Starting phenix.real_space_refine on Mon Jul 28 09:14:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdz_14678/07_2025/7zdz_14678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdz_14678/07_2025/7zdz_14678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zdz_14678/07_2025/7zdz_14678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdz_14678/07_2025/7zdz_14678.map" model { file = "/net/cci-nas-00/data/ceres_data/7zdz_14678/07_2025/7zdz_14678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdz_14678/07_2025/7zdz_14678.cif" } resolution = 4.3 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= 1.000 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: 6 Type Number sf(0) Gaussians Sr 2 13.11 5 K 1 8.98 5 S 79 5.16 5 C 6687 2.51 5 N 1736 2.21 5 O 1864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10369 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2611 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "B" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2575 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 8, 'TRANS': 312} Chain: "C" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2572 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 8, 'TRANS': 312} Chain: "D" Number of atoms: 2608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2608 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' SR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' SR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.77, per 1000 atoms: 0.65 Number of scatterers: 10369 At special positions: 0 Unit cell: (99.76, 96.32, 132.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Sr 2 37.98 K 1 19.00 S 79 16.00 O 1864 8.00 N 1736 7.00 C 6687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 154 " distance=2.03 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: 2.91 Conformation dependent library (CDL) restraints added in 1.2 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 19 sheets defined 31.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 83 through 110 Processing helix chain 'A' and resid 128 through 141 Processing helix chain 'A' and resid 154 through 185 removed outlier: 3.909A pdb=" N LYS A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 removed outlier: 3.542A pdb=" N ILE A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.910A pdb=" N TYR A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 removed outlier: 4.212A pdb=" N LYS B 64 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 removed outlier: 3.688A pdb=" N ILE B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 80 " --> pdb=" O CYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 115 removed outlier: 3.849A pdb=" N LEU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 141 Processing helix chain 'B' and resid 154 through 185 Processing helix chain 'B' and resid 283 through 290 removed outlier: 3.535A pdb=" N ILE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 344 Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 83 through 111 Processing helix chain 'C' and resid 128 through 141 removed outlier: 3.832A pdb=" N ALA C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 181 removed outlier: 3.643A pdb=" N VAL C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 340 through 344 removed outlier: 4.392A pdb=" N ARG C 343 " --> pdb=" O ASP C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 110 removed outlier: 4.712A pdb=" N THR D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS D 76 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG D 80 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TRP D 81 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ARG D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP D 83 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET D 84 " --> pdb=" O ARG D 80 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL D 86 " --> pdb=" O ARG D 82 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'D' and resid 129 through 141 Processing helix chain 'D' and resid 154 through 184 removed outlier: 4.169A pdb=" N VAL D 158 " --> pdb=" O CYS D 154 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 357 through 364 removed outlier: 3.941A pdb=" N LEU D 361 " --> pdb=" O SER D 357 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194 Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269 removed outlier: 3.703A pdb=" N TRP A 212 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 249 removed outlier: 4.587A pdb=" N ARG A 235 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 293 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 313 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 58 removed outlier: 6.610A pdb=" N GLN B 57 " --> pdb=" O VAL C 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 204 Processing sheet with id=AA7, first strand: chain 'B' and resid 222 through 223 Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 249 removed outlier: 5.201A pdb=" N ARG B 235 " --> pdb=" O PRO B 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 325 Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 333 Processing sheet with id=AB2, first strand: chain 'C' and resid 194 through 195 removed outlier: 3.551A pdb=" N VAL C 200 " --> pdb=" O MET C 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AB4, first strand: chain 'C' and resid 242 through 249 removed outlier: 4.080A pdb=" N LEU C 245 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS C 233 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN C 247 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 231 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP C 249 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA C 229 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU C 224 " --> pdb=" O MET C 301 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N MET C 301 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 299 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AB6, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.908A pdb=" N VAL D 200 " --> pdb=" O MET D 211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 193 through 195 Processing sheet with id=AB8, first strand: chain 'D' and resid 242 through 249 removed outlier: 5.281A pdb=" N ARG D 235 " --> pdb=" O PRO D 244 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D 293 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 294 " --> pdb=" O TYR D 315 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 315 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER D 313 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 300 through 301 Processing sheet with id=AC1, first strand: chain 'D' and resid 324 through 325 389 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3293 1.34 - 1.46: 1831 1.46 - 1.58: 5368 1.58 - 1.70: 0 1.70 - 1.81: 111 Bond restraints: 10603 Sorted by residual: bond pdb=" CA TYR C 68 " pdb=" C TYR C 68 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.34e-02 5.57e+03 1.65e+01 bond pdb=" N ILE C 72 " pdb=" CA ILE C 72 " ideal model delta sigma weight residual 1.459 1.413 0.046 1.25e-02 6.40e+03 1.38e+01 bond pdb=" CA ASP C 71 " pdb=" C ASP C 71 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 9.80e+00 bond pdb=" CA LEU C 69 " pdb=" C LEU C 69 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.34e-02 5.57e+03 8.86e+00 bond pdb=" CA TYR D 280 " pdb=" C TYR D 280 " ideal model delta sigma weight residual 1.522 1.485 0.038 1.37e-02 5.33e+03 7.62e+00 ... (remaining 10598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 14188 3.20 - 6.39: 141 6.39 - 9.59: 17 9.59 - 12.78: 6 12.78 - 15.98: 1 Bond angle restraints: 14353 Sorted by residual: angle pdb=" N ASN A 127 " pdb=" CA ASN A 127 " pdb=" C ASN A 127 " ideal model delta sigma weight residual 112.03 96.05 15.98 1.31e+00 5.83e-01 1.49e+02 angle pdb=" N LYS B 334 " pdb=" CA LYS B 334 " pdb=" C LYS B 334 " ideal model delta sigma weight residual 108.67 98.31 10.36 1.67e+00 3.59e-01 3.85e+01 angle pdb=" N HIS C 335 " pdb=" CA HIS C 335 " pdb=" C HIS C 335 " ideal model delta sigma weight residual 113.17 105.47 7.70 1.26e+00 6.30e-01 3.73e+01 angle pdb=" N VAL D 264 " pdb=" CA VAL D 264 " pdb=" C VAL D 264 " ideal model delta sigma weight residual 113.71 108.30 5.41 9.50e-01 1.11e+00 3.25e+01 angle pdb=" C ILE C 72 " pdb=" N PHE C 73 " pdb=" CA PHE C 73 " ideal model delta sigma weight residual 121.54 110.92 10.62 1.91e+00 2.74e-01 3.09e+01 ... (remaining 14348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 5502 17.00 - 33.99: 619 33.99 - 50.99: 136 50.99 - 67.99: 15 67.99 - 84.98: 11 Dihedral angle restraints: 6283 sinusoidal: 2506 harmonic: 3777 Sorted by residual: dihedral pdb=" CB CYS C 122 " pdb=" SG CYS C 122 " pdb=" SG CYS C 154 " pdb=" CB CYS C 154 " ideal model delta sinusoidal sigma weight residual 93.00 27.40 65.60 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS D 122 " pdb=" SG CYS D 122 " pdb=" SG CYS D 154 " pdb=" CB CYS D 154 " ideal model delta sinusoidal sigma weight residual 93.00 143.20 -50.20 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CA TYR C 336 " pdb=" C TYR C 336 " pdb=" N TYR C 337 " pdb=" CA TYR C 337 " ideal model delta harmonic sigma weight residual -180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 6280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1205 0.049 - 0.098: 313 0.098 - 0.147: 85 0.147 - 0.196: 6 0.196 - 0.245: 7 Chirality restraints: 1616 Sorted by residual: chirality pdb=" CA ARG C 312 " pdb=" N ARG C 312 " pdb=" C ARG C 312 " pdb=" CB ARG C 312 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA GLU B 303 " pdb=" N GLU B 303 " pdb=" C GLU B 303 " pdb=" CB GLU B 303 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ARG A 312 " pdb=" N ARG A 312 " pdb=" C ARG A 312 " pdb=" CB ARG A 312 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1613 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 96 " -0.029 2.00e-02 2.50e+03 2.37e-02 1.40e+01 pdb=" CG TRP C 96 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP C 96 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 96 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 96 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 96 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 96 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 96 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 96 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 333 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C GLU C 333 " -0.046 2.00e-02 2.50e+03 pdb=" O GLU C 333 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS C 334 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 96 " -0.021 2.00e-02 2.50e+03 1.68e-02 7.05e+00 pdb=" CG TRP D 96 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 96 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP D 96 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 96 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 96 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 96 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 96 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 96 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 96 " 0.002 2.00e-02 2.50e+03 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 2205 2.78 - 3.37: 11861 3.37 - 3.96: 18161 3.96 - 4.55: 23246 4.55 - 5.14: 35191 Nonbonded interactions: 90664 Sorted by model distance: nonbonded pdb=" O ARG C 67 " pdb=" C TYR C 68 " model vdw 2.192 3.270 nonbonded pdb=" O ARG D 325 " pdb=" OG1 THR D 347 " model vdw 2.228 3.040 nonbonded pdb=" NH2 ARG D 46 " pdb=" OD2 ASP D 51 " model vdw 2.261 3.120 nonbonded pdb=" O ILE C 137 " pdb=" OG1 THR C 141 " model vdw 2.262 3.040 nonbonded pdb=" O VAL C 61 " pdb=" OH TYR D 341 " model vdw 2.281 3.040 ... (remaining 90659 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' and resid 44 through 363) selection = (chain 'B' and resid 44 through 363) selection = (chain 'C' and resid 44 through 363) selection = (chain 'D' and resid 44 through 363) } 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.310 Find NCS groups from input model: 0.560 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10607 Z= 0.209 Angle : 0.860 15.979 14361 Z= 0.503 Chirality : 0.048 0.245 1616 Planarity : 0.004 0.032 1808 Dihedral : 15.046 84.983 3823 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.14 % Favored : 88.55 % Rotamer: Outliers : 0.35 % Allowed : 1.14 % Favored : 98.50 % 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: -1.61 (0.23), residues: 1284 helix: 1.13 (0.27), residues: 367 sheet: -1.09 (0.39), residues: 157 loop : -2.32 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP C 96 HIS 0.008 0.001 HIS D 221 PHE 0.029 0.002 PHE D 103 TYR 0.019 0.001 TYR C 337 ARG 0.006 0.000 ARG C 312 Details of bonding type rmsd hydrogen bonds : bond 0.14555 ( 385) hydrogen bonds : angle 6.12263 ( 1086) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.58953 ( 8) covalent geometry : bond 0.00337 (10603) covalent geometry : angle 0.85984 (14353) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 259 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8594 (tm-30) REVERT: A 211 MET cc_start: 0.3964 (ttm) cc_final: 0.3406 (ttm) REVERT: A 247 GLN cc_start: 0.7961 (mp10) cc_final: 0.7543 (mp10) REVERT: A 295 VAL cc_start: 0.9078 (t) cc_final: 0.8826 (m) REVERT: B 134 LEU cc_start: 0.8661 (tt) cc_final: 0.8427 (tt) REVERT: B 360 ASP cc_start: 0.8541 (m-30) cc_final: 0.8277 (m-30) REVERT: C 211 MET cc_start: 0.4424 (ptm) cc_final: 0.3492 (ptm) REVERT: C 310 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7933 (tm-30) REVERT: C 312 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8621 (mtt180) REVERT: D 103 PHE cc_start: 0.7728 (m-80) cc_final: 0.7405 (m-80) REVERT: D 160 MET cc_start: 0.7867 (ttt) cc_final: 0.7550 (tpt) REVERT: D 285 GLN cc_start: 0.8382 (pp30) cc_final: 0.8008 (pp30) REVERT: D 299 GLU cc_start: 0.7847 (pt0) cc_final: 0.7631 (pp20) REVERT: D 341 TYR cc_start: 0.5369 (p90) cc_final: 0.5123 (p90) outliers start: 4 outliers final: 1 residues processed: 262 average time/residue: 0.1844 time to fit residues: 71.7515 Evaluate side-chains 228 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.174061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140458 restraints weight = 22755.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142644 restraints weight = 17469.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144814 restraints weight = 13929.500| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10607 Z= 0.260 Angle : 0.736 6.846 14361 Z= 0.402 Chirality : 0.048 0.152 1616 Planarity : 0.005 0.043 1808 Dihedral : 5.914 29.989 1397 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.55 % Favored : 86.29 % Rotamer: Outliers : 0.09 % Allowed : 10.48 % Favored : 89.44 % 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: -2.02 (0.23), residues: 1284 helix: 0.58 (0.26), residues: 365 sheet: -1.31 (0.39), residues: 163 loop : -2.47 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 96 HIS 0.012 0.002 HIS C 221 PHE 0.033 0.003 PHE D 133 TYR 0.020 0.002 TYR D 280 ARG 0.010 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.05461 ( 385) hydrogen bonds : angle 5.40246 ( 1086) SS BOND : bond 0.00384 ( 4) SS BOND : angle 0.36894 ( 8) covalent geometry : bond 0.00569 (10603) covalent geometry : angle 0.73649 (14353) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 247 GLN cc_start: 0.8204 (mp10) cc_final: 0.7751 (mp10) REVERT: A 310 GLN cc_start: 0.8610 (pp30) cc_final: 0.8332 (pp30) REVERT: B 134 LEU cc_start: 0.8984 (tt) cc_final: 0.8763 (tp) REVERT: B 299 GLU cc_start: 0.8024 (tt0) cc_final: 0.7808 (tt0) REVERT: C 211 MET cc_start: 0.5268 (ptm) cc_final: 0.4597 (ptm) REVERT: C 216 ASN cc_start: 0.7939 (m110) cc_final: 0.7676 (m-40) REVERT: D 211 MET cc_start: 0.7123 (ptp) cc_final: 0.6752 (ptp) REVERT: D 285 GLN cc_start: 0.8442 (pp30) cc_final: 0.8010 (pp30) REVERT: D 331 PHE cc_start: 0.8028 (t80) cc_final: 0.7740 (t80) REVERT: D 336 TYR cc_start: 0.7550 (m-10) cc_final: 0.7204 (m-10) REVERT: D 341 TYR cc_start: 0.5329 (p90) cc_final: 0.5058 (p90) outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.1772 time to fit residues: 66.8415 Evaluate side-chains 210 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 105 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 0.0020 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 140 GLN B 190 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 221 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.185217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.151205 restraints weight = 22155.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.154565 restraints weight = 15758.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.156573 restraints weight = 11992.403| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10607 Z= 0.119 Angle : 0.630 8.844 14361 Z= 0.333 Chirality : 0.045 0.162 1616 Planarity : 0.003 0.038 1808 Dihedral : 5.108 26.337 1397 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.44 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % 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: -1.62 (0.23), residues: 1284 helix: 1.14 (0.26), residues: 370 sheet: -0.87 (0.39), residues: 171 loop : -2.44 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 96 HIS 0.005 0.001 HIS B 335 PHE 0.040 0.002 PHE D 103 TYR 0.019 0.001 TYR B 337 ARG 0.009 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 385) hydrogen bonds : angle 4.73848 ( 1086) SS BOND : bond 0.00242 ( 4) SS BOND : angle 0.31210 ( 8) covalent geometry : bond 0.00242 (10603) covalent geometry : angle 0.62980 (14353) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7550 (mmp-170) cc_final: 0.6821 (tpp-160) REVERT: A 247 GLN cc_start: 0.8180 (mp10) cc_final: 0.7595 (mp10) REVERT: A 310 GLN cc_start: 0.8489 (pp30) cc_final: 0.8207 (pp30) REVERT: B 134 LEU cc_start: 0.9007 (tt) cc_final: 0.8793 (tp) REVERT: C 189 ARG cc_start: 0.7267 (ptp90) cc_final: 0.6712 (ptp90) REVERT: C 211 MET cc_start: 0.5042 (ptm) cc_final: 0.4378 (ptm) REVERT: C 216 ASN cc_start: 0.7806 (m110) cc_final: 0.7514 (m-40) REVERT: C 310 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8080 (tm-30) REVERT: D 103 PHE cc_start: 0.7928 (m-80) cc_final: 0.7680 (m-80) REVERT: D 285 GLN cc_start: 0.8435 (pp30) cc_final: 0.8004 (pp30) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1994 time to fit residues: 83.7021 Evaluate side-chains 231 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.177063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143131 restraints weight = 22254.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.146270 restraints weight = 16268.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.148623 restraints weight = 12565.852| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10607 Z= 0.192 Angle : 0.686 8.295 14361 Z= 0.368 Chirality : 0.047 0.163 1616 Planarity : 0.004 0.043 1808 Dihedral : 5.538 26.855 1397 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.63 % Favored : 86.21 % Rotamer: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.23), residues: 1284 helix: 0.80 (0.26), residues: 367 sheet: -1.17 (0.39), residues: 166 loop : -2.46 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 96 HIS 0.015 0.002 HIS D 221 PHE 0.029 0.002 PHE B 159 TYR 0.019 0.002 TYR B 337 ARG 0.009 0.001 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 385) hydrogen bonds : angle 5.02534 ( 1086) SS BOND : bond 0.00451 ( 4) SS BOND : angle 0.81655 ( 8) covalent geometry : bond 0.00427 (10603) covalent geometry : angle 0.68585 (14353) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7837 (mmp-170) cc_final: 0.7496 (mmt-90) REVERT: A 164 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8772 (tm-30) REVERT: A 310 GLN cc_start: 0.8504 (pp30) cc_final: 0.8262 (pp30) REVERT: B 360 ASP cc_start: 0.8588 (m-30) cc_final: 0.8289 (m-30) REVERT: C 164 GLN cc_start: 0.8985 (pp30) cc_final: 0.8742 (pp30) REVERT: C 189 ARG cc_start: 0.7022 (ptp90) cc_final: 0.6623 (ttt180) REVERT: C 200 VAL cc_start: 0.7966 (p) cc_final: 0.7719 (p) REVERT: C 211 MET cc_start: 0.5292 (ptm) cc_final: 0.4727 (ptm) REVERT: C 216 ASN cc_start: 0.8075 (m110) cc_final: 0.7466 (m-40) REVERT: C 310 GLN cc_start: 0.8505 (tm-30) cc_final: 0.7996 (tm-30) REVERT: D 211 MET cc_start: 0.6924 (ptp) cc_final: 0.6684 (ptp) REVERT: D 285 GLN cc_start: 0.8505 (pp30) cc_final: 0.8078 (pp30) REVERT: D 331 PHE cc_start: 0.7947 (t80) cc_final: 0.7723 (t80) REVERT: D 341 TYR cc_start: 0.5099 (p90) cc_final: 0.4756 (p90) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1856 time to fit residues: 71.8015 Evaluate side-chains 234 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 73 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.175425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.141660 restraints weight = 22383.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.145040 restraints weight = 16123.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.146721 restraints weight = 12360.144| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10607 Z= 0.211 Angle : 0.705 8.434 14361 Z= 0.381 Chirality : 0.048 0.201 1616 Planarity : 0.005 0.085 1808 Dihedral : 5.842 27.761 1397 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.02 % Favored : 85.83 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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: -2.16 (0.22), residues: 1284 helix: 0.50 (0.25), residues: 368 sheet: -1.40 (0.38), residues: 170 loop : -2.60 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 96 HIS 0.015 0.002 HIS D 271 PHE 0.047 0.002 PHE D 133 TYR 0.020 0.002 TYR C 145 ARG 0.008 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 385) hydrogen bonds : angle 5.18944 ( 1086) SS BOND : bond 0.00374 ( 4) SS BOND : angle 0.45819 ( 8) covalent geometry : bond 0.00470 (10603) covalent geometry : angle 0.70540 (14353) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7920 (mmp-170) cc_final: 0.7471 (mmt-90) REVERT: A 310 GLN cc_start: 0.8501 (pp30) cc_final: 0.8212 (pp30) REVERT: B 360 ASP cc_start: 0.8560 (m-30) cc_final: 0.8238 (m-30) REVERT: C 103 PHE cc_start: 0.7721 (m-80) cc_final: 0.7173 (m-80) REVERT: C 164 GLN cc_start: 0.9012 (pp30) cc_final: 0.8752 (pp30) REVERT: C 189 ARG cc_start: 0.6900 (ptp90) cc_final: 0.6387 (ttt180) REVERT: C 200 VAL cc_start: 0.8061 (p) cc_final: 0.7807 (p) REVERT: C 211 MET cc_start: 0.5444 (ptm) cc_final: 0.4964 (ptm) REVERT: C 216 ASN cc_start: 0.8121 (m110) cc_final: 0.7568 (m-40) REVERT: C 331 PHE cc_start: 0.8613 (m-80) cc_final: 0.8392 (m-80) REVERT: D 211 MET cc_start: 0.7184 (ptp) cc_final: 0.6767 (ptp) REVERT: D 285 GLN cc_start: 0.8521 (pp30) cc_final: 0.8072 (pp30) REVERT: D 331 PHE cc_start: 0.7980 (t80) cc_final: 0.7764 (t80) REVERT: D 341 TYR cc_start: 0.5321 (p90) cc_final: 0.4692 (p90) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1771 time to fit residues: 70.5872 Evaluate side-chains 226 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 9 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 HIS ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.178270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.144648 restraints weight = 22337.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.148057 restraints weight = 16295.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.149678 restraints weight = 12448.681| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10607 Z= 0.160 Angle : 0.672 9.449 14361 Z= 0.357 Chirality : 0.046 0.190 1616 Planarity : 0.004 0.055 1808 Dihedral : 5.595 28.686 1397 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.93 % Favored : 86.92 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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: -2.03 (0.23), residues: 1284 helix: 0.70 (0.25), residues: 368 sheet: -1.17 (0.40), residues: 165 loop : -2.61 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 96 HIS 0.011 0.001 HIS D 271 PHE 0.034 0.002 PHE D 133 TYR 0.017 0.002 TYR D 341 ARG 0.008 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 385) hydrogen bonds : angle 4.99868 ( 1086) SS BOND : bond 0.00267 ( 4) SS BOND : angle 0.53812 ( 8) covalent geometry : bond 0.00357 (10603) covalent geometry : angle 0.67172 (14353) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8007 (mmp-170) cc_final: 0.7533 (mmt-90) REVERT: B 50 LYS cc_start: 0.7889 (tptp) cc_final: 0.7575 (tppt) REVERT: B 360 ASP cc_start: 0.8596 (m-30) cc_final: 0.8222 (m-30) REVERT: C 103 PHE cc_start: 0.7608 (m-80) cc_final: 0.7297 (m-80) REVERT: C 164 GLN cc_start: 0.8983 (pp30) cc_final: 0.8745 (pp30) REVERT: C 189 ARG cc_start: 0.6759 (ptp90) cc_final: 0.6286 (ttt180) REVERT: C 211 MET cc_start: 0.5279 (ptm) cc_final: 0.4740 (ptm) REVERT: C 216 ASN cc_start: 0.8021 (m110) cc_final: 0.7760 (m-40) REVERT: C 310 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8305 (tm-30) REVERT: D 211 MET cc_start: 0.7170 (ptp) cc_final: 0.6787 (ptp) REVERT: D 285 GLN cc_start: 0.8490 (pp30) cc_final: 0.8036 (pp30) REVERT: D 299 GLU cc_start: 0.8224 (tt0) cc_final: 0.7945 (tt0) REVERT: D 331 PHE cc_start: 0.7936 (t80) cc_final: 0.7727 (t80) REVERT: D 341 TYR cc_start: 0.5331 (p90) cc_final: 0.5008 (p90) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1908 time to fit residues: 77.4582 Evaluate side-chains 229 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 120 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 HIS ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.180343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146697 restraints weight = 22557.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.150113 restraints weight = 16076.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.152304 restraints weight = 12169.138| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10607 Z= 0.143 Angle : 0.667 9.836 14361 Z= 0.350 Chirality : 0.046 0.218 1616 Planarity : 0.004 0.042 1808 Dihedral : 5.449 28.076 1397 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.77 % Favored : 87.07 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: -1.90 (0.23), residues: 1284 helix: 0.91 (0.26), residues: 366 sheet: -1.05 (0.40), residues: 165 loop : -2.59 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 96 HIS 0.008 0.001 HIS D 271 PHE 0.035 0.002 PHE D 129 TYR 0.019 0.001 TYR D 341 ARG 0.007 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 385) hydrogen bonds : angle 4.80945 ( 1086) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.44396 ( 8) covalent geometry : bond 0.00313 (10603) covalent geometry : angle 0.66675 (14353) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8018 (mmp-170) cc_final: 0.7502 (mmt-90) REVERT: A 183 MET cc_start: 0.7769 (mmm) cc_final: 0.7471 (mtt) REVERT: B 50 LYS cc_start: 0.7833 (tptp) cc_final: 0.7491 (tppt) REVERT: B 360 ASP cc_start: 0.8591 (m-30) cc_final: 0.8260 (m-30) REVERT: C 164 GLN cc_start: 0.8994 (pp30) cc_final: 0.8767 (pp30) REVERT: C 211 MET cc_start: 0.5298 (ptm) cc_final: 0.4746 (ptm) REVERT: C 216 ASN cc_start: 0.7953 (m110) cc_final: 0.7681 (m-40) REVERT: D 211 MET cc_start: 0.7109 (ptp) cc_final: 0.6714 (ptp) REVERT: D 285 GLN cc_start: 0.8435 (pp30) cc_final: 0.7982 (pp30) REVERT: D 299 GLU cc_start: 0.8150 (tt0) cc_final: 0.7903 (tt0) REVERT: D 341 TYR cc_start: 0.5303 (p90) cc_final: 0.5101 (p90) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1855 time to fit residues: 77.1236 Evaluate side-chains 236 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 73 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.173159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138990 restraints weight = 22609.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.142208 restraints weight = 16582.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144029 restraints weight = 12824.192| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10607 Z= 0.253 Angle : 0.779 8.778 14361 Z= 0.420 Chirality : 0.051 0.242 1616 Planarity : 0.005 0.053 1808 Dihedral : 6.226 30.992 1397 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.19 % Favored : 84.66 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.42 (0.22), residues: 1284 helix: 0.10 (0.25), residues: 369 sheet: -1.28 (0.40), residues: 167 loop : -2.73 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 96 HIS 0.022 0.002 HIS C 271 PHE 0.046 0.003 PHE D 133 TYR 0.023 0.002 TYR B 337 ARG 0.016 0.001 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.05516 ( 385) hydrogen bonds : angle 5.37899 ( 1086) SS BOND : bond 0.00263 ( 4) SS BOND : angle 0.38915 ( 8) covalent geometry : bond 0.00564 (10603) covalent geometry : angle 0.77872 (14353) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 ASP cc_start: 0.8544 (m-30) cc_final: 0.8176 (m-30) REVERT: C 103 PHE cc_start: 0.7820 (m-80) cc_final: 0.7224 (m-80) REVERT: C 164 GLN cc_start: 0.8976 (pp30) cc_final: 0.8738 (pp30) REVERT: C 200 VAL cc_start: 0.8075 (p) cc_final: 0.7829 (p) REVERT: C 211 MET cc_start: 0.5684 (ptm) cc_final: 0.5250 (ptm) REVERT: C 216 ASN cc_start: 0.8182 (m110) cc_final: 0.7516 (m-40) REVERT: C 310 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8250 (tm-30) REVERT: D 211 MET cc_start: 0.7278 (ptp) cc_final: 0.6900 (ptp) REVERT: D 285 GLN cc_start: 0.8502 (pp30) cc_final: 0.8029 (pp30) REVERT: D 299 GLU cc_start: 0.8218 (tt0) cc_final: 0.7876 (tt0) REVERT: D 331 PHE cc_start: 0.8053 (t80) cc_final: 0.7815 (t80) REVERT: D 341 TYR cc_start: 0.5584 (p90) cc_final: 0.5210 (p90) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1861 time to fit residues: 73.9353 Evaluate side-chains 223 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 271 HIS B 335 HIS ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 HIS ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 HIS ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.177362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143962 restraints weight = 22411.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.147326 restraints weight = 16343.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.149364 restraints weight = 12304.971| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10607 Z= 0.169 Angle : 0.727 9.773 14361 Z= 0.382 Chirality : 0.048 0.170 1616 Planarity : 0.004 0.056 1808 Dihedral : 5.833 30.362 1397 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.02 % Favored : 85.83 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.21 (0.22), residues: 1284 helix: 0.40 (0.25), residues: 368 sheet: -1.18 (0.40), residues: 167 loop : -2.67 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 96 HIS 0.016 0.002 HIS C 271 PHE 0.032 0.002 PHE B 159 TYR 0.027 0.002 TYR D 341 ARG 0.009 0.001 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04872 ( 385) hydrogen bonds : angle 5.04261 ( 1086) SS BOND : bond 0.00323 ( 4) SS BOND : angle 0.38603 ( 8) covalent geometry : bond 0.00376 (10603) covalent geometry : angle 0.72677 (14353) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.7685 (tptp) cc_final: 0.7415 (tppt) REVERT: B 164 GLN cc_start: 0.9134 (pp30) cc_final: 0.8882 (pp30) REVERT: B 360 ASP cc_start: 0.8587 (m-30) cc_final: 0.8255 (m-30) REVERT: C 103 PHE cc_start: 0.7677 (m-80) cc_final: 0.7334 (m-80) REVERT: C 164 GLN cc_start: 0.8998 (pp30) cc_final: 0.8780 (pp30) REVERT: C 200 VAL cc_start: 0.7946 (p) cc_final: 0.7702 (p) REVERT: C 211 MET cc_start: 0.5526 (ptm) cc_final: 0.5056 (ptm) REVERT: C 216 ASN cc_start: 0.8088 (m110) cc_final: 0.7484 (m-40) REVERT: D 211 MET cc_start: 0.7127 (ptp) cc_final: 0.6738 (ptp) REVERT: D 285 GLN cc_start: 0.8494 (pp30) cc_final: 0.8057 (pp30) REVERT: D 299 GLU cc_start: 0.8117 (tt0) cc_final: 0.7827 (tt0) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1898 time to fit residues: 75.9470 Evaluate side-chains 220 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 78 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 24 optimal weight: 0.0870 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.181667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147764 restraints weight = 22213.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.151304 restraints weight = 16200.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.153440 restraints weight = 12157.918| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10607 Z= 0.136 Angle : 0.715 10.045 14361 Z= 0.372 Chirality : 0.047 0.158 1616 Planarity : 0.004 0.035 1808 Dihedral : 5.466 28.954 1397 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.08 % Favored : 86.76 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -1.99 (0.23), residues: 1284 helix: 0.64 (0.26), residues: 369 sheet: -0.91 (0.41), residues: 160 loop : -2.59 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 96 HIS 0.009 0.001 HIS C 271 PHE 0.034 0.002 PHE A 159 TYR 0.019 0.001 TYR B 337 ARG 0.007 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04543 ( 385) hydrogen bonds : angle 4.86219 ( 1086) SS BOND : bond 0.00291 ( 4) SS BOND : angle 0.34577 ( 8) covalent geometry : bond 0.00296 (10603) covalent geometry : angle 0.71525 (14353) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8051 (mmp-170) cc_final: 0.7618 (mmt-90) REVERT: A 103 PHE cc_start: 0.7577 (m-80) cc_final: 0.7329 (m-80) REVERT: B 50 LYS cc_start: 0.7686 (tptp) cc_final: 0.7336 (tppt) REVERT: B 164 GLN cc_start: 0.9116 (pp30) cc_final: 0.8884 (pp30) REVERT: B 293 GLU cc_start: 0.8092 (tp30) cc_final: 0.7471 (tm-30) REVERT: B 360 ASP cc_start: 0.8626 (m-30) cc_final: 0.8264 (m-30) REVERT: C 103 PHE cc_start: 0.7712 (m-80) cc_final: 0.7495 (m-80) REVERT: C 164 GLN cc_start: 0.8973 (pp30) cc_final: 0.8741 (pp30) REVERT: C 211 MET cc_start: 0.5275 (ptm) cc_final: 0.4745 (ptm) REVERT: C 216 ASN cc_start: 0.7915 (m110) cc_final: 0.7299 (m-40) REVERT: D 72 ILE cc_start: 0.8534 (mt) cc_final: 0.8260 (mt) REVERT: D 211 MET cc_start: 0.7050 (ptp) cc_final: 0.6631 (ptp) REVERT: D 285 GLN cc_start: 0.8526 (pp30) cc_final: 0.7968 (pp30) REVERT: D 299 GLU cc_start: 0.7989 (tt0) cc_final: 0.7764 (tt0) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1780 time to fit residues: 71.5203 Evaluate side-chains 229 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.178165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.144040 restraints weight = 22175.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.147278 restraints weight = 16296.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.149832 restraints weight = 12263.381| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10607 Z= 0.181 Angle : 0.741 9.171 14361 Z= 0.389 Chirality : 0.048 0.180 1616 Planarity : 0.004 0.046 1808 Dihedral : 5.732 29.061 1397 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.71 % Favored : 86.14 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -2.10 (0.22), residues: 1284 helix: 0.51 (0.25), residues: 369 sheet: -0.99 (0.41), residues: 160 loop : -2.63 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 96 HIS 0.011 0.002 HIS C 271 PHE 0.041 0.002 PHE D 92 TYR 0.022 0.002 TYR B 337 ARG 0.010 0.001 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 385) hydrogen bonds : angle 4.96507 ( 1086) SS BOND : bond 0.00296 ( 4) SS BOND : angle 0.33122 ( 8) covalent geometry : bond 0.00402 (10603) covalent geometry : angle 0.74076 (14353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3309.35 seconds wall clock time: 58 minutes 27.41 seconds (3507.41 seconds total)