Starting phenix.real_space_refine on Tue Feb 11 22:12:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8teq_41195/02_2025/8teq_41195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8teq_41195/02_2025/8teq_41195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8teq_41195/02_2025/8teq_41195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8teq_41195/02_2025/8teq_41195.map" model { file = "/net/cci-nas-00/data/ceres_data/8teq_41195/02_2025/8teq_41195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8teq_41195/02_2025/8teq_41195.cif" } resolution = 2.84 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: 3 Type Number sf(0) Gaussians C 4185 2.51 5 N 1155 2.21 5 O 1365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6705 Number of models: 1 Model: "" Number of chains: 2 Chain: "0" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "1" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 211 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Restraints were copied for chains: 3, B, D, F, H, J, L, N, P, R, T, V, X, Z, 2, A, C, E, G, I, K, M, O, Q, S, U, W, Y Time building chain proxies: 2.95, per 1000 atoms: 0.44 Number of scatterers: 6705 At special positions: 0 Unit cell: (65.36, 65.36, 89.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1365 8.00 N 1155 7.00 C 4185 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: 1.46 Conformation dependent library (CDL) restraints added in 637.4 milliseconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1530 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing sheet with id=AA1, first strand: chain '0' and resid 266 through 274 removed outlier: 6.765A pdb=" N GLN W 266 " --> pdb=" O GLN 0 267 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL 0 269 " --> pdb=" O GLN W 266 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR W 268 " --> pdb=" O VAL 0 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN 0 271 " --> pdb=" O TYR W 268 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE W 270 " --> pdb=" O GLN 0 271 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER 0 273 " --> pdb=" O ILE W 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR W 272 " --> pdb=" O SER 0 273 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN S 266 " --> pdb=" O GLN W 267 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL W 269 " --> pdb=" O GLN S 266 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR S 268 " --> pdb=" O VAL W 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN W 271 " --> pdb=" O TYR S 268 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE S 270 " --> pdb=" O GLN W 271 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER W 273 " --> pdb=" O ILE S 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR S 272 " --> pdb=" O SER W 273 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN O 266 " --> pdb=" O GLN S 267 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL S 269 " --> pdb=" O GLN O 266 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR O 268 " --> pdb=" O VAL S 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN S 271 " --> pdb=" O TYR O 268 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE O 270 " --> pdb=" O GLN S 271 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER S 273 " --> pdb=" O ILE O 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR O 272 " --> pdb=" O SER S 273 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN K 266 " --> pdb=" O GLN O 267 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL O 269 " --> pdb=" O GLN K 266 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR K 268 " --> pdb=" O VAL O 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN O 271 " --> pdb=" O TYR K 268 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE K 270 " --> pdb=" O GLN O 271 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N SER O 273 " --> pdb=" O ILE K 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR K 272 " --> pdb=" O SER O 273 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN G 266 " --> pdb=" O GLN K 267 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL K 269 " --> pdb=" O GLN G 266 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR G 268 " --> pdb=" O VAL K 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN K 271 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE G 270 " --> pdb=" O GLN K 271 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER K 273 " --> pdb=" O ILE G 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR G 272 " --> pdb=" O SER K 273 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN C 266 " --> pdb=" O GLN G 267 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL G 269 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR C 268 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN G 271 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE C 270 " --> pdb=" O GLN G 271 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER G 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR C 272 " --> pdb=" O SER G 273 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN A 266 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL C 269 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR A 268 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN C 271 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 270 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N SER C 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR A 272 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 278 through 279 removed outlier: 6.832A pdb=" N GLN W 278 " --> pdb=" O GLN 0 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN S 278 " --> pdb=" O GLN W 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN O 278 " --> pdb=" O GLN S 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN K 278 " --> pdb=" O GLN O 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN G 278 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN C 278 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN A 278 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 286 through 289 removed outlier: 6.544A pdb=" N GLN A 287 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN E 287 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN I 287 " --> pdb=" O PHE M 288 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN M 287 " --> pdb=" O PHE Q 288 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN Q 287 " --> pdb=" O PHE U 288 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN U 287 " --> pdb=" O PHE Y 288 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN Y 287 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 266 through 273 removed outlier: 6.401A pdb=" N GLN X 267 " --> pdb=" O TYR 1 268 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE 1 270 " --> pdb=" O GLN X 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL X 269 " --> pdb=" O ILE 1 270 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR 1 272 " --> pdb=" O VAL X 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN X 271 " --> pdb=" O TYR 1 272 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN T 267 " --> pdb=" O TYR X 268 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE X 270 " --> pdb=" O GLN T 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL T 269 " --> pdb=" O ILE X 270 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR X 272 " --> pdb=" O VAL T 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN T 271 " --> pdb=" O TYR X 272 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN P 267 " --> pdb=" O TYR T 268 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE T 270 " --> pdb=" O GLN P 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL P 269 " --> pdb=" O ILE T 270 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR T 272 " --> pdb=" O VAL P 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN P 271 " --> pdb=" O TYR T 272 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN L 267 " --> pdb=" O TYR P 268 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE P 270 " --> pdb=" O GLN L 267 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL L 269 " --> pdb=" O ILE P 270 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR P 272 " --> pdb=" O VAL L 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN L 271 " --> pdb=" O TYR P 272 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN H 267 " --> pdb=" O TYR L 268 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE L 270 " --> pdb=" O GLN H 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL H 269 " --> pdb=" O ILE L 270 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR L 272 " --> pdb=" O VAL H 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN H 271 " --> pdb=" O TYR L 272 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN D 267 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE H 270 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL D 269 " --> pdb=" O ILE H 270 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR H 272 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN D 271 " --> pdb=" O TYR H 272 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN B 267 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE D 270 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 269 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR D 272 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN B 271 " --> pdb=" O TYR D 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 278 through 279 removed outlier: 6.653A pdb=" N GLN B 278 " --> pdb=" O GLN F 279 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN F 278 " --> pdb=" O GLN J 279 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN J 278 " --> pdb=" O GLN N 279 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN N 278 " --> pdb=" O GLN R 279 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN R 278 " --> pdb=" O GLN V 279 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN V 278 " --> pdb=" O GLN Z 279 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN Z 278 " --> pdb=" O GLN 3 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 286 through 289 removed outlier: 6.508A pdb=" N GLN X 287 " --> pdb=" O PHE 1 288 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN T 287 " --> pdb=" O PHE X 288 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN P 287 " --> pdb=" O PHE T 288 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN L 287 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN H 287 " --> pdb=" O PHE L 288 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN D 287 " --> pdb=" O PHE H 288 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN B 287 " --> pdb=" O PHE D 288 " (cutoff:3.500A) 161 hydrogen bonds defined for protein. 483 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: 1.71 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1155 1.29 - 1.35: 1125 1.35 - 1.41: 813 1.41 - 1.48: 1047 1.48 - 1.54: 2760 Bond restraints: 6900 Sorted by residual: bond pdb=" C GLN F 284 " pdb=" N PRO F 285 " ideal model delta sigma weight residual 1.329 1.338 -0.008 1.22e-02 6.72e+03 4.72e-01 bond pdb=" C GLN X 284 " pdb=" N PRO X 285 " ideal model delta sigma weight residual 1.329 1.338 -0.008 1.22e-02 6.72e+03 4.65e-01 bond pdb=" C GLN V 284 " pdb=" N PRO V 285 " ideal model delta sigma weight residual 1.329 1.337 -0.008 1.22e-02 6.72e+03 4.26e-01 bond pdb=" C GLN T 284 " pdb=" N PRO T 285 " ideal model delta sigma weight residual 1.329 1.337 -0.008 1.22e-02 6.72e+03 4.19e-01 bond pdb=" CB PRO 3 285 " pdb=" CG PRO 3 285 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.11e-01 ... (remaining 6895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.63: 7837 0.63 - 1.27: 1051 1.27 - 1.90: 322 1.90 - 2.53: 105 2.53 - 3.16: 45 Bond angle restraints: 9360 Sorted by residual: angle pdb=" CA PRO F 285 " pdb=" C PRO F 285 " pdb=" N GLN F 286 " ideal model delta sigma weight residual 114.58 116.46 -1.88 1.16e+00 7.43e-01 2.62e+00 angle pdb=" CA PRO H 285 " pdb=" C PRO H 285 " pdb=" N GLN H 286 " ideal model delta sigma weight residual 114.58 116.45 -1.87 1.16e+00 7.43e-01 2.59e+00 angle pdb=" CA PRO N 285 " pdb=" C PRO N 285 " pdb=" N GLN N 286 " ideal model delta sigma weight residual 114.58 116.45 -1.87 1.16e+00 7.43e-01 2.59e+00 angle pdb=" CA PRO P 285 " pdb=" C PRO P 285 " pdb=" N GLN P 286 " ideal model delta sigma weight residual 114.58 116.45 -1.87 1.16e+00 7.43e-01 2.59e+00 angle pdb=" CA PRO T 285 " pdb=" C PRO T 285 " pdb=" N GLN T 286 " ideal model delta sigma weight residual 114.58 116.45 -1.87 1.16e+00 7.43e-01 2.59e+00 ... (remaining 9355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3795 17.70 - 35.40: 165 35.40 - 53.10: 150 53.10 - 70.80: 30 70.80 - 88.50: 30 Dihedral angle restraints: 4170 sinusoidal: 1755 harmonic: 2415 Sorted by residual: dihedral pdb=" N GLN V 289 " pdb=" CA GLN V 289 " pdb=" CB GLN V 289 " pdb=" CG GLN V 289 " ideal model delta sinusoidal sigma weight residual -60.00 -92.51 32.51 3 1.50e+01 4.44e-03 5.36e+00 dihedral pdb=" N GLN 1 289 " pdb=" CA GLN 1 289 " pdb=" CB GLN 1 289 " pdb=" CG GLN 1 289 " ideal model delta sinusoidal sigma weight residual -60.00 -92.51 32.51 3 1.50e+01 4.44e-03 5.36e+00 dihedral pdb=" N GLN N 289 " pdb=" CA GLN N 289 " pdb=" CB GLN N 289 " pdb=" CG GLN N 289 " ideal model delta sinusoidal sigma weight residual -60.00 -92.49 32.49 3 1.50e+01 4.44e-03 5.36e+00 ... (remaining 4167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 393 0.024 - 0.047: 319 0.047 - 0.071: 67 0.071 - 0.094: 44 0.094 - 0.118: 32 Chirality restraints: 855 Sorted by residual: chirality pdb=" CA VAL G 269 " pdb=" N VAL G 269 " pdb=" C VAL G 269 " pdb=" CB VAL G 269 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA VAL C 269 " pdb=" N VAL C 269 " pdb=" C VAL C 269 " pdb=" CB VAL C 269 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA VAL U 269 " pdb=" N VAL U 269 " pdb=" C VAL U 269 " pdb=" CB VAL U 269 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 852 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR V 268 " 0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C TYR V 268 " -0.020 2.00e-02 2.50e+03 pdb=" O TYR V 268 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL V 269 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR 3 268 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C TYR 3 268 " -0.020 2.00e-02 2.50e+03 pdb=" O TYR 3 268 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL 3 269 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 268 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C TYR F 268 " -0.020 2.00e-02 2.50e+03 pdb=" O TYR F 268 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL F 269 " 0.007 2.00e-02 2.50e+03 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1603 2.82 - 3.34: 5072 3.34 - 3.86: 11821 3.86 - 4.38: 14455 4.38 - 4.90: 23248 Nonbonded interactions: 56199 Sorted by model distance: nonbonded pdb=" O ALA B 274 " pdb=" OG SER B 277 " model vdw 2.300 3.040 nonbonded pdb=" O ALA V 274 " pdb=" OG SER V 277 " model vdw 2.301 3.040 nonbonded pdb=" O ALA X 274 " pdb=" OG SER X 277 " model vdw 2.301 3.040 nonbonded pdb=" O ALA Z 274 " pdb=" OG SER Z 277 " model vdw 2.301 3.040 nonbonded pdb=" O ALA T 274 " pdb=" OG SER T 277 " model vdw 2.301 3.040 ... (remaining 56194 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: 0.07 Found NCS groups: ncs_group { reference = chain '1' selection = chain '3' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain '0' selection = chain '2' selection = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 16.670 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 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 0.032 6900 Z= 0.201 Angle : 0.561 3.163 9360 Z= 0.321 Chirality : 0.040 0.118 855 Planarity : 0.007 0.026 1320 Dihedral : 17.773 88.500 2640 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: -4.35 (0.15), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.11), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE T 288 TYR 0.013 0.002 TYR Y 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.727 Fit side-chains REVERT: I 286 GLN cc_start: 0.9189 (mt0) cc_final: 0.8957 (mt0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 1.0940 time to fit residues: 98.8609 Evaluate side-chains 56 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 284 GLN ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 289 GLN C 278 GLN ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN D 289 GLN E 278 GLN E 284 GLN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 GLN F 289 GLN G 278 GLN G 284 GLN ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 GLN H 289 GLN I 278 GLN I 284 GLN ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 271 GLN J 289 GLN K 278 GLN K 284 GLN ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 GLN L 289 GLN M 278 GLN ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 271 GLN N 289 GLN O 278 GLN O 284 GLN ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN P 289 GLN Q 278 GLN Q 284 GLN ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 GLN R 289 GLN S 278 GLN S 284 GLN ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN T 289 GLN U 278 GLN U 284 GLN ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN V 289 GLN W 278 GLN W 284 GLN ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 271 GLN X 289 GLN Y 278 GLN ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 271 GLN Z 289 GLN 0 278 GLN 0 284 GLN ** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 271 GLN 1 289 GLN 2 278 GLN 2 284 GLN 3 271 GLN 3 289 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.072412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.060602 restraints weight = 10146.000| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.75 r_work: 0.2772 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.032 6900 Z= 0.527 Angle : 0.777 4.971 9360 Z= 0.463 Chirality : 0.049 0.152 855 Planarity : 0.006 0.041 1320 Dihedral : 5.948 15.726 885 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.63 % Allowed : 7.89 % Favored : 90.48 % 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: -3.28 (0.17), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.13), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE P 288 TYR 0.024 0.003 TYR E 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.766 Fit side-chains REVERT: A 289 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8755 (tt0) REVERT: E 263 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8247 (mt0) REVERT: I 286 GLN cc_start: 0.9289 (mt0) cc_final: 0.8987 (mt0) REVERT: M 289 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: O 263 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: 0 263 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8412 (mt0) outliers start: 12 outliers final: 1 residues processed: 76 average time/residue: 0.9365 time to fit residues: 76.5547 Evaluate side-chains 74 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain M residue 289 GLN Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain 0 residue 263 GLN Chi-restraints excluded: chain 1 residue 280 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 289 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 = 0.3134 r_free = 0.3134 target = 0.078756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.066849 restraints weight = 9944.989| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.74 r_work: 0.2926 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6900 Z= 0.202 Angle : 0.570 4.564 9360 Z= 0.329 Chirality : 0.045 0.141 855 Planarity : 0.005 0.034 1320 Dihedral : 5.223 16.343 885 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.36 % Allowed : 8.84 % Favored : 89.80 % 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: -3.04 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE 0 288 TYR 0.022 0.002 TYR E 272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.864 Fit side-chains REVERT: C 263 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: I 286 GLN cc_start: 0.9226 (mt0) cc_final: 0.8938 (mt0) REVERT: M 263 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8035 (mt0) REVERT: M 289 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: O 263 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: 0 263 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8342 (mt0) outliers start: 10 outliers final: 1 residues processed: 75 average time/residue: 0.9045 time to fit residues: 73.2182 Evaluate side-chains 72 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 289 GLN Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain S residue 263 GLN Chi-restraints excluded: chain 0 residue 263 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.072077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.060283 restraints weight = 10304.074| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.76 r_work: 0.2779 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 6900 Z= 0.479 Angle : 0.727 4.842 9360 Z= 0.429 Chirality : 0.049 0.156 855 Planarity : 0.006 0.042 1320 Dihedral : 5.875 16.471 885 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.31 % Allowed : 8.71 % Favored : 88.98 % 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: -3.20 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE P 288 TYR 0.024 0.003 TYR E 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.753 Fit side-chains REVERT: A 263 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8344 (mt0) REVERT: E 263 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: K 263 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: M 289 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: O 263 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8144 (mt0) outliers start: 17 outliers final: 4 residues processed: 80 average time/residue: 0.8987 time to fit residues: 77.4632 Evaluate side-chains 80 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain K residue 263 GLN Chi-restraints excluded: chain M residue 289 GLN Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain Q residue 269 VAL Chi-restraints excluded: chain 1 residue 280 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.082072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.070588 restraints weight = 9718.358| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.67 r_work: 0.2944 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6900 Z= 0.187 Angle : 0.559 4.429 9360 Z= 0.321 Chirality : 0.044 0.146 855 Planarity : 0.005 0.035 1320 Dihedral : 5.198 16.348 885 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.59 % Allowed : 9.12 % Favored : 88.30 % 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: -3.05 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE W 288 TYR 0.022 0.002 TYR I 272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.770 Fit side-chains REVERT: A 263 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8296 (mt0) REVERT: C 263 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8236 (mt0) REVERT: E 263 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: I 279 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8047 (mp10) REVERT: I 286 GLN cc_start: 0.9194 (mt0) cc_final: 0.8919 (mt0) REVERT: M 263 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: O 263 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: Q 263 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: 0 279 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.7746 (mp10) outliers start: 19 outliers final: 5 residues processed: 87 average time/residue: 0.9559 time to fit residues: 89.1818 Evaluate side-chains 85 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain Q residue 263 GLN Chi-restraints excluded: chain Q residue 269 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain 0 residue 279 GLN Chi-restraints excluded: chain 1 residue 280 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 289 GLN ** S 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 289 GLN ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 289 GLN ** 0 289 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 = 0.3136 r_free = 0.3136 target = 0.078421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.067009 restraints weight = 9910.184| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.66 r_work: 0.2836 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 6900 Z= 0.277 Angle : 0.614 4.563 9360 Z= 0.357 Chirality : 0.046 0.149 855 Planarity : 0.005 0.037 1320 Dihedral : 5.405 16.603 885 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.40 % Allowed : 8.44 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE 3 288 TYR 0.023 0.002 TYR E 272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.837 Fit side-chains REVERT: A 263 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8323 (mt0) REVERT: A 279 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: C 263 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8262 (mt0) REVERT: E 263 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: I 279 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: I 286 GLN cc_start: 0.9219 (mt0) cc_final: 0.8952 (mt0) REVERT: I 289 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: K 263 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: O 263 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: W 279 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: 0 279 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.7902 (mp10) outliers start: 25 outliers final: 6 residues processed: 87 average time/residue: 0.9280 time to fit residues: 86.7048 Evaluate side-chains 88 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 289 GLN Chi-restraints excluded: chain K residue 263 GLN Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain Q residue 269 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain W residue 279 GLN Chi-restraints excluded: chain 0 residue 279 GLN Chi-restraints excluded: chain 1 residue 280 THR Chi-restraints excluded: chain 2 residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 GLN ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 289 GLN ** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 289 GLN ** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 289 GLN 0 289 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.075553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.063677 restraints weight = 9979.560| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.75 r_work: 0.2820 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 6900 Z= 0.261 Angle : 0.604 4.520 9360 Z= 0.350 Chirality : 0.045 0.148 855 Planarity : 0.005 0.036 1320 Dihedral : 5.359 16.749 885 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.40 % Allowed : 8.57 % Favored : 88.03 % 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: -3.09 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE 3 288 TYR 0.023 0.002 TYR E 272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.788 Fit side-chains REVERT: A 263 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8302 (mt0) REVERT: A 279 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: C 263 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8217 (mt0) REVERT: E 263 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8261 (mt0) REVERT: E 279 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7493 (mp10) REVERT: I 279 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.7393 (mp10) REVERT: I 289 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: M 263 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: O 263 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: W 279 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: 0 279 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.7904 (mp10) outliers start: 25 outliers final: 10 residues processed: 90 average time/residue: 0.9126 time to fit residues: 88.2209 Evaluate side-chains 91 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 289 GLN Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain Q residue 269 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain W residue 279 GLN Chi-restraints excluded: chain 0 residue 279 GLN Chi-restraints excluded: chain 1 residue 280 THR Chi-restraints excluded: chain 2 residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.074809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.063019 restraints weight = 10079.252| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.74 r_work: 0.2819 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 6900 Z= 0.278 Angle : 0.615 4.622 9360 Z= 0.357 Chirality : 0.046 0.154 855 Planarity : 0.005 0.036 1320 Dihedral : 5.414 16.796 885 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.40 % Allowed : 8.57 % Favored : 88.03 % 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: -3.09 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE 3 288 TYR 0.023 0.002 TYR I 272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.862 Fit side-chains REVERT: A 263 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8356 (mt0) REVERT: A 279 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7425 (mp10) REVERT: C 263 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: E 263 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8379 (mt0) REVERT: E 279 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: I 289 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: K 263 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: M 263 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8314 (mt0) REVERT: O 263 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: W 279 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: 0 279 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.7919 (mp10) outliers start: 25 outliers final: 10 residues processed: 87 average time/residue: 0.9194 time to fit residues: 86.6406 Evaluate side-chains 90 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain I residue 289 GLN Chi-restraints excluded: chain K residue 263 GLN Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain Q residue 269 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain W residue 279 GLN Chi-restraints excluded: chain 0 residue 279 GLN Chi-restraints excluded: chain 1 residue 280 THR Chi-restraints excluded: chain 2 residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 45 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.073939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.062309 restraints weight = 10159.675| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.67 r_work: 0.2825 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 6900 Z= 0.334 Angle : 0.649 4.663 9360 Z= 0.378 Chirality : 0.047 0.155 855 Planarity : 0.005 0.039 1320 Dihedral : 5.559 16.828 885 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.27 % Allowed : 9.12 % Favored : 87.62 % 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: -3.14 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE 3 288 TYR 0.023 0.002 TYR I 272 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 263 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8348 (mt0) REVERT: A 279 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: C 263 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8269 (mt0) REVERT: E 263 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8373 (mt0) REVERT: I 289 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: K 263 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: M 263 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8336 (mt0) REVERT: O 263 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: W 279 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: 0 279 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.7937 (mp10) outliers start: 24 outliers final: 11 residues processed: 88 average time/residue: 0.8952 time to fit residues: 84.8683 Evaluate side-chains 91 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain I residue 289 GLN Chi-restraints excluded: chain K residue 263 GLN Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 279 GLN Chi-restraints excluded: chain Q residue 269 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain W residue 279 GLN Chi-restraints excluded: chain 0 residue 279 GLN Chi-restraints excluded: chain 1 residue 280 THR Chi-restraints excluded: chain 2 residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.078723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.067280 restraints weight = 10005.862| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.66 r_work: 0.2844 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 6900 Z= 0.248 Angle : 0.597 4.535 9360 Z= 0.346 Chirality : 0.045 0.150 855 Planarity : 0.005 0.037 1320 Dihedral : 5.369 17.073 885 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.99 % Allowed : 9.12 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.18), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE 3 288 TYR 0.022 0.002 TYR I 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.829 Fit side-chains REVERT: A 263 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8371 (mt0) REVERT: A 279 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7428 (mp10) REVERT: C 263 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: E 263 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8380 (mt0) REVERT: E 279 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: I 289 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: M 263 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8311 (mt0) REVERT: O 263 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: W 279 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.7581 (mp10) outliers start: 22 outliers final: 10 residues processed: 88 average time/residue: 0.8722 time to fit residues: 82.9598 Evaluate side-chains 90 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain I residue 289 GLN Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain O residue 263 GLN Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain Q residue 269 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain W residue 279 GLN Chi-restraints excluded: chain 1 residue 280 THR Chi-restraints excluded: chain 2 residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.078527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.066759 restraints weight = 10001.993| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.70 r_work: 0.2897 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6900 Z= 0.191 Angle : 0.555 4.489 9360 Z= 0.318 Chirality : 0.044 0.149 855 Planarity : 0.005 0.035 1320 Dihedral : 5.125 17.213 885 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.72 % Allowed : 9.66 % Favored : 87.62 % 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: -2.96 (0.19), residues: 765 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.14), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE W 288 TYR 0.022 0.002 TYR I 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3854.36 seconds wall clock time: 69 minutes 13.21 seconds (4153.21 seconds total)