Starting phenix.real_space_refine on Tue Feb 11 00:58:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ci8_16671/02_2025/8ci8_16671.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ci8_16671/02_2025/8ci8_16671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ci8_16671/02_2025/8ci8_16671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ci8_16671/02_2025/8ci8_16671.map" model { file = "/net/cci-nas-00/data/ceres_data/8ci8_16671/02_2025/8ci8_16671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ci8_16671/02_2025/8ci8_16671.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2145 2.51 5 N 560 2.21 5 O 710 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: 3430 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 70 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 178 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "C" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "D" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Restraints were copied for chains: F, K, P, U, G, L, Q, V, H, M, R, W, I, N, S, X, J, O, T, Y Time building chain proxies: 1.71, per 1000 atoms: 0.50 Number of scatterers: 3430 At special positions: 0 Unit cell: (87.15, 81.9, 44.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 710 8.00 N 560 7.00 C 2145 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: 0.80 Conformation dependent library (CDL) restraints added in 402.8 milliseconds 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 39.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 319 removed outlier: 6.551A pdb=" N LEU A 318 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU F 318 " --> pdb=" O PHE K 319 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU K 318 " --> pdb=" O PHE P 319 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU P 318 " --> pdb=" O PHE U 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 325 removed outlier: 6.149A pdb=" N GLN A 323 " --> pdb=" O ALA F 324 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN K 323 " --> pdb=" O ALA P 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 306 through 309 removed outlier: 6.494A pdb=" N SER B 306 " --> pdb=" O THR G 307 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY G 309 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 308 " --> pdb=" O GLY G 309 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER G 306 " --> pdb=" O THR L 307 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLY L 309 " --> pdb=" O SER G 306 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE G 308 " --> pdb=" O GLY L 309 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER L 306 " --> pdb=" O THR Q 307 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLY Q 309 " --> pdb=" O SER L 306 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE L 308 " --> pdb=" O GLY Q 309 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER Q 306 " --> pdb=" O THR V 307 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLY V 309 " --> pdb=" O SER Q 306 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE Q 308 " --> pdb=" O GLY V 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 312 through 322 removed outlier: 6.293A pdb=" N SER B 312 " --> pdb=" O THR G 313 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR G 315 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASN B 314 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLY G 317 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N MET B 316 " --> pdb=" O GLY G 317 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE G 319 " --> pdb=" O MET B 316 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU B 318 " --> pdb=" O PHE G 319 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL G 321 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY B 320 " --> pdb=" O VAL G 321 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER G 312 " --> pdb=" O THR L 313 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR L 315 " --> pdb=" O SER G 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ASN G 314 " --> pdb=" O THR L 315 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY L 317 " --> pdb=" O ASN G 314 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N MET G 316 " --> pdb=" O GLY L 317 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE L 319 " --> pdb=" O MET G 316 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU G 318 " --> pdb=" O PHE L 319 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL L 321 " --> pdb=" O LEU G 318 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY G 320 " --> pdb=" O VAL L 321 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N SER L 312 " --> pdb=" O THR Q 313 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR Q 315 " --> pdb=" O SER L 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASN L 314 " --> pdb=" O THR Q 315 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY Q 317 " --> pdb=" O ASN L 314 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET L 316 " --> pdb=" O GLY Q 317 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE Q 319 " --> pdb=" O MET L 316 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU L 318 " --> pdb=" O PHE Q 319 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL Q 321 " --> pdb=" O LEU L 318 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY L 320 " --> pdb=" O VAL Q 321 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER Q 312 " --> pdb=" O THR V 313 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR V 315 " --> pdb=" O SER Q 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASN Q 314 " --> pdb=" O THR V 315 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLY V 317 " --> pdb=" O ASN Q 314 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N MET Q 316 " --> pdb=" O GLY V 317 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE V 319 " --> pdb=" O MET Q 316 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU Q 318 " --> pdb=" O PHE V 319 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL V 321 " --> pdb=" O LEU Q 318 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY Q 320 " --> pdb=" O VAL V 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 300 through 301 Processing sheet with id=AA6, first strand: chain 'C' and resid 304 through 309 removed outlier: 6.829A pdb=" N ASN C 304 " --> pdb=" O THR H 305 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N THR H 307 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER C 306 " --> pdb=" O THR H 307 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLY H 309 " --> pdb=" O SER C 306 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE C 308 " --> pdb=" O GLY H 309 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN H 304 " --> pdb=" O THR M 305 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR M 307 " --> pdb=" O ASN H 304 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER H 306 " --> pdb=" O THR M 307 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY M 309 " --> pdb=" O SER H 306 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE H 308 " --> pdb=" O GLY M 309 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN M 304 " --> pdb=" O THR R 305 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR R 307 " --> pdb=" O ASN M 304 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER M 306 " --> pdb=" O THR R 307 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLY R 309 " --> pdb=" O SER M 306 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE M 308 " --> pdb=" O GLY R 309 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN R 304 " --> pdb=" O THR W 305 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N THR W 307 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER R 306 " --> pdb=" O THR W 307 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY W 309 " --> pdb=" O SER R 306 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE R 308 " --> pdb=" O GLY W 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 312 through 313 removed outlier: 6.279A pdb=" N SER C 312 " --> pdb=" O THR H 313 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER H 312 " --> pdb=" O THR M 313 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER M 312 " --> pdb=" O THR R 313 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER R 312 " --> pdb=" O THR W 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 316 through 319 Processing sheet with id=AA9, first strand: chain 'C' and resid 322 through 323 Processing sheet with id=AB1, first strand: chain 'D' and resid 301 through 302 removed outlier: 6.247A pdb=" N SER N 301 " --> pdb=" O PHE I 302 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 308 through 309 removed outlier: 6.314A pdb=" N ILE D 308 " --> pdb=" O GLY I 309 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE I 308 " --> pdb=" O GLY N 309 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE N 308 " --> pdb=" O GLY S 309 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE S 308 " --> pdb=" O GLY X 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 312 through 315 removed outlier: 6.712A pdb=" N SER D 312 " --> pdb=" O THR I 313 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR I 315 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN D 314 " --> pdb=" O THR I 315 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER I 312 " --> pdb=" O THR N 313 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N THR N 315 " --> pdb=" O SER I 312 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN I 314 " --> pdb=" O THR N 315 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER N 312 " --> pdb=" O THR S 313 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR S 315 " --> pdb=" O SER N 312 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN N 314 " --> pdb=" O THR S 315 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N SER S 312 " --> pdb=" O THR X 313 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR X 315 " --> pdb=" O SER S 312 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN S 314 " --> pdb=" O THR X 315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 318 through 321 removed outlier: 5.835A pdb=" N LEU D 318 " --> pdb=" O PHE I 319 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL I 321 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLY D 320 " --> pdb=" O VAL I 321 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU I 318 " --> pdb=" O PHE N 319 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL N 321 " --> pdb=" O LEU I 318 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLY I 320 " --> pdb=" O VAL N 321 " (cutoff:3.500A) removed outlier: 9.948A pdb=" N GLN N 323 " --> pdb=" O GLY I 320 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU N 318 " --> pdb=" O PHE S 319 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL S 321 " --> pdb=" O LEU N 318 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLY N 320 " --> pdb=" O VAL S 321 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLN S 323 " --> pdb=" O GLY N 320 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N THR N 322 " --> pdb=" O GLN S 323 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU S 318 " --> pdb=" O PHE X 319 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL X 321 " --> pdb=" O LEU S 318 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY S 320 " --> pdb=" O VAL X 321 " (cutoff:3.500A) removed outlier: 9.948A pdb=" N GLN X 323 " --> pdb=" O GLY S 320 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N THR S 322 " --> pdb=" O GLN X 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 301 through 302 33 hydrogen bonds defined for protein. 99 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: 0.88 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 561 1.32 - 1.44: 1044 1.44 - 1.56: 1845 1.56 - 1.68: 0 1.68 - 1.80: 30 Bond restraints: 3480 Sorted by residual: bond pdb=" N GLY X 317 " pdb=" CA GLY X 317 " ideal model delta sigma weight residual 1.447 1.477 -0.029 9.40e-03 1.13e+04 9.71e+00 bond pdb=" N GLY N 317 " pdb=" CA GLY N 317 " ideal model delta sigma weight residual 1.447 1.476 -0.029 9.40e-03 1.13e+04 9.59e+00 bond pdb=" N GLY D 317 " pdb=" CA GLY D 317 " ideal model delta sigma weight residual 1.447 1.476 -0.029 9.40e-03 1.13e+04 9.52e+00 bond pdb=" N GLY I 317 " pdb=" CA GLY I 317 " ideal model delta sigma weight residual 1.447 1.476 -0.029 9.40e-03 1.13e+04 9.43e+00 bond pdb=" N GLY S 317 " pdb=" CA GLY S 317 " ideal model delta sigma weight residual 1.447 1.476 -0.029 9.40e-03 1.13e+04 9.32e+00 ... (remaining 3475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 3867 1.88 - 3.75: 686 3.75 - 5.63: 107 5.63 - 7.50: 5 7.50 - 9.38: 15 Bond angle restraints: 4680 Sorted by residual: angle pdb=" N GLY R 309 " pdb=" CA GLY R 309 " pdb=" C GLY R 309 " ideal model delta sigma weight residual 113.18 103.80 9.38 2.37e+00 1.78e-01 1.57e+01 angle pdb=" N GLY W 309 " pdb=" CA GLY W 309 " pdb=" C GLY W 309 " ideal model delta sigma weight residual 113.18 103.82 9.36 2.37e+00 1.78e-01 1.56e+01 angle pdb=" N GLY H 309 " pdb=" CA GLY H 309 " pdb=" C GLY H 309 " ideal model delta sigma weight residual 113.18 103.82 9.36 2.37e+00 1.78e-01 1.56e+01 angle pdb=" N GLY C 309 " pdb=" CA GLY C 309 " pdb=" C GLY C 309 " ideal model delta sigma weight residual 113.18 103.83 9.35 2.37e+00 1.78e-01 1.56e+01 angle pdb=" N GLY M 309 " pdb=" CA GLY M 309 " pdb=" C GLY M 309 " ideal model delta sigma weight residual 113.18 103.84 9.34 2.37e+00 1.78e-01 1.55e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.82: 1685 12.82 - 25.65: 125 25.65 - 38.47: 35 38.47 - 51.30: 40 51.30 - 64.12: 5 Dihedral angle restraints: 1890 sinusoidal: 650 harmonic: 1240 Sorted by residual: dihedral pdb=" CA ILE J 308 " pdb=" CB ILE J 308 " pdb=" CG1 ILE J 308 " pdb=" CD1 ILE J 308 " ideal model delta sinusoidal sigma weight residual 60.00 109.72 -49.72 3 1.50e+01 4.44e-03 8.81e+00 dihedral pdb=" CA ILE E 308 " pdb=" CB ILE E 308 " pdb=" CG1 ILE E 308 " pdb=" CD1 ILE E 308 " ideal model delta sinusoidal sigma weight residual 60.00 109.69 -49.69 3 1.50e+01 4.44e-03 8.81e+00 dihedral pdb=" CA ILE Y 308 " pdb=" CB ILE Y 308 " pdb=" CG1 ILE Y 308 " pdb=" CD1 ILE Y 308 " ideal model delta sinusoidal sigma weight residual 60.00 109.67 -49.67 3 1.50e+01 4.44e-03 8.81e+00 ... (remaining 1887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 316 0.051 - 0.103: 109 0.103 - 0.154: 75 0.154 - 0.205: 25 0.205 - 0.257: 15 Chirality restraints: 540 Sorted by residual: chirality pdb=" CA LEU S 318 " pdb=" N LEU S 318 " pdb=" C LEU S 318 " pdb=" CB LEU S 318 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LEU N 318 " pdb=" N LEU N 318 " pdb=" C LEU N 318 " pdb=" CB LEU N 318 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LEU D 318 " pdb=" N LEU D 318 " pdb=" C LEU D 318 " pdb=" CB LEU D 318 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 537 not shown) Planarity restraints: 610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 319 " 0.005 2.00e-02 2.50e+03 2.55e-02 1.13e+01 pdb=" CG PHE H 319 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE H 319 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE H 319 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE H 319 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE H 319 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE H 319 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE W 319 " 0.005 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE W 319 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE W 319 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE W 319 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE W 319 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE W 319 " 0.046 2.00e-02 2.50e+03 pdb=" CZ PHE W 319 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 319 " 0.005 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE M 319 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE M 319 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE M 319 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE M 319 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE M 319 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE M 319 " -0.033 2.00e-02 2.50e+03 ... (remaining 607 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 1963 3.00 - 3.47: 3088 3.47 - 3.95: 6276 3.95 - 4.42: 6988 4.42 - 4.90: 13102 Nonbonded interactions: 31417 Sorted by model distance: nonbonded pdb=" NE2 GLN B 323 " pdb=" OE1 GLN G 323 " model vdw 2.521 3.120 nonbonded pdb=" O LEU N 318 " pdb=" N PHE S 319 " model vdw 2.540 3.120 nonbonded pdb=" O LEU S 318 " pdb=" N PHE X 319 " model vdw 2.559 3.120 nonbonded pdb=" OE1 GLN I 310 " pdb=" NE2 GLN N 310 " model vdw 2.565 3.120 nonbonded pdb=" NE2 GLN S 323 " pdb=" OG1 THR W 322 " model vdw 2.571 3.120 ... (remaining 31412 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' selection = chain 'P' selection = chain 'U' } ncs_group { reference = chain 'B' selection = (chain 'C' and resid 299 through 323) selection = (chain 'D' and resid 299 through 323) selection = chain 'G' selection = (chain 'H' and resid 299 through 323) selection = (chain 'I' and resid 299 through 323) selection = chain 'L' selection = (chain 'M' and resid 299 through 323) selection = (chain 'N' and resid 299 through 323) selection = chain 'Q' selection = (chain 'R' and resid 299 through 323) selection = (chain 'S' and resid 299 through 323) selection = chain 'V' selection = (chain 'W' and resid 299 through 323) selection = (chain 'X' and resid 299 through 323) } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' selection = chain 'T' 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: 0.460 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.750 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.009 0.043 3480 Z= 0.628 Angle : 1.458 9.380 4680 Z= 1.007 Chirality : 0.081 0.257 540 Planarity : 0.005 0.028 610 Dihedral : 13.632 64.121 1110 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % 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: -4.96 (0.25), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.19), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.046 0.003 PHE W 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.382 Fit side-chains REVERT: J 301 SER cc_start: 0.8632 (t) cc_final: 0.8058 (m) REVERT: J 307 THR cc_start: 0.8459 (m) cc_final: 0.8242 (t) REVERT: O 307 THR cc_start: 0.8468 (m) cc_final: 0.8242 (t) REVERT: T 307 THR cc_start: 0.8589 (m) cc_final: 0.8144 (t) REVERT: Y 307 THR cc_start: 0.8583 (m) cc_final: 0.8232 (p) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.4370 time to fit residues: 52.9726 Evaluate side-chains 80 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN D 323 GLN ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 314 ASN I 323 GLN ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 323 GLN S 314 ASN S 323 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.111056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.099483 restraints weight = 4841.348| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.63 r_work: 0.3574 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3480 Z= 0.247 Angle : 0.525 4.106 4680 Z= 0.270 Chirality : 0.042 0.155 540 Planarity : 0.003 0.025 610 Dihedral : 4.313 12.551 460 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 5.87 % Allowed : 17.33 % Favored : 76.80 % 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: -4.19 (0.28), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.22), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHE R 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.407 Fit side-chains REVERT: B 313 THR cc_start: 0.8733 (m) cc_final: 0.8500 (m) REVERT: C 315 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8722 (m) REVERT: J 301 SER cc_start: 0.8626 (t) cc_final: 0.8014 (m) outliers start: 22 outliers final: 16 residues processed: 103 average time/residue: 0.4856 time to fit residues: 53.4999 Evaluate side-chains 89 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain L residue 305 THR Chi-restraints excluded: chain L residue 313 THR Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 322 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain V residue 307 THR Chi-restraints excluded: chain V residue 313 THR Chi-restraints excluded: chain V residue 322 THR Chi-restraints excluded: chain W residue 315 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 GLN D 304 ASN ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 314 ASN S 314 ASN ** W 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.102874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.091895 restraints weight = 4935.074| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.58 r_work: 0.3460 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 3480 Z= 0.407 Angle : 0.593 4.678 4680 Z= 0.298 Chirality : 0.044 0.155 540 Planarity : 0.003 0.018 610 Dihedral : 4.774 12.449 460 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 9.07 % Allowed : 17.33 % Favored : 73.60 % 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: -3.60 (0.31), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.001 PHE R 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.354 Fit side-chains REVERT: F 326 GLN cc_start: 0.6565 (mt0) cc_final: 0.6315 (tp-100) REVERT: J 301 SER cc_start: 0.8393 (t) cc_final: 0.7914 (m) REVERT: K 321 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7732 (p) REVERT: Y 308 ILE cc_start: 0.9242 (mp) cc_final: 0.8969 (mm) outliers start: 34 outliers final: 23 residues processed: 96 average time/residue: 0.5105 time to fit residues: 52.2198 Evaluate side-chains 97 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain I residue 312 SER Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain L residue 305 THR Chi-restraints excluded: chain L residue 313 THR Chi-restraints excluded: chain L residue 318 LEU Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain Q residue 305 THR Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 322 THR Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 313 THR Chi-restraints excluded: chain V residue 322 THR Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain W residue 315 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 304 ASN ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 ASN ** 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 = 0.3740 r_free = 0.3740 target = 0.105794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094909 restraints weight = 4921.442| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.61 r_work: 0.3508 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3480 Z= 0.257 Angle : 0.525 4.331 4680 Z= 0.262 Chirality : 0.042 0.157 540 Planarity : 0.002 0.012 610 Dihedral : 4.451 11.957 460 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 8.00 % Allowed : 19.73 % Favored : 72.27 % 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: -3.53 (0.30), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.23), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE R 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.395 Fit side-chains REVERT: J 301 SER cc_start: 0.8500 (t) cc_final: 0.7948 (m) REVERT: K 321 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7909 (p) REVERT: R 304 ASN cc_start: 0.8802 (m110) cc_final: 0.8543 (m110) REVERT: U 326 GLN cc_start: 0.6897 (mp-120) cc_final: 0.5695 (tm-30) REVERT: Y 308 ILE cc_start: 0.9194 (mp) cc_final: 0.8928 (mm) outliers start: 30 outliers final: 23 residues processed: 90 average time/residue: 0.5229 time to fit residues: 50.1460 Evaluate side-chains 97 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain I residue 312 SER Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain L residue 305 THR Chi-restraints excluded: chain L residue 313 THR Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain Q residue 305 THR Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 322 THR Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 313 THR Chi-restraints excluded: chain V residue 318 LEU Chi-restraints excluded: chain V residue 322 THR Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain W residue 315 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 314 ASN ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 314 ASN ** W 304 ASN ** 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 = 0.3666 r_free = 0.3666 target = 0.100473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.089395 restraints weight = 5127.739| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.65 r_work: 0.3420 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3480 Z= 0.468 Angle : 0.615 4.554 4680 Z= 0.308 Chirality : 0.045 0.171 540 Planarity : 0.002 0.014 610 Dihedral : 4.927 13.249 460 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 9.60 % Allowed : 18.40 % Favored : 72.00 % 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: -3.50 (0.30), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.23), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE R 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.427 Fit side-chains REVERT: I 314 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8581 (m-40) REVERT: J 301 SER cc_start: 0.8388 (t) cc_final: 0.7859 (m) REVERT: K 321 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.8028 (p) REVERT: P 326 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: R 304 ASN cc_start: 0.8864 (m110) cc_final: 0.8635 (m110) REVERT: U 326 GLN cc_start: 0.6982 (mp-120) cc_final: 0.5745 (tm-30) REVERT: Y 308 ILE cc_start: 0.9206 (mp) cc_final: 0.8953 (mm) outliers start: 36 outliers final: 26 residues processed: 91 average time/residue: 0.5383 time to fit residues: 52.0452 Evaluate side-chains 99 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain I residue 312 SER Chi-restraints excluded: chain I residue 314 ASN Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain L residue 301 SER Chi-restraints excluded: chain L residue 305 THR Chi-restraints excluded: chain L residue 313 THR Chi-restraints excluded: chain L residue 316 MET Chi-restraints excluded: chain L residue 318 LEU Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain P residue 326 GLN Chi-restraints excluded: chain Q residue 305 THR Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 313 THR Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 322 THR Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain W residue 315 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN F 326 GLN ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 323 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.106595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.095470 restraints weight = 4935.618| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.66 r_work: 0.3501 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3480 Z= 0.258 Angle : 0.539 4.171 4680 Z= 0.267 Chirality : 0.042 0.127 540 Planarity : 0.002 0.010 610 Dihedral : 4.544 12.178 460 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 8.00 % Allowed : 20.53 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.31), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE R 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.379 Fit side-chains REVERT: J 301 SER cc_start: 0.8508 (t) cc_final: 0.7925 (m) REVERT: P 326 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6245 (tp40) REVERT: Q 304 ASN cc_start: 0.8764 (m-40) cc_final: 0.8439 (m-40) REVERT: R 304 ASN cc_start: 0.8868 (m110) cc_final: 0.8406 (m-40) REVERT: U 326 GLN cc_start: 0.6904 (mp-120) cc_final: 0.5693 (tm-30) REVERT: Y 308 ILE cc_start: 0.9200 (mp) cc_final: 0.8900 (mm) outliers start: 30 outliers final: 22 residues processed: 90 average time/residue: 0.5476 time to fit residues: 52.4535 Evaluate side-chains 95 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain L residue 301 SER Chi-restraints excluded: chain L residue 305 THR Chi-restraints excluded: chain L residue 313 THR Chi-restraints excluded: chain L residue 316 MET Chi-restraints excluded: chain L residue 318 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain P residue 326 GLN Chi-restraints excluded: chain Q residue 305 THR Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 313 THR Chi-restraints excluded: chain V residue 322 THR Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain W residue 315 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN ** G 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 314 ASN ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 314 ASN ** W 304 ASN ** 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 = 0.3638 r_free = 0.3638 target = 0.097882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.086768 restraints weight = 5158.933| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.65 r_work: 0.3387 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.056 3480 Z= 0.653 Angle : 0.722 6.088 4680 Z= 0.359 Chirality : 0.049 0.185 540 Planarity : 0.003 0.013 610 Dihedral : 5.293 14.594 460 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 9.60 % Allowed : 19.47 % Favored : 70.93 % 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: -3.41 (0.30), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE R 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 0.363 Fit side-chains REVERT: I 314 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8591 (m-40) REVERT: J 301 SER cc_start: 0.8350 (t) cc_final: 0.7846 (m) REVERT: K 326 GLN cc_start: 0.7414 (tp-100) cc_final: 0.6926 (tp-100) REVERT: P 326 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6800 (mp10) REVERT: R 304 ASN cc_start: 0.8867 (m110) cc_final: 0.8640 (m110) REVERT: U 326 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.5808 (tm-30) REVERT: Y 308 ILE cc_start: 0.9225 (mp) cc_final: 0.8972 (mm) outliers start: 36 outliers final: 28 residues processed: 87 average time/residue: 0.5249 time to fit residues: 48.5407 Evaluate side-chains 100 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain I residue 312 SER Chi-restraints excluded: chain I residue 314 ASN Chi-restraints excluded: chain L residue 301 SER Chi-restraints excluded: chain L residue 305 THR Chi-restraints excluded: chain L residue 313 THR Chi-restraints excluded: chain L residue 316 MET Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain M residue 315 THR Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 305 THR Chi-restraints excluded: chain P residue 326 GLN Chi-restraints excluded: chain Q residue 305 THR Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain S residue 301 SER Chi-restraints excluded: chain U residue 326 GLN Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 313 THR Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 322 THR Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain W residue 315 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN E 304 ASN G 314 ASN ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 ASN ** 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 = 0.3769 r_free = 0.3769 target = 0.106683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.095911 restraints weight = 4880.858| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.60 r_work: 0.3523 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3480 Z= 0.241 Angle : 0.545 7.082 4680 Z= 0.266 Chirality : 0.042 0.122 540 Planarity : 0.002 0.011 610 Dihedral : 4.548 12.359 460 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 7.20 % Allowed : 23.20 % Favored : 69.60 % 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: -3.23 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE R 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.365 Fit side-chains REVERT: F 326 GLN cc_start: 0.6715 (tp-100) cc_final: 0.5751 (mp10) REVERT: J 301 SER cc_start: 0.8508 (t) cc_final: 0.7911 (m) REVERT: K 326 GLN cc_start: 0.7409 (tp-100) cc_final: 0.6936 (tp-100) REVERT: R 304 ASN cc_start: 0.8831 (m110) cc_final: 0.8453 (m-40) REVERT: U 326 GLN cc_start: 0.6992 (mp-120) cc_final: 0.5661 (tm-30) REVERT: Y 308 ILE cc_start: 0.9177 (mp) cc_final: 0.8890 (mm) outliers start: 27 outliers final: 21 residues processed: 89 average time/residue: 0.5077 time to fit residues: 48.1819 Evaluate side-chains 99 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain L residue 301 SER Chi-restraints excluded: chain L residue 305 THR Chi-restraints excluded: chain L residue 313 THR Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain Q residue 305 THR Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 313 THR Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain W residue 315 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 314 ASN ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 ASN ** 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 = 0.3688 r_free = 0.3688 target = 0.100119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.089022 restraints weight = 5059.545| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.65 r_work: 0.3436 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3480 Z= 0.474 Angle : 0.636 6.690 4680 Z= 0.315 Chirality : 0.046 0.162 540 Planarity : 0.002 0.012 610 Dihedral : 5.016 14.696 460 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 6.93 % Allowed : 22.93 % Favored : 70.13 % 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: -3.22 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE R 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.401 Fit side-chains REVERT: I 314 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8517 (m-40) REVERT: J 301 SER cc_start: 0.8470 (t) cc_final: 0.7914 (m) REVERT: K 326 GLN cc_start: 0.7535 (tp-100) cc_final: 0.7110 (tp-100) REVERT: R 304 ASN cc_start: 0.8782 (m110) cc_final: 0.8574 (m110) REVERT: U 326 GLN cc_start: 0.6901 (mp-120) cc_final: 0.5763 (tm-30) REVERT: Y 308 ILE cc_start: 0.9199 (mp) cc_final: 0.8939 (mm) outliers start: 26 outliers final: 24 residues processed: 81 average time/residue: 0.5552 time to fit residues: 47.7662 Evaluate side-chains 96 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain I residue 314 ASN Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain L residue 301 SER Chi-restraints excluded: chain L residue 305 THR Chi-restraints excluded: chain L residue 313 THR Chi-restraints excluded: chain L residue 316 MET Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 305 THR Chi-restraints excluded: chain Q residue 305 THR Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 313 THR Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain W residue 315 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 314 ASN ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 ASN ** 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 = 0.3729 r_free = 0.3729 target = 0.103480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.092458 restraints weight = 4941.553| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.63 r_work: 0.3481 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3480 Z= 0.334 Angle : 0.588 6.925 4680 Z= 0.288 Chirality : 0.044 0.141 540 Planarity : 0.002 0.011 610 Dihedral : 4.821 14.253 460 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 6.40 % Allowed : 24.00 % Favored : 69.60 % 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: -3.19 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE R 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.391 Fit side-chains REVERT: I 314 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8462 (m-40) REVERT: J 301 SER cc_start: 0.8490 (t) cc_final: 0.7914 (m) REVERT: K 326 GLN cc_start: 0.7489 (tp-100) cc_final: 0.7121 (tp-100) REVERT: U 326 GLN cc_start: 0.6833 (mp-120) cc_final: 0.5705 (tm-30) REVERT: Y 308 ILE cc_start: 0.9176 (mp) cc_final: 0.8894 (mm) outliers start: 24 outliers final: 22 residues processed: 82 average time/residue: 0.5596 time to fit residues: 48.7261 Evaluate side-chains 95 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain I residue 314 ASN Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain L residue 301 SER Chi-restraints excluded: chain L residue 305 THR Chi-restraints excluded: chain L residue 313 THR Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain Q residue 305 THR Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain V residue 305 THR Chi-restraints excluded: chain V residue 313 THR Chi-restraints excluded: chain W residue 305 THR Chi-restraints excluded: chain W residue 315 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.0010 chunk 22 optimal weight: 0.9980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 314 ASN ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 ASN ** 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 = 0.3755 r_free = 0.3755 target = 0.105017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.093963 restraints weight = 4879.067| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.62 r_work: 0.3506 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3480 Z= 0.289 Angle : 0.571 6.997 4680 Z= 0.278 Chirality : 0.043 0.133 540 Planarity : 0.002 0.012 610 Dihedral : 4.693 13.797 460 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 6.67 % Allowed : 23.47 % Favored : 69.87 % 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: -3.13 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE R 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.54 seconds wall clock time: 41 minutes 49.63 seconds (2509.63 seconds total)