pdb=" CB TYR R 191 " pdb=" CG TYR R 191 " ideal model delta sigma weight residual 113.90 119.99 -6.09 1.80e+00 3.09e-01 1.15e+01 angle pdb=" CA ARG R 219 " pdb=" C ARG R 219 " pdb=" O ARG R 219 " ideal model delta sigma weight residual 120.82 117.50 3.32 1.05e+00 9.07e-01 9.99e+00 ... (remaining 12374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4893 17.93 - 35.86: 365 35.86 - 53.79: 75 53.79 - 71.72: 14 71.72 - 89.65: 9 Dihedral angle restraints: 5356 sinusoidal: 2023 harmonic: 3333 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 136.17 -43.17 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 5353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1092 0.049 - 0.099: 235 0.099 - 0.148: 52 0.148 - 0.198: 7 0.198 - 0.247: 1 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA CYS R 217 " pdb=" N CYS R 217 " pdb=" C CYS R 217 " pdb=" CB CYS R 217 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE P 31 " pdb=" N ILE P 31 " pdb=" C ILE P 31 " pdb=" CB ILE P 31 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA PHE R 335 " pdb=" N PHE R 335 " pdb=" C PHE R 335 " pdb=" CB PHE R 335 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1384 not shown) Planarity restraints: 1575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS R 216 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C HIS R 216 " 0.039 2.00e-02 2.50e+03 pdb=" O HIS R 216 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS R 217 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 376 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ILE R 376 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE R 376 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU R 377 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 236 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 ... (remaining 1572 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 701 2.74 - 3.28: 8964 3.28 - 3.82: 15715 3.82 - 4.36: 19096 4.36 - 4.90: 32751 Nonbonded interactions: 77227 Sorted by model distance: nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.201 2.440 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.207 2.520 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.216 2.440 nonbonded pdb=" O ALA R 242 " pdb=" OG SER R 246 " model vdw 2.218 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.221 2.440 ... (remaining 77222 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.430 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.520 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 0.037 9120 Z= 0.224 Angle : 0.589 9.776 12379 Z= 0.365 Chirality : 0.044 0.247 1387 Planarity : 0.004 0.042 1575 Dihedral : 13.800 89.652 3184 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.11 % Allowed : 0.65 % Favored : 99.24 % 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: 1.23 (0.25), residues: 1125 helix: 2.06 (0.25), residues: 442 sheet: -0.27 (0.32), residues: 226 loop : 0.28 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.020 0.001 TYR N 60 ARG 0.009 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6587 (p0) cc_final: 0.6264 (p0) REVERT: B 153 ASP cc_start: 0.7840 (p0) cc_final: 0.7570 (p0) REVERT: R 189 MET cc_start: 0.7184 (tmm) cc_final: 0.6880 (tmt) REVERT: R 390 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7294 (ttm170) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 1.1091 time to fit residues: 166.8970 Evaluate side-chains 113 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 0.3980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 125 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9120 Z= 0.254 Angle : 0.558 14.677 12379 Z= 0.293 Chirality : 0.042 0.187 1387 Planarity : 0.004 0.047 1575 Dihedral : 4.432 25.303 1244 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.74 % Allowed : 6.10 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1125 helix: 2.59 (0.24), residues: 435 sheet: -0.16 (0.32), residues: 227 loop : 0.19 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 298 HIS 0.007 0.001 HIS A 357 PHE 0.034 0.002 PHE R 335 TYR 0.036 0.002 TYR R 191 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6505 (p0) cc_final: 0.6249 (p0) REVERT: B 153 ASP cc_start: 0.7979 (p0) cc_final: 0.7700 (p0) REVERT: B 155 ASN cc_start: 0.7586 (t0) cc_final: 0.7303 (m-40) outliers start: 16 outliers final: 10 residues processed: 128 average time/residue: 1.1216 time to fit residues: 154.0698 Evaluate side-chains 118 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER 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: 3.9990 chunk 84 optimal weight: 50.0000 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9120 Z= 0.258 Angle : 0.557 15.896 12379 Z= 0.290 Chirality : 0.042 0.165 1387 Planarity : 0.004 0.048 1575 Dihedral : 4.440 25.699 1244 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.29 % Allowed : 9.37 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1125 helix: 2.65 (0.24), residues: 434 sheet: -0.28 (0.31), residues: 229 loop : 0.19 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 298 HIS 0.007 0.001 HIS A 357 PHE 0.030 0.002 PHE R 335 TYR 0.031 0.002 TYR R 191 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6545 (p0) cc_final: 0.6324 (p0) REVERT: B 153 ASP cc_start: 0.8032 (p0) cc_final: 0.7741 (p0) REVERT: B 155 ASN cc_start: 0.7636 (t0) cc_final: 0.7338 (m-40) outliers start: 21 outliers final: 12 residues processed: 129 average time/residue: 1.1989 time to fit residues: 166.0593 Evaluate side-chains 116 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0370 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9120 Z= 0.165 Angle : 0.501 13.010 12379 Z= 0.263 Chirality : 0.040 0.162 1387 Planarity : 0.004 0.052 1575 Dihedral : 4.244 25.495 1244 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.18 % Allowed : 11.33 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.26), residues: 1125 helix: 2.86 (0.24), residues: 436 sheet: -0.24 (0.32), residues: 229 loop : 0.28 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.009 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6529 (p0) cc_final: 0.6250 (p0) REVERT: B 153 ASP cc_start: 0.8041 (p0) cc_final: 0.7763 (p0) REVERT: B 155 ASN cc_start: 0.7599 (t0) cc_final: 0.7329 (m-40) outliers start: 20 outliers final: 12 residues processed: 127 average time/residue: 1.0694 time to fit residues: 146.9722 Evaluate side-chains 122 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 40.0000 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9120 Z= 0.286 Angle : 0.576 16.738 12379 Z= 0.298 Chirality : 0.042 0.161 1387 Planarity : 0.004 0.057 1575 Dihedral : 4.511 26.315 1244 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.72 % Allowed : 12.85 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1125 helix: 2.53 (0.24), residues: 442 sheet: -0.29 (0.32), residues: 229 loop : 0.18 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 298 HIS 0.007 0.001 HIS A 357 PHE 0.032 0.002 PHE R 335 TYR 0.026 0.002 TYR R 191 ARG 0.011 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASP cc_start: 0.6589 (p0) cc_final: 0.6373 (p0) REVERT: B 153 ASP cc_start: 0.8062 (p0) cc_final: 0.7812 (p0) REVERT: N 29 PHE cc_start: 0.7426 (t80) cc_final: 0.7100 (t80) REVERT: R 411 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8134 (mp) outliers start: 25 outliers final: 18 residues processed: 121 average time/residue: 1.0830 time to fit residues: 141.4308 Evaluate side-chains 121 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 0.0670 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 chunk 50 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9120 Z= 0.138 Angle : 0.482 12.743 12379 Z= 0.253 Chirality : 0.039 0.154 1387 Planarity : 0.004 0.055 1575 Dihedral : 4.113 23.184 1244 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.63 % Allowed : 14.27 % Favored : 84.10 % 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: 1.73 (0.26), residues: 1125 helix: 2.85 (0.25), residues: 442 sheet: -0.16 (0.32), residues: 228 loop : 0.21 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.030 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.010 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6810 (mtt90) REVERT: A 240 ASP cc_start: 0.6507 (p0) cc_final: 0.6256 (p0) REVERT: B 153 ASP cc_start: 0.7997 (p0) cc_final: 0.7773 (p0) REVERT: B 155 ASN cc_start: 0.7669 (t0) cc_final: 0.7399 (m-40) REVERT: N 29 PHE cc_start: 0.7414 (t80) cc_final: 0.7146 (t80) outliers start: 15 outliers final: 8 residues processed: 130 average time/residue: 0.9868 time to fit residues: 139.1143 Evaluate side-chains 119 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 91 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9120 Z= 0.175 Angle : 0.506 13.469 12379 Z= 0.263 Chirality : 0.040 0.220 1387 Planarity : 0.004 0.054 1575 Dihedral : 4.131 23.346 1244 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.96 % Allowed : 15.03 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1125 helix: 2.88 (0.24), residues: 442 sheet: -0.17 (0.32), residues: 229 loop : 0.25 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.012 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: B 153 ASP cc_start: 0.8018 (p0) cc_final: 0.7791 (p0) REVERT: B 155 ASN cc_start: 0.7675 (t0) cc_final: 0.7398 (m-40) REVERT: N 29 PHE cc_start: 0.7408 (t80) cc_final: 0.7157 (t80) outliers start: 18 outliers final: 13 residues processed: 121 average time/residue: 1.0244 time to fit residues: 134.3774 Evaluate side-chains 125 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 84 optimal weight: 40.0000 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9120 Z= 0.166 Angle : 0.499 13.310 12379 Z= 0.260 Chirality : 0.040 0.207 1387 Planarity : 0.004 0.054 1575 Dihedral : 4.085 23.049 1244 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.51 % Allowed : 15.03 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.26), residues: 1125 helix: 2.93 (0.24), residues: 443 sheet: -0.15 (0.32), residues: 229 loop : 0.28 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.026 0.001 TYR R 191 ARG 0.013 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: B 153 ASP cc_start: 0.8015 (p0) cc_final: 0.7788 (p0) REVERT: B 155 ASN cc_start: 0.7660 (t0) cc_final: 0.7383 (m-40) REVERT: N 29 PHE cc_start: 0.7401 (t80) cc_final: 0.7154 (t80) outliers start: 23 outliers final: 16 residues processed: 129 average time/residue: 1.0235 time to fit residues: 142.9761 Evaluate side-chains 132 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9120 Z= 0.175 Angle : 0.510 13.505 12379 Z= 0.265 Chirality : 0.040 0.199 1387 Planarity : 0.004 0.058 1575 Dihedral : 4.096 23.127 1244 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.51 % Allowed : 15.25 % Favored : 82.24 % 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: 1.82 (0.26), residues: 1125 helix: 2.92 (0.24), residues: 443 sheet: -0.14 (0.32), residues: 229 loop : 0.27 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS B 62 PHE 0.013 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.013 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: B 153 ASP cc_start: 0.8027 (p0) cc_final: 0.7807 (p0) REVERT: B 155 ASN cc_start: 0.7665 (t0) cc_final: 0.7376 (m-40) REVERT: N 29 PHE cc_start: 0.7405 (t80) cc_final: 0.7115 (t80) outliers start: 23 outliers final: 18 residues processed: 130 average time/residue: 0.9690 time to fit residues: 137.2865 Evaluate side-chains 131 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 409 SER Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 73 optimal weight: 0.0040 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 357 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9120 Z= 0.134 Angle : 0.486 11.673 12379 Z= 0.254 Chirality : 0.039 0.201 1387 Planarity : 0.004 0.059 1575 Dihedral : 3.948 21.625 1244 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.96 % Allowed : 15.58 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.26), residues: 1125 helix: 2.97 (0.25), residues: 446 sheet: -0.05 (0.32), residues: 232 loop : 0.38 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.002 0.000 HIS B 62 PHE 0.035 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.015 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6112 (mmm) cc_final: 0.5847 (mmm) REVERT: B 59 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: B 153 ASP cc_start: 0.7997 (p0) cc_final: 0.7780 (p0) REVERT: B 155 ASN cc_start: 0.7636 (t0) cc_final: 0.7366 (m-40) REVERT: B 220 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: N 29 PHE cc_start: 0.7394 (t80) cc_final: 0.7086 (t80) REVERT: R 189 MET cc_start: 0.7198 (tmm) cc_final: 0.6941 (tmt) outliers start: 18 outliers final: 15 residues processed: 127 average time/residue: 1.0236 time to fit residues: 140.9050 Evaluate side-chains 130 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 138 PHE Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS A 390 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.204102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.160536 restraints weight = 8945.241| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.72 r_work: 0.3568 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9120 Z= 0.175 Angle : 0.510 12.657 12379 Z= 0.266 Chirality : 0.040 0.198 1387 Planarity : 0.004 0.061 1575 Dihedral : 4.046 22.496 1244 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.18 % Allowed : 15.36 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.26), residues: 1125 helix: 3.00 (0.24), residues: 442 sheet: -0.04 (0.32), residues: 231 loop : 0.35 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS B 62 PHE 0.034 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.014 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3270.42 seconds wall clock time: 58 minutes 59.02 seconds (3539.02 seconds total)