Starting phenix.real_space_refine on Tue Feb 13 16:27:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mby_23750/02_2024/7mby_23750.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mby_23750/02_2024/7mby_23750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mby_23750/02_2024/7mby_23750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mby_23750/02_2024/7mby_23750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mby_23750/02_2024/7mby_23750.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mby_23750/02_2024/7mby_23750.pdb" } resolution = 2.44 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 4416 2.51 5 N 1164 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 6881 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2501 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 83 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 407 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'NH2': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2250 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 3, 'TRANS': 200} Chain breaks: 4 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.22, per 1000 atoms: 0.61 Number of scatterers: 6881 At special positions: 0 Unit cell: (73.45, 102.7, 121.55, 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 57 16.00 O 1244 8.00 N 1164 7.00 C 4416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " 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: 3.04 Conformation dependent library (CDL) restraints added in 1.4 seconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 47.6% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.561A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.614A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 39 through 69 removed outlier: 4.052A pdb=" N VAL R 62 " --> pdb=" O GLY R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 95 removed outlier: 3.838A pdb=" N PHE R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 105 Processing helix chain 'R' and resid 110 through 145 removed outlier: 3.511A pdb=" N GLY R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 153 removed outlier: 4.334A pdb=" N VAL R 151 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP R 152 " --> pdb=" O GLN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 173 Processing helix chain 'R' and resid 174 through 179 removed outlier: 4.270A pdb=" N ILE R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 218 removed outlier: 3.539A pdb=" N SER R 208 " --> pdb=" O VAL R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 238 removed outlier: 3.978A pdb=" N MET R 226 " --> pdb=" O GLY R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 339 removed outlier: 3.547A pdb=" N ARG R 313 " --> pdb=" O LYS R 309 " (cutoff:3.500A) Proline residue: R 328 - end of helix removed outlier: 3.644A pdb=" N TYR R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 347 removed outlier: 3.930A pdb=" N ALA R 343 " --> pdb=" O ASP R 339 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 361 Processing helix chain 'R' and resid 361 through 371 Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 385 removed outlier: 3.511A pdb=" N LEU R 379 " --> pdb=" O LYS R 375 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 39 removed outlier: 3.541A pdb=" N LYS A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 4.147A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.506A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.767A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 4.172A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.946A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.014A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.568A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.516A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.668A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.810A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.512A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.775A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 180 through 186 removed outlier: 3.599A pdb=" N ASN R 181 " --> pdb=" O ARG R 197 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG R 197 " --> pdb=" O ASN R 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.916A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 219 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 292 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1095 1.31 - 1.44: 1910 1.44 - 1.56: 3926 1.56 - 1.69: 6 1.69 - 1.82: 84 Bond restraints: 7021 Sorted by residual: bond pdb=" CAI Y01 R 501 " pdb=" CAK Y01 R 501 " ideal model delta sigma weight residual 1.492 1.582 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" CAZ Y01 R 501 " pdb=" CBH Y01 R 501 " ideal model delta sigma weight residual 1.519 1.441 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CAK Y01 R 501 " pdb=" CBD Y01 R 501 " ideal model delta sigma weight residual 1.525 1.598 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CAP Y01 R 501 " pdb=" CAQ Y01 R 501 " ideal model delta sigma weight residual 1.541 1.610 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" CAY Y01 R 501 " pdb=" OAW Y01 R 501 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 7016 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.31: 160 106.31 - 113.27: 3837 113.27 - 120.24: 2551 120.24 - 127.20: 2919 127.20 - 134.16: 76 Bond angle restraints: 9543 Sorted by residual: angle pdb=" C ARG R 376 " pdb=" CA ARG R 376 " pdb=" CB ARG R 376 " ideal model delta sigma weight residual 110.79 100.70 10.09 1.68e+00 3.54e-01 3.61e+01 angle pdb=" O1 TYS P 2 " pdb=" S TYS P 2 " pdb=" O3 TYS P 2 " ideal model delta sigma weight residual 115.16 100.64 14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 125.66 132.89 -7.23 1.85e+00 2.92e-01 1.53e+01 angle pdb=" OH TYS P 2 " pdb=" S TYS P 2 " pdb=" O3 TYS P 2 " ideal model delta sigma weight residual 100.21 111.53 -11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CA GLY B 319 " pdb=" C GLY B 319 " pdb=" O GLY B 319 " ideal model delta sigma weight residual 121.19 117.83 3.36 9.10e-01 1.21e+00 1.36e+01 ... (remaining 9538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 4005 21.72 - 43.44: 176 43.44 - 65.15: 18 65.15 - 86.87: 7 86.87 - 108.59: 1 Dihedral angle restraints: 4207 sinusoidal: 1603 harmonic: 2604 Sorted by residual: dihedral pdb=" C ARG R 376 " pdb=" N ARG R 376 " pdb=" CA ARG R 376 " pdb=" CB ARG R 376 " ideal model delta harmonic sigma weight residual -122.60 -108.99 -13.61 0 2.50e+00 1.60e-01 2.96e+01 dihedral pdb=" CBC Y01 R 501 " pdb=" CAR Y01 R 501 " pdb=" CAT Y01 R 501 " pdb=" CBH Y01 R 501 " ideal model delta sinusoidal sigma weight residual -57.13 51.46 -108.59 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" N ARG R 376 " pdb=" C ARG R 376 " pdb=" CA ARG R 376 " pdb=" CB ARG R 376 " ideal model delta harmonic sigma weight residual 122.80 114.15 8.65 0 2.50e+00 1.60e-01 1.20e+01 ... (remaining 4204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 941 0.079 - 0.158: 161 0.158 - 0.236: 14 0.236 - 0.315: 3 0.315 - 0.394: 4 Chirality restraints: 1123 Sorted by residual: chirality pdb=" CG LEU B 146 " pdb=" CB LEU B 146 " pdb=" CD1 LEU B 146 " pdb=" CD2 LEU B 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CBG Y01 R 501 " pdb=" CAQ Y01 R 501 " pdb=" CBD Y01 R 501 " pdb=" CBI Y01 R 501 " both_signs ideal model delta sigma weight residual False -2.33 -2.69 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA ARG R 376 " pdb=" N ARG R 376 " pdb=" C ARG R 376 " pdb=" CB ARG R 376 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1120 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 200 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO R 201 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO R 201 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 201 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 174 " -0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO R 175 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 175 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 175 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 152 " -0.018 2.00e-02 2.50e+03 1.40e-02 4.92e+00 pdb=" CG TRP R 152 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP R 152 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 152 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 152 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP R 152 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 152 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 152 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP R 152 " -0.001 2.00e-02 2.50e+03 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1752 2.80 - 3.33: 6294 3.33 - 3.85: 11771 3.85 - 4.38: 13697 4.38 - 4.90: 23660 Nonbonded interactions: 57174 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.280 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.319 2.440 nonbonded pdb=" O CYS R 114 " pdb=" OG1 THR R 118 " model vdw 2.334 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.346 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.354 2.440 ... (remaining 57169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.000 Extract box with map and model: 7.050 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 26.830 Find NCS groups from input model: 0.190 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:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 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 0.090 7021 Z= 0.392 Angle : 0.946 14.524 9543 Z= 0.504 Chirality : 0.061 0.394 1123 Planarity : 0.007 0.077 1190 Dihedral : 12.467 108.587 2506 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.12 % 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: -1.45 (0.26), residues: 869 helix: -0.90 (0.23), residues: 383 sheet: 0.10 (0.39), residues: 185 loop : -1.52 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP R 152 HIS 0.007 0.002 HIS A 357 PHE 0.023 0.003 PHE B 151 TYR 0.037 0.003 TYR B 59 ARG 0.016 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7564 (mmm160) cc_final: 0.7137 (mmp-170) REVERT: B 65 THR cc_start: 0.7138 (m) cc_final: 0.6775 (p) REVERT: B 217 MET cc_start: 0.7681 (ptt) cc_final: 0.6510 (ptt) REVERT: B 269 ILE cc_start: 0.5407 (mm) cc_final: 0.4956 (mt) REVERT: R 105 LYS cc_start: 0.8712 (mttp) cc_final: 0.8509 (mtmt) REVERT: R 126 SER cc_start: 0.8362 (t) cc_final: 0.7868 (p) REVERT: R 145 LYS cc_start: 0.7389 (pttt) cc_final: 0.7160 (pttp) REVERT: R 195 MET cc_start: 0.7015 (mtm) cc_final: 0.6807 (mtt) REVERT: A 25 MET cc_start: 0.6445 (ttm) cc_final: 0.5929 (ttm) REVERT: A 36 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7612 (mtmm) REVERT: A 218 ASN cc_start: 0.7201 (t0) cc_final: 0.6513 (m-40) REVERT: A 253 TYR cc_start: 0.7023 (m-80) cc_final: 0.6536 (m-80) REVERT: A 343 LYS cc_start: 0.6797 (tmtt) cc_final: 0.6445 (tptp) REVERT: A 347 ASP cc_start: 0.4691 (p0) cc_final: 0.4244 (p0) REVERT: A 380 LYS cc_start: 0.7234 (tmtt) cc_final: 0.6851 (tttm) outliers start: 0 outliers final: 1 residues processed: 186 average time/residue: 1.1191 time to fit residues: 219.9371 Evaluate side-chains 102 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 0.0070 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS R 98 ASN R 191 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 292 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7021 Z= 0.191 Angle : 0.649 7.978 9543 Z= 0.334 Chirality : 0.044 0.170 1123 Planarity : 0.005 0.066 1190 Dihedral : 6.580 52.602 1025 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.36 % Allowed : 15.00 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.28), residues: 869 helix: 0.90 (0.26), residues: 384 sheet: 0.07 (0.38), residues: 189 loop : -1.35 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 297 HIS 0.007 0.001 HIS A 362 PHE 0.027 0.002 PHE A 219 TYR 0.010 0.001 TYR R 237 ARG 0.006 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7753 (ptt) cc_final: 0.7447 (ptt) REVERT: B 234 PHE cc_start: 0.5191 (OUTLIER) cc_final: 0.4841 (t80) REVERT: B 269 ILE cc_start: 0.5332 (mm) cc_final: 0.4881 (mt) REVERT: R 92 LEU cc_start: 0.7526 (mt) cc_final: 0.7172 (mp) REVERT: R 105 LYS cc_start: 0.8679 (mttp) cc_final: 0.8382 (mtmt) REVERT: R 126 SER cc_start: 0.8381 (t) cc_final: 0.8117 (p) REVERT: R 220 ILE cc_start: 0.7782 (mm) cc_final: 0.7322 (mt) REVERT: A 39 ARG cc_start: 0.5828 (mtt-85) cc_final: 0.5192 (mtm-85) REVERT: A 218 ASN cc_start: 0.6986 (t0) cc_final: 0.6426 (m-40) REVERT: A 253 TYR cc_start: 0.7009 (m-80) cc_final: 0.6327 (m-80) REVERT: A 380 LYS cc_start: 0.7222 (tmtt) cc_final: 0.6918 (ttpt) REVERT: A 390 GLU cc_start: 0.8212 (tm-30) cc_final: 0.8008 (tm-30) outliers start: 17 outliers final: 6 residues processed: 123 average time/residue: 1.1159 time to fit residues: 145.2876 Evaluate side-chains 101 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain A residue 254 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7021 Z= 0.213 Angle : 0.645 12.806 9543 Z= 0.324 Chirality : 0.044 0.227 1123 Planarity : 0.004 0.049 1190 Dihedral : 5.828 59.322 1023 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.19 % Allowed : 17.08 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.29), residues: 869 helix: 1.59 (0.27), residues: 380 sheet: -0.00 (0.37), residues: 192 loop : -1.11 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 326 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.002 PHE A 219 TYR 0.027 0.002 TYR A 360 ARG 0.006 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.822 Fit side-chains REVERT: B 217 MET cc_start: 0.7638 (ptt) cc_final: 0.6815 (ptt) REVERT: B 234 PHE cc_start: 0.5376 (OUTLIER) cc_final: 0.4819 (t80) REVERT: B 269 ILE cc_start: 0.5216 (mm) cc_final: 0.4773 (mt) REVERT: R 105 LYS cc_start: 0.8642 (mttp) cc_final: 0.8418 (mtmt) REVERT: R 126 SER cc_start: 0.8342 (t) cc_final: 0.8009 (p) REVERT: R 220 ILE cc_start: 0.7701 (mm) cc_final: 0.7330 (mt) REVERT: A 380 LYS cc_start: 0.7214 (tmtt) cc_final: 0.6693 (tptt) REVERT: A 390 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8013 (tm-30) outliers start: 23 outliers final: 9 residues processed: 115 average time/residue: 1.1430 time to fit residues: 139.5795 Evaluate side-chains 98 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain A residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7021 Z= 0.192 Angle : 0.621 10.677 9543 Z= 0.315 Chirality : 0.043 0.165 1123 Planarity : 0.004 0.060 1190 Dihedral : 5.690 58.402 1023 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.61 % Allowed : 18.33 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.29), residues: 869 helix: 1.85 (0.27), residues: 382 sheet: 0.16 (0.38), residues: 189 loop : -1.15 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 326 HIS 0.009 0.001 HIS R 210 PHE 0.021 0.001 PHE A 219 TYR 0.012 0.001 TYR R 237 ARG 0.006 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 0.847 Fit side-chains REVERT: B 217 MET cc_start: 0.7759 (ptt) cc_final: 0.6857 (ptt) REVERT: B 234 PHE cc_start: 0.5396 (OUTLIER) cc_final: 0.4806 (t80) REVERT: B 269 ILE cc_start: 0.5135 (mm) cc_final: 0.4693 (mt) REVERT: R 92 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7194 (mp) REVERT: R 126 SER cc_start: 0.8287 (t) cc_final: 0.7961 (p) REVERT: R 187 LYS cc_start: 0.6882 (mttt) cc_final: 0.6619 (mtpt) REVERT: R 220 ILE cc_start: 0.7697 (mm) cc_final: 0.7338 (mt) REVERT: R 306 MET cc_start: 0.4887 (OUTLIER) cc_final: 0.4349 (pp-130) REVERT: R 368 ILE cc_start: 0.8543 (pt) cc_final: 0.8291 (pp) REVERT: A 380 LYS cc_start: 0.7212 (tmtt) cc_final: 0.6689 (tptt) REVERT: A 390 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7982 (tm-30) outliers start: 26 outliers final: 9 residues processed: 119 average time/residue: 1.0009 time to fit residues: 126.9621 Evaluate side-chains 103 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 55 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 20 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN R 190 ASN A 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7021 Z= 0.217 Angle : 0.640 9.442 9543 Z= 0.324 Chirality : 0.044 0.200 1123 Planarity : 0.004 0.058 1190 Dihedral : 5.640 56.773 1023 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.61 % Allowed : 19.44 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.29), residues: 869 helix: 1.87 (0.27), residues: 386 sheet: -0.03 (0.37), residues: 197 loop : -1.11 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 326 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE A 219 TYR 0.036 0.002 TYR R 176 ARG 0.005 0.001 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5470 (OUTLIER) cc_final: 0.4869 (t80) REVERT: B 269 ILE cc_start: 0.5236 (mm) cc_final: 0.4764 (mt) REVERT: R 92 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7098 (mp) REVERT: R 126 SER cc_start: 0.8263 (t) cc_final: 0.8010 (p) REVERT: R 155 LYS cc_start: 0.6810 (OUTLIER) cc_final: 0.6448 (mptp) REVERT: R 187 LYS cc_start: 0.6874 (mttt) cc_final: 0.6659 (mtpt) REVERT: R 205 MET cc_start: 0.4416 (ptm) cc_final: 0.3952 (pmm) REVERT: R 306 MET cc_start: 0.4810 (OUTLIER) cc_final: 0.4489 (pp-130) REVERT: A 360 TYR cc_start: 0.6126 (m-80) cc_final: 0.5923 (m-80) REVERT: A 380 LYS cc_start: 0.7185 (tmtt) cc_final: 0.6681 (tptt) REVERT: A 390 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8011 (tm-30) outliers start: 26 outliers final: 15 residues processed: 113 average time/residue: 0.9627 time to fit residues: 115.9433 Evaluate side-chains 104 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 LYS Chi-restraints excluded: chain R residue 190 ASN Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 299 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7021 Z= 0.365 Angle : 0.752 8.970 9543 Z= 0.382 Chirality : 0.047 0.197 1123 Planarity : 0.005 0.059 1190 Dihedral : 6.030 55.573 1023 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.89 % Allowed : 20.00 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.29), residues: 869 helix: 1.62 (0.26), residues: 384 sheet: -0.20 (0.38), residues: 184 loop : -1.20 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 326 HIS 0.009 0.002 HIS A 357 PHE 0.023 0.002 PHE A 246 TYR 0.025 0.002 TYR R 176 ARG 0.007 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.4775 (t80) REVERT: B 269 ILE cc_start: 0.5240 (mm) cc_final: 0.4750 (mt) REVERT: R 92 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7123 (mp) REVERT: R 126 SER cc_start: 0.8313 (t) cc_final: 0.7946 (p) REVERT: R 155 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6501 (mptp) REVERT: R 205 MET cc_start: 0.4433 (ptm) cc_final: 0.3165 (pmm) REVERT: R 235 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7042 (mp0) REVERT: R 306 MET cc_start: 0.5006 (OUTLIER) cc_final: 0.4672 (pp-130) REVERT: A 380 LYS cc_start: 0.7215 (tmtt) cc_final: 0.6686 (tptt) REVERT: A 390 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7999 (tm-30) outliers start: 28 outliers final: 15 residues processed: 110 average time/residue: 0.9766 time to fit residues: 114.5771 Evaluate side-chains 110 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 155 LYS Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7021 Z= 0.226 Angle : 0.679 9.044 9543 Z= 0.344 Chirality : 0.044 0.170 1123 Planarity : 0.004 0.055 1190 Dihedral : 5.813 55.748 1023 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.75 % Allowed : 21.39 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.29), residues: 869 helix: 1.76 (0.27), residues: 379 sheet: -0.20 (0.38), residues: 186 loop : -1.19 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 326 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.002 PHE B 151 TYR 0.028 0.002 TYR A 360 ARG 0.005 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.807 Fit side-chains REVERT: B 55 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7826 (mt) REVERT: B 234 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.4983 (t80) REVERT: B 269 ILE cc_start: 0.5208 (mm) cc_final: 0.4762 (mt) REVERT: R 92 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7153 (mp) REVERT: R 126 SER cc_start: 0.8272 (t) cc_final: 0.8050 (p) REVERT: R 205 MET cc_start: 0.4327 (ptm) cc_final: 0.3892 (pmm) REVERT: R 235 GLU cc_start: 0.7263 (mm-30) cc_final: 0.7057 (mp0) REVERT: R 306 MET cc_start: 0.5015 (OUTLIER) cc_final: 0.4728 (pp-130) REVERT: R 373 MET cc_start: 0.5792 (OUTLIER) cc_final: 0.5084 (tmt) REVERT: A 380 LYS cc_start: 0.7188 (tmtt) cc_final: 0.6654 (tptt) REVERT: A 390 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7973 (tm-30) outliers start: 27 outliers final: 15 residues processed: 104 average time/residue: 0.9919 time to fit residues: 110.0898 Evaluate side-chains 106 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 308 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7021 Z= 0.191 Angle : 0.660 9.640 9543 Z= 0.333 Chirality : 0.043 0.187 1123 Planarity : 0.004 0.050 1190 Dihedral : 5.634 55.064 1023 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.19 % Allowed : 22.22 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.29), residues: 869 helix: 1.77 (0.27), residues: 380 sheet: -0.20 (0.38), residues: 192 loop : -1.12 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 326 HIS 0.006 0.001 HIS R 210 PHE 0.015 0.001 PHE B 222 TYR 0.020 0.001 TYR R 176 ARG 0.004 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 0.850 Fit side-chains REVERT: B 234 PHE cc_start: 0.5571 (OUTLIER) cc_final: 0.4895 (t80) REVERT: B 269 ILE cc_start: 0.5242 (mm) cc_final: 0.4769 (mt) REVERT: R 126 SER cc_start: 0.8314 (t) cc_final: 0.8039 (p) REVERT: R 205 MET cc_start: 0.4169 (ptm) cc_final: 0.2932 (pmm) REVERT: R 306 MET cc_start: 0.5041 (OUTLIER) cc_final: 0.4784 (pp-130) REVERT: R 329 ILE cc_start: 0.7861 (tp) cc_final: 0.7554 (mp) REVERT: A 390 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7994 (tm-30) outliers start: 23 outliers final: 12 residues processed: 102 average time/residue: 0.9438 time to fit residues: 102.7822 Evaluate side-chains 99 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 190 ASN Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 55 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 0.0970 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7021 Z= 0.235 Angle : 0.730 13.767 9543 Z= 0.361 Chirality : 0.045 0.240 1123 Planarity : 0.004 0.049 1190 Dihedral : 5.690 54.536 1023 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.06 % Allowed : 23.06 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.29), residues: 869 helix: 1.72 (0.27), residues: 381 sheet: -0.36 (0.38), residues: 193 loop : -1.08 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 326 HIS 0.008 0.002 HIS R 210 PHE 0.027 0.002 PHE R 93 TYR 0.051 0.002 TYR A 360 ARG 0.003 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7783 (mt) REVERT: B 234 PHE cc_start: 0.5689 (OUTLIER) cc_final: 0.4908 (t80) REVERT: B 269 ILE cc_start: 0.5277 (mm) cc_final: 0.4790 (mt) REVERT: R 126 SER cc_start: 0.8305 (t) cc_final: 0.8066 (p) REVERT: R 235 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: R 306 MET cc_start: 0.5066 (OUTLIER) cc_final: 0.4856 (pp-130) REVERT: R 329 ILE cc_start: 0.7894 (tp) cc_final: 0.7562 (mp) REVERT: A 380 LYS cc_start: 0.7180 (tmtt) cc_final: 0.6653 (tptt) REVERT: A 390 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8000 (tm-30) outliers start: 22 outliers final: 14 residues processed: 97 average time/residue: 0.9919 time to fit residues: 102.5805 Evaluate side-chains 100 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 190 ASN Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 308 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 189 ASN ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7021 Z= 0.194 Angle : 0.725 13.063 9543 Z= 0.358 Chirality : 0.044 0.229 1123 Planarity : 0.004 0.048 1190 Dihedral : 5.597 54.189 1023 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.92 % Allowed : 23.33 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.29), residues: 869 helix: 1.78 (0.27), residues: 380 sheet: -0.38 (0.38), residues: 194 loop : -1.07 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 326 HIS 0.007 0.001 HIS R 210 PHE 0.023 0.001 PHE R 93 TYR 0.026 0.001 TYR R 176 ARG 0.008 0.000 ARG A 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: B 43 ILE cc_start: 0.6305 (OUTLIER) cc_final: 0.5901 (mp) REVERT: B 55 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7698 (mt) REVERT: B 234 PHE cc_start: 0.5607 (OUTLIER) cc_final: 0.4948 (t80) REVERT: B 269 ILE cc_start: 0.5235 (mm) cc_final: 0.4757 (mt) REVERT: R 126 SER cc_start: 0.8332 (t) cc_final: 0.8094 (p) REVERT: R 235 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: R 306 MET cc_start: 0.5017 (OUTLIER) cc_final: 0.4816 (pp-130) REVERT: R 329 ILE cc_start: 0.7860 (tp) cc_final: 0.7529 (mp) REVERT: A 390 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8012 (tm-30) outliers start: 21 outliers final: 13 residues processed: 98 average time/residue: 0.9608 time to fit residues: 100.8958 Evaluate side-chains 100 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 18 optimal weight: 0.0980 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 0.0370 chunk 70 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 ASN ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.155979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.130336 restraints weight = 14657.892| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.87 r_work: 0.4113 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7021 Z= 0.180 Angle : 0.729 12.901 9543 Z= 0.355 Chirality : 0.044 0.242 1123 Planarity : 0.004 0.048 1190 Dihedral : 5.865 59.983 1023 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.64 % Allowed : 23.89 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.29), residues: 869 helix: 1.84 (0.27), residues: 379 sheet: -0.22 (0.39), residues: 189 loop : -1.04 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 326 HIS 0.006 0.001 HIS R 210 PHE 0.020 0.001 PHE R 93 TYR 0.035 0.002 TYR A 360 ARG 0.007 0.000 ARG A 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.60 seconds wall clock time: 56 minutes 58.22 seconds (3418.22 seconds total)