Starting phenix.real_space_refine on Fri Dec 27 13:16:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gsz_34244/12_2024/8gsz_34244.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gsz_34244/12_2024/8gsz_34244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gsz_34244/12_2024/8gsz_34244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gsz_34244/12_2024/8gsz_34244.map" model { file = "/net/cci-nas-00/data/ceres_data/8gsz_34244/12_2024/8gsz_34244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gsz_34244/12_2024/8gsz_34244.cif" } resolution = 3.65 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 140 atoms to isotropic. 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 26 5.16 5 C 3118 2.51 5 N 854 2.21 5 O 872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2435 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 295} Chain breaks: 5 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Restraints were copied for chains: B Time building chain proxies: 4.04, per 1000 atoms: 0.83 Number of scatterers: 4870 At special positions: 0 Unit cell: (84.609, 73.899, 106.029, 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 26 16.00 O 872 8.00 N 854 7.00 C 3118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.15 Conformation dependent library (CDL) restraints added in 561.0 milliseconds 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 62.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.551A pdb=" N ALA A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.678A pdb=" N GLU A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 65 removed outlier: 3.593A pdb=" N VAL A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 4.025A pdb=" N ARG A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 80 through 90 removed outlier: 3.844A pdb=" N THR A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 108 removed outlier: 4.134A pdb=" N ARG A 95 " --> pdb=" O CYS A 91 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 134 removed outlier: 4.115A pdb=" N LEU A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 151 removed outlier: 3.505A pdb=" N LEU A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 167 removed outlier: 3.590A pdb=" N SER A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.655A pdb=" N ARG A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 186 " --> pdb=" O TYR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 removed outlier: 3.717A pdb=" N GLN A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.643A pdb=" N ALA A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.978A pdb=" N GLU A 296 " --> pdb=" O CYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.719A pdb=" N GLN A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 307 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 307' Processing helix chain 'A' and resid 324 through 335 removed outlier: 4.250A pdb=" N GLU A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.551A pdb=" N ALA B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 23 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 38 removed outlier: 3.678A pdb=" N GLU B 38 " --> pdb=" O TRP B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 65 removed outlier: 3.593A pdb=" N VAL B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 4.025A pdb=" N ARG B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 78 Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.844A pdb=" N THR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 108 removed outlier: 4.134A pdb=" N ARG B 95 " --> pdb=" O CYS B 91 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 134 removed outlier: 4.115A pdb=" N LEU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 132 " --> pdb=" O GLN B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 removed outlier: 3.505A pdb=" N LEU B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 167 removed outlier: 3.590A pdb=" N SER B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.655A pdb=" N ARG B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 186 " --> pdb=" O TYR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 273 removed outlier: 3.717A pdb=" N GLN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 removed outlier: 3.643A pdb=" N ALA B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 302 removed outlier: 3.978A pdb=" N GLU B 296 " --> pdb=" O CYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 307 removed outlier: 3.719A pdb=" N GLN B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 307' Processing helix chain 'B' and resid 324 through 335 removed outlier: 4.250A pdb=" N GLU B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 249 removed outlier: 3.691A pdb=" N GLY A 255 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU A 249 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 198 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE A 312 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 200 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 249 removed outlier: 3.691A pdb=" N GLY B 255 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU B 249 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ARG B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 198 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE B 312 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 200 " --> pdb=" O ILE B 312 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 612 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: 1.25 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1588 1.34 - 1.46: 1126 1.46 - 1.58: 2226 1.58 - 1.70: 0 1.70 - 1.81: 32 Bond restraints: 4972 Sorted by residual: bond pdb=" N VAL A 194 " pdb=" CA VAL A 194 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.66e+00 bond pdb=" N VAL B 194 " pdb=" CA VAL B 194 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.66e+00 bond pdb=" N HIS B 72 " pdb=" CA HIS B 72 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.18e-02 7.18e+03 8.92e+00 bond pdb=" N HIS A 72 " pdb=" CA HIS A 72 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.18e-02 7.18e+03 8.92e+00 bond pdb=" N ILE A 73 " pdb=" CA ILE A 73 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.70e+00 ... (remaining 4967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 6328 1.58 - 3.16: 326 3.16 - 4.74: 54 4.74 - 6.32: 28 6.32 - 7.90: 4 Bond angle restraints: 6740 Sorted by residual: angle pdb=" C TYR A 77 " pdb=" N ARG A 78 " pdb=" CA ARG A 78 " ideal model delta sigma weight residual 122.08 127.51 -5.43 1.47e+00 4.63e-01 1.37e+01 angle pdb=" C TYR B 77 " pdb=" N ARG B 78 " pdb=" CA ARG B 78 " ideal model delta sigma weight residual 122.08 127.51 -5.43 1.47e+00 4.63e-01 1.37e+01 angle pdb=" C GLU B 249 " pdb=" N ASN B 250 " pdb=" CA ASN B 250 " ideal model delta sigma weight residual 122.46 127.15 -4.69 1.41e+00 5.03e-01 1.11e+01 angle pdb=" C GLU A 249 " pdb=" N ASN A 250 " pdb=" CA ASN A 250 " ideal model delta sigma weight residual 122.46 127.15 -4.69 1.41e+00 5.03e-01 1.11e+01 angle pdb=" CA ILE B 73 " pdb=" C ILE B 73 " pdb=" O ILE B 73 " ideal model delta sigma weight residual 120.95 117.51 3.44 1.04e+00 9.25e-01 1.09e+01 ... (remaining 6735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 2532 14.97 - 29.95: 302 29.95 - 44.92: 106 44.92 - 59.89: 12 59.89 - 74.86: 14 Dihedral angle restraints: 2966 sinusoidal: 1164 harmonic: 1802 Sorted by residual: dihedral pdb=" CA ASN B 154 " pdb=" C ASN B 154 " pdb=" N VAL B 155 " pdb=" CA VAL B 155 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ASN A 154 " pdb=" C ASN A 154 " pdb=" N VAL A 155 " pdb=" CA VAL A 155 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA GLU B 328 " pdb=" C GLU B 328 " pdb=" N VAL B 329 " pdb=" CA VAL B 329 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 2963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 442 0.040 - 0.079: 242 0.079 - 0.118: 54 0.118 - 0.158: 16 0.158 - 0.197: 8 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA LEU A 198 " pdb=" N LEU A 198 " pdb=" C LEU A 198 " pdb=" CB LEU A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA LEU B 198 " pdb=" N LEU B 198 " pdb=" C LEU B 198 " pdb=" CB LEU B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA ARG B 71 " pdb=" N ARG B 71 " pdb=" C ARG B 71 " pdb=" CB ARG B 71 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 759 not shown) Planarity restraints: 854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 263 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO B 264 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 264 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 264 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 263 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 264 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 172 " 0.036 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO B 173 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " 0.030 5.00e-02 4.00e+02 ... (remaining 851 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1064 2.77 - 3.30: 4390 3.30 - 3.84: 7845 3.84 - 4.37: 9309 4.37 - 4.90: 15438 Nonbonded interactions: 38046 Sorted by model distance: nonbonded pdb=" NH2 ARG A 197 " pdb=" CG ARG A 310 " model vdw 2.241 3.520 nonbonded pdb=" NH2 ARG B 197 " pdb=" CG ARG B 310 " model vdw 2.241 3.520 nonbonded pdb=" OE1 GLU B 246 " pdb=" OG1 THR B 256 " model vdw 2.279 3.040 nonbonded pdb=" OE1 GLU A 246 " pdb=" OG1 THR A 256 " model vdw 2.279 3.040 nonbonded pdb=" O LEU B 99 " pdb=" OG SER B 102 " model vdw 2.365 3.040 ... (remaining 38041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 3.240 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: 0.380 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 15.810 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 22.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 0.099 4972 Z= 0.373 Angle : 0.862 7.903 6740 Z= 0.489 Chirality : 0.051 0.197 762 Planarity : 0.006 0.063 854 Dihedral : 15.613 74.864 1806 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.39 % Allowed : 10.85 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.38 (0.24), residues: 596 helix: -4.27 (0.12), residues: 348 sheet: -2.93 (0.62), residues: 36 loop : -1.91 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 119 HIS 0.002 0.001 HIS A 7 PHE 0.009 0.002 PHE B 117 TYR 0.007 0.001 TYR A 107 ARG 0.001 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.589 Fit side-chains REVERT: A 42 HIS cc_start: 0.6621 (m-70) cc_final: 0.6383 (m90) REVERT: A 132 ILE cc_start: 0.8956 (pt) cc_final: 0.8731 (pt) REVERT: A 223 ASP cc_start: 0.6769 (m-30) cc_final: 0.6561 (m-30) REVERT: A 269 PHE cc_start: 0.8515 (t80) cc_final: 0.7921 (t80) REVERT: A 310 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.7159 (mmm-85) REVERT: B 42 HIS cc_start: 0.6619 (m-70) cc_final: 0.6381 (m90) REVERT: B 132 ILE cc_start: 0.8957 (pt) cc_final: 0.8731 (pt) REVERT: B 223 ASP cc_start: 0.6768 (m-30) cc_final: 0.6556 (m-30) REVERT: B 269 PHE cc_start: 0.8517 (t80) cc_final: 0.7924 (t80) REVERT: B 310 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.7159 (mmm-85) outliers start: 2 outliers final: 0 residues processed: 164 average time/residue: 0.2310 time to fit residues: 47.0771 Evaluate side-chains 116 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 61 ASN A 74 HIS A 131 ASN A 154 ASN A 157 HIS A 218 ASN A 273 GLN A 307 ASN B 7 HIS B 61 ASN B 74 HIS B 131 ASN B 154 ASN B 157 HIS B 218 ASN B 273 GLN B 307 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4972 Z= 0.180 Angle : 0.619 6.330 6740 Z= 0.306 Chirality : 0.041 0.130 762 Planarity : 0.005 0.041 854 Dihedral : 4.833 25.615 684 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.33 % Allowed : 19.38 % Favored : 78.29 % 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: -3.82 (0.29), residues: 596 helix: -2.57 (0.21), residues: 378 sheet: -2.61 (0.66), residues: 42 loop : -1.80 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 34 HIS 0.002 0.001 HIS A 332 PHE 0.024 0.002 PHE B 221 TYR 0.011 0.001 TYR A 199 ARG 0.003 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.525 Fit side-chains REVERT: A 42 HIS cc_start: 0.6632 (m-70) cc_final: 0.6425 (m90) REVERT: A 199 TYR cc_start: 0.7837 (m-80) cc_final: 0.7616 (m-80) REVERT: A 269 PHE cc_start: 0.8368 (t80) cc_final: 0.7913 (t80) REVERT: B 42 HIS cc_start: 0.6628 (m-70) cc_final: 0.6420 (m90) REVERT: B 199 TYR cc_start: 0.7830 (m-80) cc_final: 0.7610 (m-80) REVERT: B 269 PHE cc_start: 0.8367 (t80) cc_final: 0.7913 (t80) outliers start: 12 outliers final: 6 residues processed: 132 average time/residue: 0.1350 time to fit residues: 23.5282 Evaluate side-chains 132 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 283 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 50 optimal weight: 0.0270 chunk 55 optimal weight: 0.3980 chunk 19 optimal weight: 0.0670 chunk 45 optimal weight: 0.7980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 61 ASN A 72 HIS B 3 HIS B 61 ASN B 72 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 4972 Z= 0.143 Angle : 0.581 5.656 6740 Z= 0.276 Chirality : 0.039 0.118 762 Planarity : 0.003 0.032 854 Dihedral : 4.371 22.542 684 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.49 % Allowed : 22.09 % Favored : 74.42 % 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: -2.64 (0.32), residues: 596 helix: -1.50 (0.25), residues: 370 sheet: -2.59 (0.70), residues: 42 loop : -1.64 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 HIS 0.004 0.001 HIS B 3 PHE 0.015 0.001 PHE A 221 TYR 0.008 0.001 TYR A 199 ARG 0.004 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.558 Fit side-chains outliers start: 18 outliers final: 4 residues processed: 132 average time/residue: 0.1558 time to fit residues: 26.6891 Evaluate side-chains 112 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 72 HIS B 3 HIS B 72 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4972 Z= 0.167 Angle : 0.597 7.954 6740 Z= 0.272 Chirality : 0.039 0.120 762 Planarity : 0.003 0.030 854 Dihedral : 4.223 22.662 684 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.88 % Allowed : 24.03 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.33), residues: 596 helix: -0.84 (0.27), residues: 372 sheet: -2.69 (0.75), residues: 36 loop : -1.82 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 34 HIS 0.004 0.001 HIS B 3 PHE 0.010 0.001 PHE A 117 TYR 0.008 0.001 TYR B 199 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.615 Fit side-chains REVERT: A 269 PHE cc_start: 0.8385 (t80) cc_final: 0.7903 (t80) REVERT: B 269 PHE cc_start: 0.8383 (t80) cc_final: 0.7903 (t80) outliers start: 20 outliers final: 16 residues processed: 126 average time/residue: 0.1750 time to fit residues: 28.5776 Evaluate side-chains 126 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 HIS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 0.0670 chunk 20 optimal weight: 0.0010 chunk 11 optimal weight: 3.9990 overall best weight: 0.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4972 Z= 0.140 Angle : 0.590 7.438 6740 Z= 0.268 Chirality : 0.038 0.143 762 Planarity : 0.003 0.027 854 Dihedral : 4.146 21.909 684 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.26 % Allowed : 26.74 % Favored : 68.99 % 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: -1.67 (0.34), residues: 596 helix: -0.47 (0.28), residues: 372 sheet: -2.59 (0.78), residues: 36 loop : -1.88 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 34 HIS 0.007 0.001 HIS B 3 PHE 0.010 0.001 PHE A 221 TYR 0.007 0.001 TYR B 274 ARG 0.003 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.881 Fit side-chains REVERT: A 269 PHE cc_start: 0.8338 (t80) cc_final: 0.7824 (t80) REVERT: B 269 PHE cc_start: 0.8336 (t80) cc_final: 0.7823 (t80) outliers start: 22 outliers final: 12 residues processed: 140 average time/residue: 0.1536 time to fit residues: 28.6840 Evaluate side-chains 131 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS A 154 ASN ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS B 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4972 Z= 0.188 Angle : 0.596 7.245 6740 Z= 0.272 Chirality : 0.040 0.120 762 Planarity : 0.003 0.027 854 Dihedral : 4.098 22.393 684 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.07 % Allowed : 26.36 % Favored : 69.57 % 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: -1.36 (0.34), residues: 596 helix: -0.21 (0.28), residues: 374 sheet: -1.81 (1.10), residues: 26 loop : -1.97 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 161 HIS 0.005 0.001 HIS B 3 PHE 0.005 0.001 PHE A 117 TYR 0.008 0.001 TYR A 199 ARG 0.002 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.663 Fit side-chains REVERT: A 269 PHE cc_start: 0.8443 (t80) cc_final: 0.8082 (t80) REVERT: B 269 PHE cc_start: 0.8440 (t80) cc_final: 0.8076 (t80) outliers start: 21 outliers final: 15 residues processed: 136 average time/residue: 0.1533 time to fit residues: 27.5712 Evaluate side-chains 137 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4972 Z= 0.239 Angle : 0.634 7.409 6740 Z= 0.290 Chirality : 0.041 0.134 762 Planarity : 0.003 0.029 854 Dihedral : 4.241 24.180 684 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.62 % Allowed : 26.74 % Favored : 67.64 % 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: -1.13 (0.34), residues: 596 helix: -0.00 (0.28), residues: 362 sheet: -2.35 (0.89), residues: 32 loop : -1.70 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 161 HIS 0.007 0.001 HIS A 3 PHE 0.007 0.001 PHE A 117 TYR 0.010 0.001 TYR B 199 ARG 0.006 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.619 Fit side-chains REVERT: A 260 GLU cc_start: 0.7985 (pp20) cc_final: 0.7646 (pp20) REVERT: A 269 PHE cc_start: 0.8507 (t80) cc_final: 0.8136 (t80) REVERT: B 260 GLU cc_start: 0.7991 (pp20) cc_final: 0.7647 (pp20) REVERT: B 269 PHE cc_start: 0.8507 (t80) cc_final: 0.8135 (t80) outliers start: 29 outliers final: 21 residues processed: 136 average time/residue: 0.1880 time to fit residues: 33.1223 Evaluate side-chains 134 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4972 Z= 0.213 Angle : 0.609 7.473 6740 Z= 0.282 Chirality : 0.041 0.145 762 Planarity : 0.003 0.030 854 Dihedral : 4.189 23.458 684 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.26 % Allowed : 28.49 % Favored : 67.25 % 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: -0.94 (0.34), residues: 596 helix: 0.13 (0.28), residues: 360 sheet: -2.50 (0.87), residues: 32 loop : -1.51 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 161 HIS 0.012 0.001 HIS B 3 PHE 0.005 0.001 PHE B 117 TYR 0.009 0.001 TYR B 199 ARG 0.006 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.614 Fit side-chains REVERT: A 81 TYR cc_start: 0.7832 (m-80) cc_final: 0.7491 (m-80) REVERT: A 269 PHE cc_start: 0.8472 (t80) cc_final: 0.8089 (t80) REVERT: B 81 TYR cc_start: 0.7826 (m-80) cc_final: 0.7486 (m-80) REVERT: B 260 GLU cc_start: 0.7993 (pp20) cc_final: 0.7706 (pp20) REVERT: B 269 PHE cc_start: 0.8472 (t80) cc_final: 0.8110 (t80) outliers start: 22 outliers final: 18 residues processed: 128 average time/residue: 0.1506 time to fit residues: 25.3439 Evaluate side-chains 136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4972 Z= 0.204 Angle : 0.626 7.772 6740 Z= 0.293 Chirality : 0.040 0.145 762 Planarity : 0.004 0.039 854 Dihedral : 4.235 23.062 684 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.07 % Allowed : 29.46 % Favored : 66.47 % 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: -0.91 (0.35), residues: 596 helix: 0.16 (0.28), residues: 372 sheet: -2.10 (0.64), residues: 54 loop : -1.54 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 161 HIS 0.008 0.001 HIS A 3 PHE 0.009 0.001 PHE B 117 TYR 0.010 0.001 TYR A 261 ARG 0.003 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.575 Fit side-chains REVERT: A 81 TYR cc_start: 0.7864 (m-80) cc_final: 0.7474 (m-80) REVERT: A 269 PHE cc_start: 0.8448 (t80) cc_final: 0.8119 (t80) REVERT: B 81 TYR cc_start: 0.7857 (m-80) cc_final: 0.7472 (m-80) REVERT: B 260 GLU cc_start: 0.8026 (pp20) cc_final: 0.7784 (pp20) REVERT: B 269 PHE cc_start: 0.8455 (t80) cc_final: 0.8117 (t80) outliers start: 21 outliers final: 16 residues processed: 133 average time/residue: 0.1574 time to fit residues: 27.1508 Evaluate side-chains 129 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 0.0370 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4972 Z= 0.160 Angle : 0.619 7.749 6740 Z= 0.290 Chirality : 0.039 0.146 762 Planarity : 0.004 0.034 854 Dihedral : 4.102 21.681 684 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.29 % Allowed : 30.23 % Favored : 66.47 % 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: -0.70 (0.36), residues: 596 helix: 0.29 (0.28), residues: 372 sheet: -2.78 (0.72), residues: 38 loop : -1.31 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 82 HIS 0.009 0.001 HIS A 3 PHE 0.019 0.001 PHE B 117 TYR 0.009 0.001 TYR A 261 ARG 0.011 0.000 ARG A 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1192 Ramachandran restraints generated. 596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.575 Fit side-chains REVERT: A 81 TYR cc_start: 0.7862 (m-80) cc_final: 0.7520 (m-10) REVERT: A 269 PHE cc_start: 0.8386 (t80) cc_final: 0.8055 (t80) REVERT: B 81 TYR cc_start: 0.7858 (m-80) cc_final: 0.7521 (m-10) REVERT: B 260 GLU cc_start: 0.8017 (pp20) cc_final: 0.7763 (pp20) REVERT: B 269 PHE cc_start: 0.8393 (t80) cc_final: 0.8060 (t80) outliers start: 17 outliers final: 13 residues processed: 136 average time/residue: 0.1626 time to fit residues: 28.6211 Evaluate side-chains 121 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 33 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.157297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.129191 restraints weight = 7963.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.132592 restraints weight = 4922.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.134928 restraints weight = 3638.201| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4972 Z= 0.165 Angle : 0.666 7.668 6740 Z= 0.324 Chirality : 0.041 0.197 762 Planarity : 0.004 0.044 854 Dihedral : 4.079 21.804 684 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.91 % Allowed : 32.95 % Favored : 64.15 % 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: -0.82 (0.35), residues: 596 helix: 0.28 (0.28), residues: 374 sheet: -2.19 (0.81), residues: 40 loop : -1.74 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 82 HIS 0.008 0.001 HIS A 3 PHE 0.007 0.001 PHE A 221 TYR 0.010 0.001 TYR A 261 ARG 0.015 0.001 ARG A 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1552.79 seconds wall clock time: 29 minutes 38.77 seconds (1778.77 seconds total)