Starting phenix.real_space_refine on Thu Aug 6 15:36:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xpq_38559/08_2026/8xpq_38559.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xpq_38559/08_2026/8xpq_38559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xpq_38559/08_2026/8xpq_38559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xpq_38559/08_2026/8xpq_38559.map" model { file = "/net/cci-nas-00/data/ceres_data/8xpq_38559/08_2026/8xpq_38559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xpq_38559/08_2026/8xpq_38559.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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 86 5.16 5 C 10334 2.51 5 N 2682 2.21 5 O 2864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15966 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 7983 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 34, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 6, 'GLU:plan': 4, 'ASN:plan1': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 107 Restraints were copied for chains: B Time building chain proxies: 9.10, per 1000 atoms: 0.57 Number of scatterers: 15966 At special positions: 0 Unit cell: (104.76, 132.84, 124.2, 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 86 16.00 O 2864 8.00 N 2682 7.00 C 10334 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: 1.42 Conformation dependent library (CDL) restraints added in 668.9 milliseconds 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3916 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 10 sheets defined 73.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 75 through 95 removed outlier: 4.305A pdb=" N VAL A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.893A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.739A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.537A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 253 removed outlier: 3.748A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.646A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 318 removed outlier: 3.969A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 376 through 379 removed outlier: 4.076A pdb=" N ALA A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 381 through 412 Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.643A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.355A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 571 through 600 removed outlier: 3.846A pdb=" N ALA A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 619 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 639 through 653 removed outlier: 4.484A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 691 Processing helix chain 'A' and resid 691 through 699 removed outlier: 3.800A pdb=" N ILE A 695 " --> pdb=" O ASN A 691 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 752 Processing helix chain 'A' and resid 763 through 776 Processing helix chain 'A' and resid 803 through 853 Proline residue: A 819 - end of helix removed outlier: 3.656A pdb=" N LEU A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 858 removed outlier: 3.942A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.548A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.676A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1069 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1122 Processing helix chain 'A' and resid 1206 through 1210 removed outlier: 4.155A pdb=" N SER A1210 " --> pdb=" O SER A1207 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 95 removed outlier: 4.305A pdb=" N VAL B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 3.894A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.739A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.537A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 223 through 253 removed outlier: 3.747A pdb=" N GLY B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 292 Proline residue: B 276 - end of helix removed outlier: 3.646A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 318 removed outlier: 3.969A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 376 through 379 removed outlier: 4.076A pdb=" N ALA B 379 " --> pdb=" O ALA B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 379' Processing helix chain 'B' and resid 381 through 412 Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.643A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 481 removed outlier: 4.355A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 513 Processing helix chain 'B' and resid 522 through 530 Processing helix chain 'B' and resid 547 through 559 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 571 through 600 removed outlier: 3.847A pdb=" N ALA B 576 " --> pdb=" O PRO B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 639 through 653 removed outlier: 4.484A pdb=" N TRP B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 691 Processing helix chain 'B' and resid 691 through 699 removed outlier: 3.800A pdb=" N ILE B 695 " --> pdb=" O ASN B 691 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 696 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 752 Processing helix chain 'B' and resid 763 through 776 Processing helix chain 'B' and resid 803 through 853 Proline residue: B 819 - end of helix removed outlier: 3.657A pdb=" N LEU B 835 " --> pdb=" O ASN B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 858 removed outlier: 3.942A pdb=" N MET B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.548A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.676A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 959 Processing helix chain 'B' and resid 966 through 976 Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1069 through 1080 Processing helix chain 'B' and resid 1085 through 1107 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1122 Processing helix chain 'B' and resid 1206 through 1210 removed outlier: 4.155A pdb=" N SER B1210 " --> pdb=" O SER B1207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 979 through 982 removed outlier: 6.270A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.647A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.430A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL A1145 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS A1165 " --> pdb=" O LEU A1147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA5, first strand: chain 'A' and resid 1203 through 1204 removed outlier: 3.855A pdb=" N SER A1213 " --> pdb=" O ASP A1204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 979 through 982 removed outlier: 6.270A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 987 through 989 removed outlier: 6.647A pdb=" N VAL B1057 " --> pdb=" O ILE B 988 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1125 through 1126 removed outlier: 6.429A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B1145 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS B1165 " --> pdb=" O LEU B1147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1135 through 1137 Processing sheet with id=AB1, first strand: chain 'B' and resid 1203 through 1204 removed outlier: 3.855A pdb=" N SER B1213 " --> pdb=" O ASP B1204 " (cutoff:3.500A) 1198 hydrogen bonds defined for protein. 3534 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: 3.17 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5081 1.34 - 1.46: 2746 1.46 - 1.58: 8273 1.58 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 16254 Sorted by residual: bond pdb=" N CYS B 559 " pdb=" CA CYS B 559 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.19e-02 7.06e+03 6.55e+00 bond pdb=" N CYS A 559 " pdb=" CA CYS A 559 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.19e-02 7.06e+03 5.97e+00 bond pdb=" CA CYS A 559 " pdb=" C CYS A 559 " ideal model delta sigma weight residual 1.525 1.549 -0.025 1.04e-02 9.25e+03 5.68e+00 bond pdb=" CA CYS B 559 " pdb=" C CYS B 559 " ideal model delta sigma weight residual 1.525 1.549 -0.024 1.04e-02 9.25e+03 5.40e+00 bond pdb=" CA ILE A1198 " pdb=" C ILE A1198 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.27e-02 6.20e+03 4.69e+00 ... (remaining 16249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 21232 1.76 - 3.53: 651 3.53 - 5.29: 125 5.29 - 7.05: 34 7.05 - 8.82: 20 Bond angle restraints: 22062 Sorted by residual: angle pdb=" N PRO A1197 " pdb=" CA PRO A1197 " pdb=" C PRO A1197 " ideal model delta sigma weight residual 114.03 105.35 8.68 1.23e+00 6.61e-01 4.98e+01 angle pdb=" N PRO B1197 " pdb=" CA PRO B1197 " pdb=" C PRO B1197 " ideal model delta sigma weight residual 114.03 105.36 8.67 1.23e+00 6.61e-01 4.97e+01 angle pdb=" C HIS B1156 " pdb=" N THR B1157 " pdb=" CA THR B1157 " ideal model delta sigma weight residual 122.46 129.86 -7.40 1.41e+00 5.03e-01 2.76e+01 angle pdb=" C HIS A1156 " pdb=" N THR A1157 " pdb=" CA THR A1157 " ideal model delta sigma weight residual 122.46 129.85 -7.39 1.41e+00 5.03e-01 2.75e+01 angle pdb=" C VAL A 558 " pdb=" N CYS A 559 " pdb=" CA CYS A 559 " ideal model delta sigma weight residual 123.46 117.49 5.97 1.35e+00 5.49e-01 1.96e+01 ... (remaining 22057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 8939 17.44 - 34.88: 627 34.88 - 52.32: 158 52.32 - 69.76: 30 69.76 - 87.20: 4 Dihedral angle restraints: 9758 sinusoidal: 3726 harmonic: 6032 Sorted by residual: dihedral pdb=" CA ARG A1190 " pdb=" C ARG A1190 " pdb=" N ASN A1191 " pdb=" CA ASN A1191 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ARG B1190 " pdb=" C ARG B1190 " pdb=" N ASN B1191 " pdb=" CA ASN B1191 " ideal model delta harmonic sigma weight residual 180.00 151.63 28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA TYR A1083 " pdb=" C TYR A1083 " pdb=" N PRO A1084 " pdb=" CA PRO A1084 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 9755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2451 0.088 - 0.177: 199 0.177 - 0.265: 8 0.265 - 0.354: 0 0.354 - 0.442: 2 Chirality restraints: 2660 Sorted by residual: chirality pdb=" CA LEU B1199 " pdb=" N LEU B1199 " pdb=" C LEU B1199 " pdb=" CB LEU B1199 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA LEU A1199 " pdb=" N LEU A1199 " pdb=" C LEU A1199 " pdb=" CB LEU A1199 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CG LEU B 552 " pdb=" CB LEU B 552 " pdb=" CD1 LEU B 552 " pdb=" CD2 LEU B 552 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2657 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 467 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C LEU B 467 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU B 467 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL B 468 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 467 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C LEU A 467 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU A 467 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 468 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 952 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO B 953 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 953 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 953 " -0.035 5.00e-02 4.00e+02 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4314 2.81 - 3.33: 15352 3.33 - 3.85: 26781 3.85 - 4.38: 29506 4.38 - 4.90: 53178 Nonbonded interactions: 129131 Sorted by model distance: nonbonded pdb=" O ALA A 307 " pdb=" OG1 THR A 311 " model vdw 2.286 3.040 nonbonded pdb=" O ALA B 307 " pdb=" OG1 THR B 311 " model vdw 2.286 3.040 nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.321 3.040 nonbonded pdb=" O ILE B 469 " pdb=" OG1 THR B 473 " model vdw 2.322 3.040 nonbonded pdb=" OE1 GLN B1177 " pdb=" OG1 THR B1179 " model vdw 2.329 3.040 ... (remaining 129126 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.010 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 16254 Z= 0.269 Angle : 0.799 8.817 22062 Z= 0.451 Chirality : 0.052 0.442 2660 Planarity : 0.007 0.064 2752 Dihedral : 13.261 87.203 5842 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 5.24 % Allowed : 9.18 % Favored : 85.58 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.16), residues: 2050 helix: -0.61 (0.12), residues: 1410 sheet: -0.94 (0.54), residues: 92 loop : -2.36 (0.22), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.012 0.002 TYR B 102 PHE 0.015 0.002 PHE A 352 TRP 0.022 0.002 TRP B 962 HIS 0.007 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.27 (16254) covalent geometry : angle 0.79876 / 0.45 (22062) hydrogen bonds : bond 0.11687 / 7.90 ( 1198) hydrogen bonds : angle 5.86608 / 4.22 ( 3534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 561 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.6922 (tp30) cc_final: 0.6347 (tp30) REVERT: A 154 MET cc_start: 0.7462 (tpp) cc_final: 0.7151 (mmm) REVERT: A 160 MET cc_start: 0.6575 (mmt) cc_final: 0.6307 (mmm) REVERT: A 248 PHE cc_start: 0.7219 (m-80) cc_final: 0.7018 (m-10) REVERT: A 321 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7321 (t) REVERT: A 337 GLU cc_start: 0.7774 (mp0) cc_final: 0.7448 (mp0) REVERT: A 366 MET cc_start: 0.8577 (mmm) cc_final: 0.8323 (mmm) REVERT: A 368 VAL cc_start: 0.7885 (t) cc_final: 0.7644 (p) REVERT: A 375 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7898 (mtmm) REVERT: A 494 MET cc_start: 0.8075 (tpp) cc_final: 0.7769 (tpp) REVERT: A 552 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7335 (tp) REVERT: A 820 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7630 (mmmt) REVERT: A 823 LEU cc_start: 0.7975 (mp) cc_final: 0.7682 (mm) REVERT: A 847 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 849 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7912 (mm-30) REVERT: A 928 HIS cc_start: 0.7543 (t-90) cc_final: 0.7340 (t-170) REVERT: A 931 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 973 ILE cc_start: 0.8656 (mm) cc_final: 0.8351 (tt) REVERT: A 987 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8562 (m) REVERT: A 993 ASP cc_start: 0.8000 (p0) cc_final: 0.7777 (p0) REVERT: A 994 GLU cc_start: 0.8185 (mp0) cc_final: 0.7876 (mp0) REVERT: A 1061 THR cc_start: 0.8316 (p) cc_final: 0.8073 (p) REVERT: A 1073 MET cc_start: 0.8579 (mmm) cc_final: 0.8113 (mmm) REVERT: A 1087 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 1094 VAL cc_start: 0.8695 (m) cc_final: 0.8364 (p) REVERT: A 1098 ILE cc_start: 0.8972 (tt) cc_final: 0.8670 (tt) REVERT: A 1122 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7176 (mm-30) REVERT: A 1131 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 1134 PHE cc_start: 0.8007 (m-80) cc_final: 0.7762 (m-10) REVERT: A 1142 LEU cc_start: 0.7806 (mp) cc_final: 0.7534 (mm) REVERT: A 1147 LEU cc_start: 0.7482 (tp) cc_final: 0.7119 (tp) REVERT: A 1166 LEU cc_start: 0.8604 (tp) cc_final: 0.8277 (tp) REVERT: A 1202 ARG cc_start: 0.7003 (ttt-90) cc_final: 0.6719 (ttt-90) REVERT: A 1215 THR cc_start: 0.8024 (p) cc_final: 0.7754 (p) REVERT: B 124 GLU cc_start: 0.6710 (tp30) cc_final: 0.6171 (tp30) REVERT: B 149 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7559 (tm-30) REVERT: B 154 MET cc_start: 0.7610 (tpp) cc_final: 0.7276 (mmm) REVERT: B 160 MET cc_start: 0.6562 (mmt) cc_final: 0.6208 (mmm) REVERT: B 220 LEU cc_start: 0.8194 (mt) cc_final: 0.7935 (mt) REVERT: B 321 VAL cc_start: 0.7713 (OUTLIER) cc_final: 0.7501 (t) REVERT: B 366 MET cc_start: 0.8460 (mmm) cc_final: 0.8211 (mmm) REVERT: B 375 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8135 (ttmm) REVERT: B 380 VAL cc_start: 0.7197 (p) cc_final: 0.6915 (p) REVERT: B 520 ASP cc_start: 0.7341 (p0) cc_final: 0.7138 (p0) REVERT: B 534 ASP cc_start: 0.6994 (t70) cc_final: 0.6746 (t0) REVERT: B 556 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7985 (mmmt) REVERT: B 569 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8319 (mp0) REVERT: B 621 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: B 820 LYS cc_start: 0.8049 (mmmt) cc_final: 0.7737 (mmmt) REVERT: B 823 LEU cc_start: 0.8007 (mp) cc_final: 0.7721 (mm) REVERT: B 841 LYS cc_start: 0.7963 (mtpm) cc_final: 0.7729 (mtpm) REVERT: B 847 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7381 (mm-30) REVERT: B 849 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7954 (mm-30) REVERT: B 942 MET cc_start: 0.8308 (tpp) cc_final: 0.8078 (tpp) REVERT: B 971 ASP cc_start: 0.8272 (m-30) cc_final: 0.7893 (m-30) REVERT: B 972 PHE cc_start: 0.7868 (t80) cc_final: 0.7662 (t80) REVERT: B 973 ILE cc_start: 0.8453 (mm) cc_final: 0.8205 (tt) REVERT: B 986 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8025 (mt-10) REVERT: B 993 ASP cc_start: 0.8081 (p0) cc_final: 0.7834 (p0) REVERT: B 994 GLU cc_start: 0.8091 (mp0) cc_final: 0.7814 (mp0) REVERT: B 1044 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7907 (mt-10) REVERT: B 1072 ASP cc_start: 0.7591 (m-30) cc_final: 0.7373 (m-30) REVERT: B 1073 MET cc_start: 0.8489 (mmm) cc_final: 0.8187 (mmm) REVERT: B 1094 VAL cc_start: 0.8689 (m) cc_final: 0.8396 (p) REVERT: B 1098 ILE cc_start: 0.8958 (tt) cc_final: 0.8679 (tt) REVERT: B 1105 GLU cc_start: 0.7925 (tt0) cc_final: 0.7723 (tt0) REVERT: B 1110 GLN cc_start: 0.8422 (mp10) cc_final: 0.8188 (mp10) REVERT: B 1122 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7291 (mm-30) REVERT: B 1127 VAL cc_start: 0.7823 (t) cc_final: 0.7482 (m) REVERT: B 1134 PHE cc_start: 0.8062 (m-80) cc_final: 0.7801 (m-80) REVERT: B 1138 ILE cc_start: 0.8451 (mt) cc_final: 0.8187 (mt) REVERT: B 1172 HIS cc_start: 0.7827 (t-170) cc_final: 0.7545 (t-170) REVERT: B 1188 VAL cc_start: 0.8748 (m) cc_final: 0.8522 (p) outliers start: 88 outliers final: 32 residues processed: 622 average time/residue: 0.1219 time to fit residues: 112.6380 Evaluate side-chains 520 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 483 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 CYS Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 559 CYS Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1161 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 600 HIS A 614 HIS A 832 GLN A 886 GLN A 917 GLN A 955 ASN A1106 GLN A1114 GLN A1120 HIS B 165 GLN B 292 HIS B 600 HIS B 614 HIS B 624 GLN ** B 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 GLN B 886 GLN B 917 GLN B 955 ASN B1149 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.151051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.132441 restraints weight = 25420.304| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.35 r_work: 0.3614 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16254 Z= 0.170 Angle : 0.632 7.364 22062 Z= 0.330 Chirality : 0.042 0.149 2660 Planarity : 0.005 0.051 2752 Dihedral : 6.675 59.511 2281 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.13 % Allowed : 16.27 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2050 helix: 0.96 (0.13), residues: 1438 sheet: 0.08 (0.58), residues: 96 loop : -2.02 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 499 TYR 0.012 0.001 TYR B 837 PHE 0.015 0.002 PHE A 455 TRP 0.014 0.002 TRP B1091 HIS 0.007 0.001 HIS B1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (16254) covalent geometry : angle 0.63171 / 0.33 (22062) hydrogen bonds : bond 0.04838 / 3.28 ( 1198) hydrogen bonds : angle 4.39362 / 3.16 ( 3534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 525 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.6825 (tp30) cc_final: 0.6439 (tp30) REVERT: A 149 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 154 MET cc_start: 0.7832 (tpp) cc_final: 0.7430 (tpp) REVERT: A 155 ASP cc_start: 0.7537 (t70) cc_final: 0.7301 (t70) REVERT: A 160 MET cc_start: 0.7128 (mmt) cc_final: 0.6784 (mmm) REVERT: A 186 MET cc_start: 0.7378 (mtp) cc_final: 0.7145 (mmm) REVERT: A 187 ASN cc_start: 0.7191 (m-40) cc_final: 0.6840 (m110) REVERT: A 248 PHE cc_start: 0.7977 (m-80) cc_final: 0.7765 (m-80) REVERT: A 265 VAL cc_start: 0.8090 (t) cc_final: 0.7820 (p) REVERT: A 289 PHE cc_start: 0.7793 (t80) cc_final: 0.7435 (t80) REVERT: A 300 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 316 ASP cc_start: 0.7558 (t0) cc_final: 0.7353 (m-30) REVERT: A 337 GLU cc_start: 0.7656 (mp0) cc_final: 0.7323 (mp0) REVERT: A 355 MET cc_start: 0.8193 (ttp) cc_final: 0.7871 (ttp) REVERT: A 375 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8246 (ttmm) REVERT: A 404 SER cc_start: 0.7972 (m) cc_final: 0.7769 (p) REVERT: A 427 TRP cc_start: 0.8206 (t-100) cc_final: 0.7683 (t-100) REVERT: A 511 MET cc_start: 0.8400 (ttt) cc_final: 0.8021 (ttp) REVERT: A 534 ASP cc_start: 0.7418 (t70) cc_final: 0.7176 (t0) REVERT: A 536 TYR cc_start: 0.7835 (m-80) cc_final: 0.7360 (m-10) REVERT: A 552 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7454 (tt) REVERT: A 578 MET cc_start: 0.7221 (mtm) cc_final: 0.6879 (mtp) REVERT: A 823 LEU cc_start: 0.8253 (mp) cc_final: 0.7923 (mm) REVERT: A 845 ILE cc_start: 0.8645 (mt) cc_final: 0.8385 (mm) REVERT: A 847 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7550 (mm-30) REVERT: A 849 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 887 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7721 (ttt90) REVERT: A 926 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7345 (mm-30) REVERT: A 971 ASP cc_start: 0.8194 (m-30) cc_final: 0.7799 (m-30) REVERT: A 987 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8606 (m) REVERT: A 993 ASP cc_start: 0.7745 (p0) cc_final: 0.7401 (p0) REVERT: A 996 ASP cc_start: 0.7558 (p0) cc_final: 0.7272 (p0) REVERT: A 1002 VAL cc_start: 0.8403 (m) cc_final: 0.8166 (p) REVERT: A 1044 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7756 (mt-10) REVERT: A 1061 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8068 (p) REVERT: A 1073 MET cc_start: 0.8554 (mmm) cc_final: 0.8122 (mmm) REVERT: A 1098 ILE cc_start: 0.8987 (tt) cc_final: 0.8663 (tt) REVERT: A 1104 MET cc_start: 0.7865 (tpp) cc_final: 0.7496 (tpp) REVERT: A 1122 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7129 (mm-30) REVERT: A 1134 PHE cc_start: 0.7952 (m-80) cc_final: 0.7737 (m-10) REVERT: A 1190 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.7039 (ttm-80) REVERT: B 124 GLU cc_start: 0.6525 (tp30) cc_final: 0.6211 (tp30) REVERT: B 140 GLN cc_start: 0.8004 (mm110) cc_final: 0.7684 (mp10) REVERT: B 154 MET cc_start: 0.7995 (tpp) cc_final: 0.7503 (tpp) REVERT: B 155 ASP cc_start: 0.7452 (t70) cc_final: 0.7224 (t70) REVERT: B 160 MET cc_start: 0.6994 (mmt) cc_final: 0.6660 (mmm) REVERT: B 176 VAL cc_start: 0.7917 (p) cc_final: 0.7709 (p) REVERT: B 231 GLU cc_start: 0.7166 (tt0) cc_final: 0.6820 (mt-10) REVERT: B 265 VAL cc_start: 0.7987 (t) cc_final: 0.7744 (p) REVERT: B 319 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7951 (mt) REVERT: B 333 ILE cc_start: 0.8039 (mt) cc_final: 0.7499 (mm) REVERT: B 337 GLU cc_start: 0.7692 (mp0) cc_final: 0.7159 (mp0) REVERT: B 375 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8235 (mtmm) REVERT: B 401 MET cc_start: 0.7333 (mmp) cc_final: 0.7008 (mtp) REVERT: B 404 SER cc_start: 0.7660 (m) cc_final: 0.7458 (p) REVERT: B 490 LYS cc_start: 0.7601 (ttmm) cc_final: 0.7320 (tttp) REVERT: B 534 ASP cc_start: 0.7516 (t70) cc_final: 0.7187 (t0) REVERT: B 565 MET cc_start: 0.4712 (ppp) cc_final: 0.4444 (ppp) REVERT: B 569 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8097 (mp0) REVERT: B 578 MET cc_start: 0.7352 (mtt) cc_final: 0.7041 (mtp) REVERT: B 595 TRP cc_start: 0.8284 (m100) cc_final: 0.7982 (m100) REVERT: B 605 ARG cc_start: 0.8358 (tpp80) cc_final: 0.8155 (tpp80) REVERT: B 624 GLN cc_start: 0.7530 (pt0) cc_final: 0.7282 (pt0) REVERT: B 820 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7664 (mmmt) REVERT: B 823 LEU cc_start: 0.8266 (mp) cc_final: 0.8012 (mm) REVERT: B 832 GLN cc_start: 0.8234 (tp40) cc_final: 0.7940 (tm-30) REVERT: B 841 LYS cc_start: 0.7818 (mtpm) cc_final: 0.7596 (mtpm) REVERT: B 847 GLU cc_start: 0.7830 (mm-30) cc_final: 0.6969 (mm-30) REVERT: B 898 THR cc_start: 0.8300 (m) cc_final: 0.8079 (p) REVERT: B 926 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7306 (mm-30) REVERT: B 971 ASP cc_start: 0.8259 (m-30) cc_final: 0.7882 (m-30) REVERT: B 973 ILE cc_start: 0.8599 (mm) cc_final: 0.8198 (tt) REVERT: B 983 ASP cc_start: 0.8130 (p0) cc_final: 0.7805 (p0) REVERT: B 987 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8665 (m) REVERT: B 991 GLU cc_start: 0.7697 (tt0) cc_final: 0.7492 (tt0) REVERT: B 994 GLU cc_start: 0.8003 (mp0) cc_final: 0.7742 (mp0) REVERT: B 996 ASP cc_start: 0.7708 (p0) cc_final: 0.7466 (p0) REVERT: B 1037 THR cc_start: 0.7958 (t) cc_final: 0.7738 (p) REVERT: B 1051 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8452 (mtpp) REVERT: B 1094 VAL cc_start: 0.8491 (m) cc_final: 0.8223 (p) REVERT: B 1098 ILE cc_start: 0.9007 (tt) cc_final: 0.8657 (tt) REVERT: B 1104 MET cc_start: 0.7808 (tpp) cc_final: 0.7416 (mmm) REVERT: B 1105 GLU cc_start: 0.7769 (tt0) cc_final: 0.7531 (tt0) REVERT: B 1110 GLN cc_start: 0.8348 (mp10) cc_final: 0.8020 (mp10) REVERT: B 1122 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7243 (mm-30) REVERT: B 1128 ASP cc_start: 0.7160 (t0) cc_final: 0.6877 (t70) REVERT: B 1134 PHE cc_start: 0.8068 (m-80) cc_final: 0.7786 (m-10) REVERT: B 1172 HIS cc_start: 0.7492 (t-170) cc_final: 0.7120 (t-170) REVERT: B 1188 VAL cc_start: 0.8667 (m) cc_final: 0.8303 (p) outliers start: 86 outliers final: 53 residues processed: 572 average time/residue: 0.1134 time to fit residues: 97.4768 Evaluate side-chains 537 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 478 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1165 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 958 LYS Chi-restraints excluded: chain B residue 961 SER Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1051 LYS Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1112 TRP Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1135 GLN Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1149 ASN Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1175 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 113 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 82 optimal weight: 0.3980 chunk 136 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 26 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN A 165 GLN A 374 GLN A 600 HIS A 614 HIS ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN A1177 GLN B 165 GLN B 614 HIS ** B 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN B1137 ASN B1149 ASN B1177 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.146004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127372 restraints weight = 25254.154| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.32 r_work: 0.3543 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16254 Z= 0.143 Angle : 0.573 6.374 22062 Z= 0.303 Chirality : 0.041 0.176 2660 Planarity : 0.004 0.040 2752 Dihedral : 5.736 59.110 2254 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.42 % Allowed : 18.06 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.19), residues: 2050 helix: 1.55 (0.14), residues: 1430 sheet: 0.58 (0.59), residues: 96 loop : -1.88 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 161 TYR 0.012 0.001 TYR A1125 PHE 0.012 0.001 PHE A 999 TRP 0.012 0.002 TRP B 962 HIS 0.005 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (16254) covalent geometry : angle 0.57327 / 0.30 (22062) hydrogen bonds : bond 0.04496 / 3.05 ( 1198) hydrogen bonds : angle 4.15668 / 2.99 ( 3534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 526 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8290 (t) REVERT: A 124 GLU cc_start: 0.6822 (tp30) cc_final: 0.6431 (tp30) REVERT: A 140 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7992 (mp10) REVERT: A 149 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7183 (tm-30) REVERT: A 154 MET cc_start: 0.7986 (tpp) cc_final: 0.7764 (tpp) REVERT: A 155 ASP cc_start: 0.7649 (t70) cc_final: 0.7410 (t70) REVERT: A 166 VAL cc_start: 0.7483 (t) cc_final: 0.7226 (t) REVERT: A 180 LEU cc_start: 0.8254 (tt) cc_final: 0.8026 (tp) REVERT: A 186 MET cc_start: 0.7414 (mtp) cc_final: 0.7103 (mtp) REVERT: A 187 ASN cc_start: 0.7281 (m-40) cc_final: 0.6801 (m-40) REVERT: A 265 VAL cc_start: 0.8206 (t) cc_final: 0.7980 (p) REVERT: A 289 PHE cc_start: 0.7903 (t80) cc_final: 0.7557 (t80) REVERT: A 296 ASP cc_start: 0.7601 (p0) cc_final: 0.7217 (p0) REVERT: A 337 GLU cc_start: 0.7680 (mp0) cc_final: 0.7334 (mp0) REVERT: A 346 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7313 (mt-10) REVERT: A 355 MET cc_start: 0.8209 (ttp) cc_final: 0.7878 (ttp) REVERT: A 427 TRP cc_start: 0.8515 (t-100) cc_final: 0.7685 (t-100) REVERT: A 477 LEU cc_start: 0.8196 (mm) cc_final: 0.7912 (mp) REVERT: A 511 MET cc_start: 0.8394 (ttt) cc_final: 0.8128 (ttt) REVERT: A 534 ASP cc_start: 0.7602 (t70) cc_final: 0.7386 (t0) REVERT: A 536 TYR cc_start: 0.8030 (m-80) cc_final: 0.7815 (m-10) REVERT: A 552 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7522 (tt) REVERT: A 599 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: A 624 GLN cc_start: 0.7623 (pt0) cc_final: 0.7323 (pp30) REVERT: A 632 LYS cc_start: 0.7767 (mtpm) cc_final: 0.7532 (mtpp) REVERT: A 820 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7757 (mmmt) REVERT: A 823 LEU cc_start: 0.8336 (mp) cc_final: 0.8020 (mm) REVERT: A 832 GLN cc_start: 0.8243 (tp40) cc_final: 0.8022 (tm-30) REVERT: A 958 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8111 (ttpp) REVERT: A 971 ASP cc_start: 0.8204 (m-30) cc_final: 0.7855 (m-30) REVERT: A 987 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8774 (t) REVERT: A 991 GLU cc_start: 0.7619 (tt0) cc_final: 0.7387 (tt0) REVERT: A 993 ASP cc_start: 0.7809 (p0) cc_final: 0.7526 (p0) REVERT: A 994 GLU cc_start: 0.7915 (mp0) cc_final: 0.7686 (mp0) REVERT: A 1044 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7718 (mt-10) REVERT: A 1061 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8180 (p) REVERT: A 1067 PHE cc_start: 0.7855 (t80) cc_final: 0.7425 (t80) REVERT: A 1073 MET cc_start: 0.8479 (mmm) cc_final: 0.8050 (mmm) REVERT: A 1094 VAL cc_start: 0.8512 (m) cc_final: 0.8202 (p) REVERT: A 1098 ILE cc_start: 0.8987 (tt) cc_final: 0.8667 (tt) REVERT: A 1122 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7239 (tp30) REVERT: A 1125 TYR cc_start: 0.8089 (p90) cc_final: 0.7826 (p90) REVERT: A 1127 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8120 (p) REVERT: A 1134 PHE cc_start: 0.8032 (m-80) cc_final: 0.7626 (m-10) REVERT: A 1190 ARG cc_start: 0.7185 (ttm-80) cc_final: 0.6786 (ttm-80) REVERT: B 79 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8297 (t) REVERT: B 140 GLN cc_start: 0.8026 (mm110) cc_final: 0.7788 (mp10) REVERT: B 149 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7248 (tp30) REVERT: B 154 MET cc_start: 0.8204 (tpp) cc_final: 0.7557 (tpp) REVERT: B 155 ASP cc_start: 0.7524 (t70) cc_final: 0.7290 (t70) REVERT: B 160 MET cc_start: 0.7129 (mmt) cc_final: 0.6793 (mmm) REVERT: B 206 SER cc_start: 0.8120 (t) cc_final: 0.7829 (t) REVERT: B 231 GLU cc_start: 0.7283 (tt0) cc_final: 0.6928 (mt-10) REVERT: B 289 PHE cc_start: 0.7871 (t80) cc_final: 0.7496 (t80) REVERT: B 319 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7827 (mt) REVERT: B 375 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8299 (ttpp) REVERT: B 401 MET cc_start: 0.7519 (mmp) cc_final: 0.7293 (mtp) REVERT: B 520 ASP cc_start: 0.7721 (p0) cc_final: 0.7454 (p0) REVERT: B 534 ASP cc_start: 0.7646 (t70) cc_final: 0.7354 (t0) REVERT: B 565 MET cc_start: 0.4907 (ppp) cc_final: 0.4475 (ppp) REVERT: B 578 MET cc_start: 0.7579 (mtt) cc_final: 0.7188 (mtp) REVERT: B 595 TRP cc_start: 0.8418 (m100) cc_final: 0.8110 (m100) REVERT: B 596 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7970 (ttmm) REVERT: B 599 GLU cc_start: 0.7746 (tp30) cc_final: 0.7535 (mm-30) REVERT: B 600 HIS cc_start: 0.8137 (m90) cc_final: 0.7893 (m-70) REVERT: B 823 LEU cc_start: 0.8312 (mp) cc_final: 0.8036 (mm) REVERT: B 832 GLN cc_start: 0.8302 (tp40) cc_final: 0.8035 (tm-30) REVERT: B 853 ILE cc_start: 0.8394 (mm) cc_final: 0.7921 (tp) REVERT: B 897 LYS cc_start: 0.8295 (mmtp) cc_final: 0.8094 (mttp) REVERT: B 898 THR cc_start: 0.8472 (m) cc_final: 0.8161 (p) REVERT: B 926 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 929 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7834 (ttmt) REVERT: B 971 ASP cc_start: 0.8194 (m-30) cc_final: 0.7827 (m-30) REVERT: B 972 PHE cc_start: 0.8078 (t80) cc_final: 0.7843 (t80) REVERT: B 987 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8737 (m) REVERT: B 1002 VAL cc_start: 0.8460 (m) cc_final: 0.8105 (p) REVERT: B 1061 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8128 (p) REVERT: B 1067 PHE cc_start: 0.7774 (t80) cc_final: 0.7308 (t80) REVERT: B 1094 VAL cc_start: 0.8456 (m) cc_final: 0.8223 (p) REVERT: B 1098 ILE cc_start: 0.9039 (tt) cc_final: 0.8679 (tt) REVERT: B 1104 MET cc_start: 0.7718 (tpp) cc_final: 0.7418 (tpp) REVERT: B 1110 GLN cc_start: 0.8341 (mp10) cc_final: 0.8085 (mp10) REVERT: B 1117 VAL cc_start: 0.8837 (t) cc_final: 0.8490 (t) REVERT: B 1127 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8021 (m) REVERT: B 1128 ASP cc_start: 0.7272 (t0) cc_final: 0.7045 (t0) REVERT: B 1134 PHE cc_start: 0.8090 (m-80) cc_final: 0.7610 (m-10) REVERT: B 1141 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 1172 HIS cc_start: 0.7432 (t-170) cc_final: 0.7123 (t-170) REVERT: B 1214 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.6922 (mm) outliers start: 91 outliers final: 52 residues processed: 568 average time/residue: 0.1291 time to fit residues: 108.0503 Evaluate side-chains 558 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 492 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 958 LYS Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1149 ASN Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1165 CYS Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1214 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 85 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 37 optimal weight: 0.0470 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 6 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.1392 > 50:) chunk 68 optimal weight: 0.9990 chunk 191 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 HIS A 614 HIS A 624 GLN A1137 ASN A1172 HIS ** B 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.142038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123369 restraints weight = 24707.233| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.26 r_work: 0.3491 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16254 Z= 0.143 Angle : 0.568 8.088 22062 Z= 0.299 Chirality : 0.041 0.181 2660 Planarity : 0.004 0.043 2752 Dihedral : 5.566 58.769 2250 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.13 % Allowed : 20.80 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 2050 helix: 1.83 (0.14), residues: 1438 sheet: 0.87 (0.60), residues: 96 loop : -1.72 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 887 TYR 0.014 0.001 TYR B1125 PHE 0.017 0.001 PHE B 517 TRP 0.011 0.001 TRP B 427 HIS 0.004 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (16254) covalent geometry : angle 0.56812 / 0.30 (22062) hydrogen bonds : bond 0.04385 / 2.99 ( 1198) hydrogen bonds : angle 4.02931 / 2.90 ( 3534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 515 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8325 (t) REVERT: A 124 GLU cc_start: 0.7061 (tp30) cc_final: 0.6697 (tp30) REVERT: A 129 ASP cc_start: 0.6315 (OUTLIER) cc_final: 0.6059 (p0) REVERT: A 140 GLN cc_start: 0.8273 (mm-40) cc_final: 0.8056 (mp10) REVERT: A 149 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7464 (tm-30) REVERT: A 154 MET cc_start: 0.8256 (tpp) cc_final: 0.7744 (ttm) REVERT: A 155 ASP cc_start: 0.7976 (t70) cc_final: 0.7706 (t70) REVERT: A 166 VAL cc_start: 0.7607 (t) cc_final: 0.7385 (t) REVERT: A 180 LEU cc_start: 0.8344 (tt) cc_final: 0.8129 (tp) REVERT: A 184 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7829 (tp) REVERT: A 186 MET cc_start: 0.7778 (mtp) cc_final: 0.7435 (mtp) REVERT: A 187 ASN cc_start: 0.7575 (m-40) cc_final: 0.7127 (m-40) REVERT: A 206 SER cc_start: 0.8438 (t) cc_final: 0.8151 (t) REVERT: A 289 PHE cc_start: 0.8247 (t80) cc_final: 0.7969 (t80) REVERT: A 319 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8094 (mt) REVERT: A 337 GLU cc_start: 0.8036 (mp0) cc_final: 0.7602 (mp0) REVERT: A 346 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7754 (mt-10) REVERT: A 355 MET cc_start: 0.8444 (ttp) cc_final: 0.8119 (ttp) REVERT: A 427 TRP cc_start: 0.8697 (t-100) cc_final: 0.7757 (t-100) REVERT: A 534 ASP cc_start: 0.7902 (t70) cc_final: 0.7690 (t0) REVERT: A 588 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8035 (tttm) REVERT: A 599 GLU cc_start: 0.8145 (tp30) cc_final: 0.7726 (mp0) REVERT: A 622 LYS cc_start: 0.8758 (tppt) cc_final: 0.8290 (tppt) REVERT: A 632 LYS cc_start: 0.8145 (mtpm) cc_final: 0.7824 (mtpp) REVERT: A 823 LEU cc_start: 0.8513 (mp) cc_final: 0.8129 (mm) REVERT: A 832 GLN cc_start: 0.8569 (tp40) cc_final: 0.8209 (tt0) REVERT: A 925 MET cc_start: 0.7607 (ttm) cc_final: 0.7406 (mtp) REVERT: A 926 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7721 (mm-30) REVERT: A 958 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8236 (ttpp) REVERT: A 971 ASP cc_start: 0.8514 (m-30) cc_final: 0.8140 (m-30) REVERT: A 987 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8731 (m) REVERT: A 996 ASP cc_start: 0.7797 (p0) cc_final: 0.7595 (p0) REVERT: A 1044 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8074 (mt-10) REVERT: A 1061 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8282 (p) REVERT: A 1067 PHE cc_start: 0.8114 (t80) cc_final: 0.7741 (t80) REVERT: A 1073 MET cc_start: 0.8575 (mmm) cc_final: 0.8114 (mmm) REVERT: A 1094 VAL cc_start: 0.8698 (m) cc_final: 0.8395 (p) REVERT: A 1098 ILE cc_start: 0.9096 (tt) cc_final: 0.8747 (tt) REVERT: A 1104 MET cc_start: 0.8137 (tpt) cc_final: 0.7847 (mmm) REVERT: A 1127 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8416 (p) REVERT: A 1134 PHE cc_start: 0.8216 (m-80) cc_final: 0.7984 (m-80) REVERT: A 1186 LEU cc_start: 0.8665 (mt) cc_final: 0.8460 (mt) REVERT: A 1190 ARG cc_start: 0.7401 (ttm-80) cc_final: 0.6865 (mtt-85) REVERT: B 79 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8394 (t) REVERT: B 93 SER cc_start: 0.8309 (m) cc_final: 0.7936 (p) REVERT: B 107 LEU cc_start: 0.8258 (tt) cc_final: 0.8030 (tp) REVERT: B 133 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7592 (mtm) REVERT: B 140 GLN cc_start: 0.8120 (mm110) cc_final: 0.7838 (mp10) REVERT: B 149 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7569 (tp30) REVERT: B 166 VAL cc_start: 0.7730 (t) cc_final: 0.7432 (t) REVERT: B 206 SER cc_start: 0.8500 (t) cc_final: 0.8232 (t) REVERT: B 208 THR cc_start: 0.8220 (m) cc_final: 0.7986 (p) REVERT: B 231 GLU cc_start: 0.7715 (tt0) cc_final: 0.7425 (mt-10) REVERT: B 233 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7242 (tt0) REVERT: B 289 PHE cc_start: 0.8188 (t80) cc_final: 0.7961 (t80) REVERT: B 319 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8107 (mt) REVERT: B 375 LYS cc_start: 0.8774 (ttpt) cc_final: 0.8499 (ttpt) REVERT: B 401 MET cc_start: 0.7910 (mmp) cc_final: 0.7677 (mtp) REVERT: B 474 ILE cc_start: 0.6851 (tp) cc_final: 0.6591 (tt) REVERT: B 534 ASP cc_start: 0.7987 (t70) cc_final: 0.7773 (t0) REVERT: B 595 TRP cc_start: 0.8724 (m100) cc_final: 0.8360 (m100) REVERT: B 596 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8218 (ttmm) REVERT: B 599 GLU cc_start: 0.8024 (tp30) cc_final: 0.7815 (mm-30) REVERT: B 600 HIS cc_start: 0.8234 (m90) cc_final: 0.7948 (m-70) REVERT: B 823 LEU cc_start: 0.8494 (mp) cc_final: 0.8182 (mm) REVERT: B 832 GLN cc_start: 0.8537 (tp40) cc_final: 0.8203 (tm-30) REVERT: B 847 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7697 (mm-30) REVERT: B 884 LEU cc_start: 0.8674 (mm) cc_final: 0.8435 (mp) REVERT: B 940 ARG cc_start: 0.8587 (tpp80) cc_final: 0.8333 (ttm-80) REVERT: B 971 ASP cc_start: 0.8483 (m-30) cc_final: 0.8145 (m-30) REVERT: B 972 PHE cc_start: 0.8289 (t80) cc_final: 0.8077 (t80) REVERT: B 976 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7124 (ttm170) REVERT: B 987 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8871 (m) REVERT: B 1002 VAL cc_start: 0.8571 (m) cc_final: 0.8201 (p) REVERT: B 1051 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8546 (mtpp) REVERT: B 1061 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8243 (p) REVERT: B 1067 PHE cc_start: 0.8155 (t80) cc_final: 0.7805 (t80) REVERT: B 1072 ASP cc_start: 0.7789 (m-30) cc_final: 0.7231 (m-30) REVERT: B 1094 VAL cc_start: 0.8606 (m) cc_final: 0.8397 (p) REVERT: B 1098 ILE cc_start: 0.9111 (tt) cc_final: 0.8719 (tt) REVERT: B 1104 MET cc_start: 0.7870 (tpp) cc_final: 0.7575 (tpp) REVERT: B 1117 VAL cc_start: 0.8970 (t) cc_final: 0.8579 (t) REVERT: B 1127 VAL cc_start: 0.8535 (t) cc_final: 0.8253 (m) REVERT: B 1134 PHE cc_start: 0.8262 (m-80) cc_final: 0.7805 (m-10) REVERT: B 1141 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8290 (p) REVERT: B 1172 HIS cc_start: 0.7641 (t-170) cc_final: 0.7419 (t-170) REVERT: B 1214 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.6896 (mm) outliers start: 86 outliers final: 53 residues processed: 557 average time/residue: 0.1276 time to fit residues: 105.9869 Evaluate side-chains 560 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 491 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1149 ASN Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1214 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 5 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 HIS A 614 HIS B 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119589 restraints weight = 24530.848| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.21 r_work: 0.3435 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16254 Z= 0.169 Angle : 0.598 10.671 22062 Z= 0.312 Chirality : 0.042 0.197 2660 Planarity : 0.004 0.064 2752 Dihedral : 5.387 59.731 2243 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.60 % Allowed : 22.11 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 2050 helix: 1.81 (0.14), residues: 1446 sheet: 0.95 (0.59), residues: 96 loop : -1.66 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 887 TYR 0.012 0.001 TYR A1125 PHE 0.020 0.002 PHE A 625 TRP 0.013 0.001 TRP B 427 HIS 0.005 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (16254) covalent geometry : angle 0.59771 / 0.31 (22062) hydrogen bonds : bond 0.04672 / 3.18 ( 1198) hydrogen bonds : angle 4.04680 / 2.91 ( 3534) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 523 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8377 (t) REVERT: A 93 SER cc_start: 0.8300 (m) cc_final: 0.7882 (p) REVERT: A 112 ILE cc_start: 0.8510 (mt) cc_final: 0.8145 (mm) REVERT: A 124 GLU cc_start: 0.7132 (tp30) cc_final: 0.6755 (tp30) REVERT: A 140 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7980 (mp10) REVERT: A 149 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 154 MET cc_start: 0.8325 (tpp) cc_final: 0.7929 (ttm) REVERT: A 160 MET cc_start: 0.7999 (mmt) cc_final: 0.7668 (mmm) REVERT: A 184 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8042 (tp) REVERT: A 197 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7629 (tt0) REVERT: A 206 SER cc_start: 0.8668 (t) cc_final: 0.8072 (t) REVERT: A 233 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7474 (tm-30) REVERT: A 289 PHE cc_start: 0.8349 (t80) cc_final: 0.8108 (t80) REVERT: A 319 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7828 (mp) REVERT: A 337 GLU cc_start: 0.8084 (mp0) cc_final: 0.7653 (mp0) REVERT: A 346 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7773 (mt-10) REVERT: A 355 MET cc_start: 0.8458 (ttp) cc_final: 0.8118 (ttp) REVERT: A 387 TYR cc_start: 0.8090 (m-10) cc_final: 0.7636 (m-10) REVERT: A 398 ILE cc_start: 0.8674 (mt) cc_final: 0.8452 (mt) REVERT: A 410 LEU cc_start: 0.7857 (mp) cc_final: 0.7628 (mt) REVERT: A 427 TRP cc_start: 0.8853 (t-100) cc_final: 0.7753 (t-100) REVERT: A 449 ASP cc_start: 0.8273 (t0) cc_final: 0.8065 (t70) REVERT: A 451 ILE cc_start: 0.8551 (tt) cc_final: 0.8204 (tt) REVERT: A 588 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7943 (ttpm) REVERT: A 599 GLU cc_start: 0.8169 (tp30) cc_final: 0.7728 (mp0) REVERT: A 624 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6834 (pp30) REVERT: A 632 LYS cc_start: 0.8416 (mtpm) cc_final: 0.8092 (mtpp) REVERT: A 643 TRP cc_start: 0.6266 (t-100) cc_final: 0.6042 (t-100) REVERT: A 861 LYS cc_start: 0.7680 (mmmt) cc_final: 0.7415 (mmtm) REVERT: A 881 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8208 (tp30) REVERT: A 958 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8218 (ttpp) REVERT: A 971 ASP cc_start: 0.8486 (m-30) cc_final: 0.8115 (m-30) REVERT: A 986 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7966 (mt-10) REVERT: A 987 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8802 (m) REVERT: A 994 GLU cc_start: 0.8171 (mp0) cc_final: 0.7866 (mp0) REVERT: A 1044 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8114 (mt-10) REVERT: A 1061 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8321 (p) REVERT: A 1067 PHE cc_start: 0.8159 (t80) cc_final: 0.7841 (t80) REVERT: A 1098 ILE cc_start: 0.9117 (tt) cc_final: 0.8872 (tt) REVERT: A 1104 MET cc_start: 0.8112 (tpt) cc_final: 0.7848 (mmm) REVERT: A 1115 GLU cc_start: 0.8126 (tt0) cc_final: 0.7863 (tp30) REVERT: A 1122 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 1128 ASP cc_start: 0.7807 (t0) cc_final: 0.7582 (t70) REVERT: A 1134 PHE cc_start: 0.8231 (m-80) cc_final: 0.7892 (m-80) REVERT: A 1139 ASP cc_start: 0.8151 (p0) cc_final: 0.7772 (p0) REVERT: A 1141 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.8050 (p) REVERT: A 1190 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.7063 (mtt-85) REVERT: A 1202 ARG cc_start: 0.6928 (ttt-90) cc_final: 0.6601 (ttt-90) REVERT: B 79 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8404 (p) REVERT: B 93 SER cc_start: 0.8352 (m) cc_final: 0.7990 (p) REVERT: B 107 LEU cc_start: 0.8330 (tt) cc_final: 0.8130 (tp) REVERT: B 113 LEU cc_start: 0.8602 (tp) cc_final: 0.8399 (tt) REVERT: B 133 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7753 (mtm) REVERT: B 140 GLN cc_start: 0.8113 (mm110) cc_final: 0.7857 (mp10) REVERT: B 149 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7619 (tp30) REVERT: B 197 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7572 (tt0) REVERT: B 233 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 289 PHE cc_start: 0.8305 (t80) cc_final: 0.8019 (t80) REVERT: B 319 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8122 (mt) REVERT: B 375 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8568 (ttpp) REVERT: B 383 MET cc_start: 0.7076 (mmm) cc_final: 0.6278 (mmt) REVERT: B 387 TYR cc_start: 0.8183 (m-10) cc_final: 0.7657 (m-10) REVERT: B 401 MET cc_start: 0.7960 (mmp) cc_final: 0.7740 (mtp) REVERT: B 579 MET cc_start: 0.7878 (tpt) cc_final: 0.7578 (tpt) REVERT: B 595 TRP cc_start: 0.8787 (m100) cc_final: 0.8323 (m100) REVERT: B 606 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: B 609 ARG cc_start: 0.8205 (tpp80) cc_final: 0.7914 (tpp80) REVERT: B 643 TRP cc_start: 0.6422 (t-100) cc_final: 0.6198 (t-100) REVERT: B 646 ARG cc_start: 0.6831 (ptp-170) cc_final: 0.6525 (ptp-170) REVERT: B 823 LEU cc_start: 0.8560 (mp) cc_final: 0.8214 (mm) REVERT: B 832 GLN cc_start: 0.8617 (tp40) cc_final: 0.8273 (tt0) REVERT: B 940 ARG cc_start: 0.8594 (tpp80) cc_final: 0.8343 (ttm-80) REVERT: B 971 ASP cc_start: 0.8448 (m-30) cc_final: 0.8165 (m-30) REVERT: B 987 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8915 (m) REVERT: B 1051 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8538 (mtpp) REVERT: B 1061 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8289 (p) REVERT: B 1067 PHE cc_start: 0.8180 (t80) cc_final: 0.7790 (t80) REVERT: B 1072 ASP cc_start: 0.7806 (m-30) cc_final: 0.7605 (m-30) REVERT: B 1094 VAL cc_start: 0.8595 (m) cc_final: 0.8380 (p) REVERT: B 1098 ILE cc_start: 0.9109 (tt) cc_final: 0.8696 (tt) REVERT: B 1117 VAL cc_start: 0.8968 (t) cc_final: 0.8744 (t) REVERT: B 1134 PHE cc_start: 0.8303 (m-80) cc_final: 0.7978 (m-80) REVERT: B 1141 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8280 (p) REVERT: B 1214 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7001 (mm) outliers start: 94 outliers final: 59 residues processed: 565 average time/residue: 0.1283 time to fit residues: 107.6885 Evaluate side-chains 580 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 504 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1050 LYS Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1081 THR Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1212 ILE Chi-restraints excluded: chain B residue 1214 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 178 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 166 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 HIS A 624 GLN A 943 ASN B 614 HIS B 908 HIS B 943 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119477 restraints weight = 24497.987| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.20 r_work: 0.3435 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16254 Z= 0.137 Angle : 0.580 8.474 22062 Z= 0.299 Chirality : 0.041 0.159 2660 Planarity : 0.004 0.037 2752 Dihedral : 5.352 59.640 2243 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.90 % Allowed : 21.45 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.19), residues: 2050 helix: 1.97 (0.14), residues: 1444 sheet: 1.02 (0.60), residues: 96 loop : -1.57 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 887 TYR 0.011 0.001 TYR B1125 PHE 0.015 0.001 PHE B 517 TRP 0.011 0.001 TRP B1112 HIS 0.004 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (16254) covalent geometry : angle 0.57995 / 0.30 (22062) hydrogen bonds : bond 0.04388 / 2.99 ( 1198) hydrogen bonds : angle 3.96143 / 2.85 ( 3534) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 521 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8406 (t) REVERT: A 112 ILE cc_start: 0.8439 (mt) cc_final: 0.8084 (mm) REVERT: A 124 GLU cc_start: 0.7116 (tp30) cc_final: 0.6807 (tm-30) REVERT: A 129 ASP cc_start: 0.6270 (OUTLIER) cc_final: 0.6005 (p0) REVERT: A 133 MET cc_start: 0.8220 (ttm) cc_final: 0.7805 (mtm) REVERT: A 137 VAL cc_start: 0.8128 (p) cc_final: 0.7846 (m) REVERT: A 140 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7905 (mp10) REVERT: A 149 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7455 (tm-30) REVERT: A 154 MET cc_start: 0.8273 (tpp) cc_final: 0.7997 (tpp) REVERT: A 155 ASP cc_start: 0.7937 (p0) cc_final: 0.7515 (p0) REVERT: A 160 MET cc_start: 0.8148 (mmt) cc_final: 0.7826 (mmm) REVERT: A 180 LEU cc_start: 0.8368 (tt) cc_final: 0.8157 (mt) REVERT: A 184 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7995 (tp) REVERT: A 186 MET cc_start: 0.7876 (mtp) cc_final: 0.7613 (mtp) REVERT: A 199 MET cc_start: 0.8270 (mmm) cc_final: 0.8069 (tmm) REVERT: A 217 LEU cc_start: 0.8428 (mt) cc_final: 0.8201 (mm) REVERT: A 233 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7551 (tm-30) REVERT: A 253 PHE cc_start: 0.8257 (m-10) cc_final: 0.7923 (m-80) REVERT: A 289 PHE cc_start: 0.8364 (t80) cc_final: 0.8125 (t80) REVERT: A 319 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7825 (mp) REVERT: A 337 GLU cc_start: 0.8060 (mp0) cc_final: 0.7607 (mp0) REVERT: A 346 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7693 (mt-10) REVERT: A 355 MET cc_start: 0.8448 (ttp) cc_final: 0.8104 (ttp) REVERT: A 372 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8563 (p) REVERT: A 387 TYR cc_start: 0.8135 (m-10) cc_final: 0.7649 (m-10) REVERT: A 398 ILE cc_start: 0.8628 (mt) cc_final: 0.8354 (mt) REVERT: A 515 ASP cc_start: 0.8346 (t0) cc_final: 0.8081 (t0) REVERT: A 552 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7677 (tt) REVERT: A 574 GLU cc_start: 0.6849 (pt0) cc_final: 0.6638 (pt0) REVERT: A 580 GLU cc_start: 0.7377 (tp30) cc_final: 0.7148 (tp30) REVERT: A 588 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7946 (ttpm) REVERT: A 599 GLU cc_start: 0.8135 (tp30) cc_final: 0.7667 (mp0) REVERT: A 622 LYS cc_start: 0.8693 (tppt) cc_final: 0.8209 (tppt) REVERT: A 632 LYS cc_start: 0.8494 (mtpm) cc_final: 0.8234 (mtpp) REVERT: A 643 TRP cc_start: 0.6217 (t-100) cc_final: 0.5935 (t-100) REVERT: A 861 LYS cc_start: 0.7759 (mmmt) cc_final: 0.7522 (mmtm) REVERT: A 881 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8081 (tp30) REVERT: A 957 LEU cc_start: 0.8692 (tp) cc_final: 0.8329 (mp) REVERT: A 958 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8190 (ttpp) REVERT: A 971 ASP cc_start: 0.8484 (m-30) cc_final: 0.8148 (m-30) REVERT: A 986 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7980 (mt-10) REVERT: A 987 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8783 (m) REVERT: A 1060 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7474 (mm-30) REVERT: A 1061 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8394 (p) REVERT: A 1067 PHE cc_start: 0.8153 (t80) cc_final: 0.7905 (t80) REVERT: A 1087 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7306 (mm-30) REVERT: A 1098 ILE cc_start: 0.9066 (tt) cc_final: 0.8824 (tt) REVERT: A 1104 MET cc_start: 0.8069 (tpt) cc_final: 0.7817 (mmm) REVERT: A 1115 GLU cc_start: 0.8115 (tt0) cc_final: 0.7861 (tp30) REVERT: A 1122 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7684 (mm-30) REVERT: A 1134 PHE cc_start: 0.8217 (m-80) cc_final: 0.7872 (m-80) REVERT: A 1190 ARG cc_start: 0.7398 (ttm-80) cc_final: 0.7053 (mtt-85) REVERT: A 1202 ARG cc_start: 0.6829 (ttt-90) cc_final: 0.6535 (ttt-90) REVERT: B 79 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8384 (p) REVERT: B 93 SER cc_start: 0.8328 (m) cc_final: 0.7969 (p) REVERT: B 113 LEU cc_start: 0.8584 (tp) cc_final: 0.8380 (tt) REVERT: B 133 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7671 (mtm) REVERT: B 149 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7657 (tp30) REVERT: B 160 MET cc_start: 0.8106 (mmt) cc_final: 0.7844 (mmm) REVERT: B 180 LEU cc_start: 0.8259 (tt) cc_final: 0.8022 (tp) REVERT: B 231 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: B 233 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 289 PHE cc_start: 0.8339 (t80) cc_final: 0.8059 (t80) REVERT: B 319 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7840 (mt) REVERT: B 383 MET cc_start: 0.6974 (mmm) cc_final: 0.6005 (mmt) REVERT: B 387 TYR cc_start: 0.8203 (m-10) cc_final: 0.7649 (m-10) REVERT: B 401 MET cc_start: 0.7980 (mmp) cc_final: 0.7751 (mtp) REVERT: B 451 ILE cc_start: 0.8563 (tt) cc_final: 0.8292 (tt) REVERT: B 588 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8013 (ttpm) REVERT: B 595 TRP cc_start: 0.8748 (m100) cc_final: 0.8346 (m100) REVERT: B 606 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: B 609 ARG cc_start: 0.8239 (tpp80) cc_final: 0.7966 (tpp80) REVERT: B 643 TRP cc_start: 0.6480 (t-100) cc_final: 0.6252 (t-100) REVERT: B 646 ARG cc_start: 0.6913 (ptp-170) cc_final: 0.6601 (ptp-170) REVERT: B 832 GLN cc_start: 0.8566 (tp40) cc_final: 0.8355 (tt0) REVERT: B 940 ARG cc_start: 0.8579 (tpp80) cc_final: 0.8377 (ttm-80) REVERT: B 967 MET cc_start: 0.8218 (mmp) cc_final: 0.7824 (mmp) REVERT: B 971 ASP cc_start: 0.8438 (m-30) cc_final: 0.8129 (m-30) REVERT: B 976 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7246 (ttm170) REVERT: B 1061 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8252 (p) REVERT: B 1067 PHE cc_start: 0.8218 (t80) cc_final: 0.7769 (t80) REVERT: B 1072 ASP cc_start: 0.7709 (m-30) cc_final: 0.7318 (m-30) REVERT: B 1094 VAL cc_start: 0.8616 (m) cc_final: 0.8386 (p) REVERT: B 1098 ILE cc_start: 0.9110 (tt) cc_final: 0.8700 (tp) REVERT: B 1117 VAL cc_start: 0.8923 (t) cc_final: 0.8707 (t) REVERT: B 1134 PHE cc_start: 0.8311 (m-80) cc_final: 0.7999 (m-80) REVERT: B 1141 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8276 (p) REVERT: B 1172 HIS cc_start: 0.7520 (t-170) cc_final: 0.7267 (t-170) REVERT: B 1214 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6798 (mm) outliers start: 99 outliers final: 60 residues processed: 567 average time/residue: 0.1278 time to fit residues: 107.3544 Evaluate side-chains 576 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 497 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1081 THR Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1212 ILE Chi-restraints excluded: chain B residue 1214 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 90 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 18 optimal weight: 0.0970 chunk 53 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN A 943 ASN B 140 GLN B1172 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118045 restraints weight = 24300.522| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.16 r_work: 0.3412 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16254 Z= 0.150 Angle : 0.602 10.364 22062 Z= 0.309 Chirality : 0.041 0.156 2660 Planarity : 0.004 0.056 2752 Dihedral : 5.307 59.564 2242 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.90 % Allowed : 22.88 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 2050 helix: 2.01 (0.14), residues: 1444 sheet: 1.05 (0.60), residues: 96 loop : -1.51 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 887 TYR 0.010 0.001 TYR B1125 PHE 0.026 0.001 PHE B 972 TRP 0.013 0.001 TRP B1112 HIS 0.005 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (16254) covalent geometry : angle 0.60229 / 0.31 (22062) hydrogen bonds : bond 0.04488 / 3.06 ( 1198) hydrogen bonds : angle 3.96150 / 2.85 ( 3534) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 503 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8358 (p) REVERT: A 112 ILE cc_start: 0.8494 (mt) cc_final: 0.8150 (mm) REVERT: A 124 GLU cc_start: 0.7136 (tp30) cc_final: 0.6834 (tm-30) REVERT: A 129 ASP cc_start: 0.6218 (OUTLIER) cc_final: 0.5946 (p0) REVERT: A 133 MET cc_start: 0.8219 (ttm) cc_final: 0.7774 (mtm) REVERT: A 137 VAL cc_start: 0.8139 (p) cc_final: 0.7855 (m) REVERT: A 140 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7904 (mp10) REVERT: A 149 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7419 (tm-30) REVERT: A 154 MET cc_start: 0.8320 (tpp) cc_final: 0.7955 (ttm) REVERT: A 160 MET cc_start: 0.8268 (mmt) cc_final: 0.7952 (mmm) REVERT: A 184 LEU cc_start: 0.8185 (tt) cc_final: 0.7926 (tp) REVERT: A 186 MET cc_start: 0.7908 (mtp) cc_final: 0.7650 (mtt) REVERT: A 217 LEU cc_start: 0.8517 (mt) cc_final: 0.8246 (mm) REVERT: A 233 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7509 (tm-30) REVERT: A 253 PHE cc_start: 0.8236 (m-10) cc_final: 0.7930 (m-80) REVERT: A 266 LEU cc_start: 0.8110 (tp) cc_final: 0.7807 (tp) REVERT: A 289 PHE cc_start: 0.8393 (t80) cc_final: 0.8123 (t80) REVERT: A 319 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7616 (mp) REVERT: A 337 GLU cc_start: 0.8040 (mp0) cc_final: 0.7624 (mp0) REVERT: A 346 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 355 MET cc_start: 0.8453 (ttp) cc_final: 0.8104 (ttp) REVERT: A 372 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8532 (p) REVERT: A 377 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8470 (mp) REVERT: A 387 TYR cc_start: 0.8214 (m-10) cc_final: 0.7661 (m-10) REVERT: A 398 ILE cc_start: 0.8665 (mt) cc_final: 0.8380 (mt) REVERT: A 427 TRP cc_start: 0.8830 (t-100) cc_final: 0.8401 (t-100) REVERT: A 484 SER cc_start: 0.8679 (p) cc_final: 0.8362 (t) REVERT: A 552 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7690 (tt) REVERT: A 580 GLU cc_start: 0.7574 (tp30) cc_final: 0.7245 (tp30) REVERT: A 588 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8144 (tttm) REVERT: A 599 GLU cc_start: 0.8112 (tp30) cc_final: 0.7660 (mp0) REVERT: A 622 LYS cc_start: 0.8660 (tppt) cc_final: 0.8376 (tppt) REVERT: A 630 ASP cc_start: 0.7402 (p0) cc_final: 0.7128 (p0) REVERT: A 632 LYS cc_start: 0.8544 (mtpm) cc_final: 0.8272 (mtpp) REVERT: A 643 TRP cc_start: 0.6437 (t-100) cc_final: 0.6048 (t-100) REVERT: A 646 ARG cc_start: 0.7038 (ptp90) cc_final: 0.6691 (ptp90) REVERT: A 818 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7706 (tp) REVERT: A 881 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8077 (tp30) REVERT: A 976 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7741 (mtm-85) REVERT: A 986 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7816 (mt-10) REVERT: A 987 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8876 (m) REVERT: A 1060 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 1061 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8400 (p) REVERT: A 1067 PHE cc_start: 0.8172 (t80) cc_final: 0.7906 (t80) REVERT: A 1087 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7438 (mm-30) REVERT: A 1098 ILE cc_start: 0.9082 (tt) cc_final: 0.8825 (tt) REVERT: A 1115 GLU cc_start: 0.8124 (tt0) cc_final: 0.7862 (tp30) REVERT: A 1122 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7613 (mm-30) REVERT: A 1139 ASP cc_start: 0.8338 (p0) cc_final: 0.7937 (p0) REVERT: A 1141 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.8045 (p) REVERT: A 1190 ARG cc_start: 0.7412 (ttm-80) cc_final: 0.7019 (mtt-85) REVERT: A 1202 ARG cc_start: 0.6803 (ttt-90) cc_final: 0.6559 (ttt-90) REVERT: B 79 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8370 (p) REVERT: B 93 SER cc_start: 0.8277 (m) cc_final: 0.7899 (p) REVERT: B 133 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7728 (mtm) REVERT: B 149 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7614 (tp30) REVERT: B 160 MET cc_start: 0.8155 (mmt) cc_final: 0.7908 (mmm) REVERT: B 233 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7490 (tm-30) REVERT: B 265 VAL cc_start: 0.8592 (p) cc_final: 0.8385 (p) REVERT: B 289 PHE cc_start: 0.8355 (t80) cc_final: 0.8126 (t80) REVERT: B 319 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7765 (mt) REVERT: B 383 MET cc_start: 0.6991 (mmm) cc_final: 0.5861 (mmt) REVERT: B 387 TYR cc_start: 0.8235 (m-10) cc_final: 0.7651 (m-10) REVERT: B 401 MET cc_start: 0.7958 (mmp) cc_final: 0.7720 (mtp) REVERT: B 484 SER cc_start: 0.8678 (p) cc_final: 0.8341 (t) REVERT: B 577 ASP cc_start: 0.7517 (m-30) cc_final: 0.7308 (m-30) REVERT: B 588 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7984 (ttpm) REVERT: B 595 TRP cc_start: 0.8773 (m100) cc_final: 0.8404 (m100) REVERT: B 609 ARG cc_start: 0.8235 (tpp80) cc_final: 0.7985 (tpp80) REVERT: B 643 TRP cc_start: 0.6719 (t-100) cc_final: 0.6420 (t-100) REVERT: B 646 ARG cc_start: 0.7060 (ptp-170) cc_final: 0.6760 (ptp-170) REVERT: B 861 LYS cc_start: 0.7794 (mmmt) cc_final: 0.7589 (mmmm) REVERT: B 872 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7514 (tp30) REVERT: B 967 MET cc_start: 0.8026 (mmp) cc_final: 0.7692 (mmp) REVERT: B 971 ASP cc_start: 0.8340 (m-30) cc_final: 0.8034 (m-30) REVERT: B 976 ARG cc_start: 0.7970 (mtt90) cc_final: 0.7265 (ttm170) REVERT: B 999 PHE cc_start: 0.7684 (m-80) cc_final: 0.7203 (m-80) REVERT: B 1061 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8192 (p) REVERT: B 1067 PHE cc_start: 0.8129 (t80) cc_final: 0.7826 (t80) REVERT: B 1072 ASP cc_start: 0.7678 (m-30) cc_final: 0.7332 (m-30) REVERT: B 1087 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7397 (tp30) REVERT: B 1094 VAL cc_start: 0.8599 (m) cc_final: 0.8368 (p) REVERT: B 1098 ILE cc_start: 0.9102 (tt) cc_final: 0.8690 (tp) REVERT: B 1117 VAL cc_start: 0.8926 (t) cc_final: 0.8715 (t) REVERT: B 1134 PHE cc_start: 0.8340 (m-80) cc_final: 0.7950 (m-10) REVERT: B 1141 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8299 (p) REVERT: B 1214 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6816 (mm) outliers start: 99 outliers final: 61 residues processed: 546 average time/residue: 0.1285 time to fit residues: 104.0292 Evaluate side-chains 570 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 491 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1212 ILE Chi-restraints excluded: chain B residue 1214 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 5 optimal weight: 0.0570 chunk 73 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 177 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN B 832 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.137028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118757 restraints weight = 24350.627| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.17 r_work: 0.3424 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16254 Z= 0.133 Angle : 0.594 10.558 22062 Z= 0.304 Chirality : 0.041 0.177 2660 Planarity : 0.004 0.053 2752 Dihedral : 5.226 59.746 2241 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.89 % Allowed : 24.14 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.19), residues: 2050 helix: 2.09 (0.14), residues: 1440 sheet: 1.05 (0.60), residues: 96 loop : -1.47 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 887 TYR 0.011 0.001 TYR A1178 PHE 0.017 0.001 PHE B 253 TRP 0.011 0.001 TRP B1112 HIS 0.004 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (16254) covalent geometry : angle 0.59353 / 0.30 (22062) hydrogen bonds : bond 0.04313 / 2.94 ( 1198) hydrogen bonds : angle 3.90848 / 2.81 ( 3534) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 498 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8318 (t) REVERT: A 112 ILE cc_start: 0.8439 (mt) cc_final: 0.8092 (mm) REVERT: A 124 GLU cc_start: 0.7088 (tp30) cc_final: 0.6753 (tp30) REVERT: A 129 ASP cc_start: 0.6179 (OUTLIER) cc_final: 0.5935 (p0) REVERT: A 137 VAL cc_start: 0.8076 (p) cc_final: 0.7815 (m) REVERT: A 140 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7955 (mp10) REVERT: A 149 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7419 (tm-30) REVERT: A 154 MET cc_start: 0.8323 (tpp) cc_final: 0.8027 (ttp) REVERT: A 160 MET cc_start: 0.8249 (mmt) cc_final: 0.7956 (mmm) REVERT: A 184 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7897 (tp) REVERT: A 186 MET cc_start: 0.7905 (mtp) cc_final: 0.7651 (mtt) REVERT: A 217 LEU cc_start: 0.8531 (mt) cc_final: 0.8256 (mm) REVERT: A 233 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7419 (tm-30) REVERT: A 266 LEU cc_start: 0.8157 (tp) cc_final: 0.7861 (tp) REVERT: A 289 PHE cc_start: 0.8397 (t80) cc_final: 0.8129 (t80) REVERT: A 300 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 319 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7544 (mp) REVERT: A 337 GLU cc_start: 0.8016 (mp0) cc_final: 0.7614 (mp0) REVERT: A 346 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7589 (mt-10) REVERT: A 355 MET cc_start: 0.8458 (ttp) cc_final: 0.8103 (ttp) REVERT: A 372 VAL cc_start: 0.8794 (p) cc_final: 0.8580 (p) REVERT: A 387 TYR cc_start: 0.8193 (m-10) cc_final: 0.7562 (m-10) REVERT: A 398 ILE cc_start: 0.8683 (mt) cc_final: 0.8382 (mt) REVERT: A 427 TRP cc_start: 0.8828 (t-100) cc_final: 0.8414 (t-100) REVERT: A 484 SER cc_start: 0.8716 (p) cc_final: 0.8421 (t) REVERT: A 580 GLU cc_start: 0.7552 (tp30) cc_final: 0.7288 (tp30) REVERT: A 588 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8156 (tttm) REVERT: A 599 GLU cc_start: 0.8124 (tp30) cc_final: 0.7668 (mp0) REVERT: A 622 LYS cc_start: 0.8614 (tppt) cc_final: 0.8343 (tppt) REVERT: A 630 ASP cc_start: 0.7441 (p0) cc_final: 0.7119 (p0) REVERT: A 632 LYS cc_start: 0.8580 (mtpm) cc_final: 0.8287 (mtpp) REVERT: A 643 TRP cc_start: 0.6545 (t-100) cc_final: 0.6088 (t-100) REVERT: A 818 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7652 (tp) REVERT: A 881 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8025 (tp30) REVERT: A 957 LEU cc_start: 0.8706 (tp) cc_final: 0.8458 (mp) REVERT: A 986 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7773 (mt-10) REVERT: A 987 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8877 (m) REVERT: A 1060 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 1061 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8368 (p) REVERT: A 1067 PHE cc_start: 0.8167 (t80) cc_final: 0.7865 (t80) REVERT: A 1087 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 1098 ILE cc_start: 0.9060 (tt) cc_final: 0.8819 (tt) REVERT: A 1115 GLU cc_start: 0.8127 (tt0) cc_final: 0.7872 (tp30) REVERT: A 1122 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7611 (mm-30) REVERT: A 1139 ASP cc_start: 0.8278 (p0) cc_final: 0.7788 (p0) REVERT: A 1141 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8039 (p) REVERT: A 1172 HIS cc_start: 0.7433 (t70) cc_final: 0.7230 (t-90) REVERT: A 1190 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.7097 (mtt-85) REVERT: A 1202 ARG cc_start: 0.6717 (ttt-90) cc_final: 0.6483 (ttt-90) REVERT: B 79 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8346 (p) REVERT: B 133 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7648 (mtm) REVERT: B 149 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7626 (tp30) REVERT: B 156 VAL cc_start: 0.8445 (t) cc_final: 0.8219 (m) REVERT: B 160 MET cc_start: 0.8329 (mmt) cc_final: 0.8065 (mmm) REVERT: B 233 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7464 (tm-30) REVERT: B 253 PHE cc_start: 0.8196 (m-10) cc_final: 0.7880 (m-80) REVERT: B 289 PHE cc_start: 0.8351 (t80) cc_final: 0.8074 (t80) REVERT: B 319 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7733 (mt) REVERT: B 383 MET cc_start: 0.7007 (mmm) cc_final: 0.5870 (mmt) REVERT: B 386 PHE cc_start: 0.8366 (t80) cc_final: 0.8138 (t80) REVERT: B 387 TYR cc_start: 0.8249 (m-10) cc_final: 0.7642 (m-10) REVERT: B 401 MET cc_start: 0.7961 (mmp) cc_final: 0.7752 (mtp) REVERT: B 484 SER cc_start: 0.8674 (p) cc_final: 0.8359 (t) REVERT: B 577 ASP cc_start: 0.7553 (m-30) cc_final: 0.7333 (m-30) REVERT: B 588 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8004 (ttpm) REVERT: B 595 TRP cc_start: 0.8775 (m100) cc_final: 0.8423 (m100) REVERT: B 609 ARG cc_start: 0.8286 (tpp80) cc_final: 0.8040 (tpp80) REVERT: B 643 TRP cc_start: 0.6805 (t-100) cc_final: 0.6504 (t-100) REVERT: B 646 ARG cc_start: 0.7110 (ptp-170) cc_final: 0.6839 (ptp-170) REVERT: B 955 ASN cc_start: 0.8094 (m-40) cc_final: 0.7757 (t0) REVERT: B 1061 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8252 (p) REVERT: B 1067 PHE cc_start: 0.8127 (t80) cc_final: 0.7820 (t80) REVERT: B 1087 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7355 (tp30) REVERT: B 1094 VAL cc_start: 0.8585 (m) cc_final: 0.8356 (p) REVERT: B 1098 ILE cc_start: 0.9085 (tt) cc_final: 0.8676 (tp) REVERT: B 1104 MET cc_start: 0.8014 (mmm) cc_final: 0.7791 (tpp) REVERT: B 1117 VAL cc_start: 0.8892 (t) cc_final: 0.8664 (t) REVERT: B 1134 PHE cc_start: 0.8311 (m-80) cc_final: 0.7941 (m-10) REVERT: B 1141 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8304 (p) REVERT: B 1214 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6802 (mm) outliers start: 82 outliers final: 53 residues processed: 528 average time/residue: 0.1267 time to fit residues: 98.9902 Evaluate side-chains 560 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 491 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1212 ILE Chi-restraints excluded: chain B residue 1214 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 7 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 79 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN B 917 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.135749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.117725 restraints weight = 24364.109| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.14 r_work: 0.3406 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16254 Z= 0.146 Angle : 0.618 9.970 22062 Z= 0.314 Chirality : 0.041 0.213 2660 Planarity : 0.004 0.054 2752 Dihedral : 5.189 58.821 2241 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.59 % Allowed : 24.91 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.19), residues: 2050 helix: 2.14 (0.14), residues: 1434 sheet: 1.11 (0.60), residues: 96 loop : -1.47 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 887 TYR 0.016 0.001 TYR B 280 PHE 0.031 0.002 PHE B 248 TRP 0.013 0.001 TRP B 193 HIS 0.004 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (16254) covalent geometry : angle 0.61840 / 0.31 (22062) hydrogen bonds : bond 0.04431 / 3.02 ( 1198) hydrogen bonds : angle 3.90817 / 2.80 ( 3534) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 508 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8358 (p) REVERT: A 112 ILE cc_start: 0.8423 (mt) cc_final: 0.8069 (mm) REVERT: A 124 GLU cc_start: 0.7144 (tp30) cc_final: 0.6802 (tp30) REVERT: A 129 ASP cc_start: 0.6207 (OUTLIER) cc_final: 0.5952 (p0) REVERT: A 133 MET cc_start: 0.8191 (ttm) cc_final: 0.7723 (mtm) REVERT: A 137 VAL cc_start: 0.8089 (p) cc_final: 0.7818 (m) REVERT: A 149 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7460 (tm-30) REVERT: A 154 MET cc_start: 0.8335 (tpp) cc_final: 0.7951 (ttm) REVERT: A 160 MET cc_start: 0.8366 (mmt) cc_final: 0.8070 (mmm) REVERT: A 184 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7937 (tp) REVERT: A 186 MET cc_start: 0.7877 (mtp) cc_final: 0.7645 (mtt) REVERT: A 199 MET cc_start: 0.8108 (tmm) cc_final: 0.7199 (tpp) REVERT: A 217 LEU cc_start: 0.8552 (mt) cc_final: 0.8269 (mm) REVERT: A 233 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7525 (tm-30) REVERT: A 249 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8198 (ttm) REVERT: A 266 LEU cc_start: 0.8241 (tp) cc_final: 0.7945 (tp) REVERT: A 289 PHE cc_start: 0.8474 (t80) cc_final: 0.8206 (t80) REVERT: A 319 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7579 (mp) REVERT: A 337 GLU cc_start: 0.7997 (mp0) cc_final: 0.7588 (mp0) REVERT: A 355 MET cc_start: 0.8465 (ttp) cc_final: 0.8120 (ttp) REVERT: A 372 VAL cc_start: 0.8821 (p) cc_final: 0.8573 (p) REVERT: A 377 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8498 (mp) REVERT: A 383 MET cc_start: 0.7389 (mmm) cc_final: 0.6105 (mmm) REVERT: A 387 TYR cc_start: 0.8233 (m-10) cc_final: 0.7340 (m-10) REVERT: A 398 ILE cc_start: 0.8713 (mt) cc_final: 0.8397 (mt) REVERT: A 427 TRP cc_start: 0.8840 (t-100) cc_final: 0.8376 (t-100) REVERT: A 484 SER cc_start: 0.8722 (p) cc_final: 0.8426 (t) REVERT: A 580 GLU cc_start: 0.7643 (tp30) cc_final: 0.7377 (tp30) REVERT: A 599 GLU cc_start: 0.8129 (tp30) cc_final: 0.7673 (mp0) REVERT: A 622 LYS cc_start: 0.8559 (tppt) cc_final: 0.8299 (tppt) REVERT: A 630 ASP cc_start: 0.7506 (p0) cc_final: 0.7185 (p0) REVERT: A 632 LYS cc_start: 0.8594 (mtpm) cc_final: 0.8305 (mtpp) REVERT: A 643 TRP cc_start: 0.6701 (t-100) cc_final: 0.5978 (t-100) REVERT: A 646 ARG cc_start: 0.7133 (ptp90) cc_final: 0.6594 (ptp90) REVERT: A 861 LYS cc_start: 0.8017 (mmmt) cc_final: 0.7735 (mmtp) REVERT: A 881 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8095 (tp30) REVERT: A 972 PHE cc_start: 0.8155 (t80) cc_final: 0.7930 (t80) REVERT: A 987 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8893 (m) REVERT: A 999 PHE cc_start: 0.7497 (m-80) cc_final: 0.7003 (m-80) REVERT: A 1060 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 1061 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8359 (p) REVERT: A 1067 PHE cc_start: 0.8221 (t80) cc_final: 0.7870 (t80) REVERT: A 1087 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 1098 ILE cc_start: 0.9111 (tt) cc_final: 0.8901 (tt) REVERT: A 1115 GLU cc_start: 0.8118 (tt0) cc_final: 0.7863 (tp30) REVERT: A 1122 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7636 (mm-30) REVERT: A 1139 ASP cc_start: 0.8310 (p0) cc_final: 0.7862 (p0) REVERT: A 1141 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.8061 (p) REVERT: A 1172 HIS cc_start: 0.7330 (t70) cc_final: 0.7126 (t-90) REVERT: A 1202 ARG cc_start: 0.6757 (ttt-90) cc_final: 0.6508 (ttt-90) REVERT: B 79 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8366 (p) REVERT: B 133 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7701 (mtm) REVERT: B 149 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7604 (tp30) REVERT: B 160 MET cc_start: 0.8350 (mmt) cc_final: 0.8118 (mmm) REVERT: B 161 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7685 (mtm-85) REVERT: B 179 VAL cc_start: 0.8395 (p) cc_final: 0.8159 (t) REVERT: B 233 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7508 (tm-30) REVERT: B 253 PHE cc_start: 0.8125 (m-10) cc_final: 0.7828 (m-80) REVERT: B 289 PHE cc_start: 0.8371 (t80) cc_final: 0.8091 (t80) REVERT: B 319 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7961 (mt) REVERT: B 351 ARG cc_start: 0.8771 (tpp80) cc_final: 0.8495 (tpp80) REVERT: B 383 MET cc_start: 0.7123 (mmm) cc_final: 0.6021 (mmt) REVERT: B 386 PHE cc_start: 0.8380 (t80) cc_final: 0.8163 (t80) REVERT: B 387 TYR cc_start: 0.8289 (m-10) cc_final: 0.7602 (m-10) REVERT: B 401 MET cc_start: 0.7950 (mmp) cc_final: 0.7739 (mtp) REVERT: B 484 SER cc_start: 0.8665 (p) cc_final: 0.8357 (t) REVERT: B 580 GLU cc_start: 0.7609 (tp30) cc_final: 0.6987 (tp30) REVERT: B 588 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7967 (ttpm) REVERT: B 643 TRP cc_start: 0.7051 (t-100) cc_final: 0.6678 (t-100) REVERT: B 646 ARG cc_start: 0.7283 (ptp-170) cc_final: 0.6956 (ptp-170) REVERT: B 955 ASN cc_start: 0.8110 (m-40) cc_final: 0.7717 (t0) REVERT: B 999 PHE cc_start: 0.7752 (m-80) cc_final: 0.7299 (m-80) REVERT: B 1061 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8221 (p) REVERT: B 1067 PHE cc_start: 0.8077 (t80) cc_final: 0.7831 (t80) REVERT: B 1087 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7345 (tp30) REVERT: B 1094 VAL cc_start: 0.8622 (m) cc_final: 0.8387 (p) REVERT: B 1098 ILE cc_start: 0.9057 (tt) cc_final: 0.8630 (tp) REVERT: B 1104 MET cc_start: 0.8007 (mmm) cc_final: 0.7793 (tpp) REVERT: B 1117 VAL cc_start: 0.8900 (t) cc_final: 0.8663 (t) REVERT: B 1141 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8299 (p) outliers start: 77 outliers final: 54 residues processed: 538 average time/residue: 0.1238 time to fit residues: 98.4065 Evaluate side-chains 566 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 497 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 143 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 127 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 41 optimal weight: 0.0170 chunk 144 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 63 optimal weight: 0.0970 chunk 149 optimal weight: 0.5980 chunk 14 optimal weight: 0.0040 overall best weight: 0.2028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN A 600 HIS A1149 ASN B 917 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.137723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.119793 restraints weight = 24546.282| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.16 r_work: 0.3433 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16254 Z= 0.126 Angle : 0.612 9.609 22062 Z= 0.311 Chirality : 0.040 0.192 2660 Planarity : 0.004 0.069 2752 Dihedral : 5.136 58.789 2241 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.11 % Allowed : 25.69 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.19), residues: 2050 helix: 2.17 (0.14), residues: 1446 sheet: 1.21 (0.65), residues: 76 loop : -1.40 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 976 TYR 0.044 0.001 TYR A1178 PHE 0.026 0.001 PHE B 248 TRP 0.013 0.001 TRP B1112 HIS 0.005 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (16254) covalent geometry : angle 0.61237 / 0.31 (22062) hydrogen bonds : bond 0.04072 / 2.77 ( 1198) hydrogen bonds : angle 3.85424 / 2.76 ( 3534) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 515 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8264 (t) REVERT: A 112 ILE cc_start: 0.8388 (mt) cc_final: 0.8030 (mm) REVERT: A 129 ASP cc_start: 0.6098 (OUTLIER) cc_final: 0.5864 (p0) REVERT: A 137 VAL cc_start: 0.7956 (p) cc_final: 0.7736 (m) REVERT: A 149 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7428 (tm-30) REVERT: A 154 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7796 (ttm) REVERT: A 155 ASP cc_start: 0.7920 (p0) cc_final: 0.7635 (p0) REVERT: A 160 MET cc_start: 0.8360 (mmt) cc_final: 0.8039 (mmm) REVERT: A 184 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7799 (tp) REVERT: A 186 MET cc_start: 0.7853 (mtp) cc_final: 0.7610 (mtt) REVERT: A 199 MET cc_start: 0.8004 (tmm) cc_final: 0.7122 (tpp) REVERT: A 217 LEU cc_start: 0.8530 (mt) cc_final: 0.8257 (mm) REVERT: A 233 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7434 (tm-30) REVERT: A 266 LEU cc_start: 0.8227 (tp) cc_final: 0.7935 (tp) REVERT: A 289 PHE cc_start: 0.8465 (t80) cc_final: 0.8203 (t80) REVERT: A 319 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7418 (mp) REVERT: A 337 GLU cc_start: 0.8067 (mp0) cc_final: 0.7649 (mp0) REVERT: A 355 MET cc_start: 0.8454 (ttp) cc_final: 0.8097 (ttp) REVERT: A 372 VAL cc_start: 0.8782 (p) cc_final: 0.8569 (p) REVERT: A 383 MET cc_start: 0.7317 (mmm) cc_final: 0.6006 (mmm) REVERT: A 387 TYR cc_start: 0.8220 (m-10) cc_final: 0.7328 (m-10) REVERT: A 398 ILE cc_start: 0.8728 (mt) cc_final: 0.8406 (mt) REVERT: A 406 PHE cc_start: 0.8299 (m-10) cc_final: 0.8096 (m-10) REVERT: A 427 TRP cc_start: 0.8821 (t-100) cc_final: 0.8372 (t-100) REVERT: A 484 SER cc_start: 0.8717 (p) cc_final: 0.8414 (t) REVERT: A 580 GLU cc_start: 0.7531 (tp30) cc_final: 0.7255 (tp30) REVERT: A 599 GLU cc_start: 0.8103 (tp30) cc_final: 0.7637 (mp0) REVERT: A 622 LYS cc_start: 0.8512 (tppt) cc_final: 0.8262 (tppt) REVERT: A 630 ASP cc_start: 0.7460 (p0) cc_final: 0.7169 (p0) REVERT: A 632 LYS cc_start: 0.8543 (mtpm) cc_final: 0.8235 (mtpp) REVERT: A 643 TRP cc_start: 0.6687 (t-100) cc_final: 0.5998 (t-100) REVERT: A 646 ARG cc_start: 0.7188 (ptp90) cc_final: 0.6775 (ptp90) REVERT: A 861 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7641 (mmtp) REVERT: A 881 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8049 (tp30) REVERT: A 957 LEU cc_start: 0.8733 (tp) cc_final: 0.8509 (mp) REVERT: A 986 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7934 (mt-10) REVERT: A 987 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8878 (m) REVERT: A 999 PHE cc_start: 0.7469 (m-80) cc_final: 0.7262 (m-80) REVERT: A 1034 ASP cc_start: 0.8091 (t0) cc_final: 0.7870 (t0) REVERT: A 1060 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7341 (mm-30) REVERT: A 1061 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8411 (p) REVERT: A 1098 ILE cc_start: 0.9077 (tt) cc_final: 0.8848 (tt) REVERT: A 1115 GLU cc_start: 0.8056 (tt0) cc_final: 0.7790 (tp30) REVERT: A 1122 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 79 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8295 (p) REVERT: B 149 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7611 (tp30) REVERT: B 160 MET cc_start: 0.8331 (mmt) cc_final: 0.8094 (mmm) REVERT: B 191 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: B 233 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 253 PHE cc_start: 0.8069 (m-10) cc_final: 0.7793 (m-80) REVERT: B 289 PHE cc_start: 0.8375 (t80) cc_final: 0.8091 (t80) REVERT: B 351 ARG cc_start: 0.8739 (tpp80) cc_final: 0.8496 (tpp80) REVERT: B 355 MET cc_start: 0.8447 (tmm) cc_final: 0.8049 (tmm) REVERT: B 383 MET cc_start: 0.7020 (mmm) cc_final: 0.5917 (mmt) REVERT: B 386 PHE cc_start: 0.8331 (t80) cc_final: 0.8109 (t80) REVERT: B 387 TYR cc_start: 0.8239 (m-10) cc_final: 0.7585 (m-10) REVERT: B 484 SER cc_start: 0.8634 (p) cc_final: 0.8322 (t) REVERT: B 499 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.7933 (ttm-80) REVERT: B 577 ASP cc_start: 0.7579 (m-30) cc_final: 0.7344 (m-30) REVERT: B 588 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7974 (ttpm) REVERT: B 626 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8029 (mt) REVERT: B 643 TRP cc_start: 0.6970 (t-100) cc_final: 0.6593 (t-100) REVERT: B 646 ARG cc_start: 0.7305 (ptp-170) cc_final: 0.7020 (ptp-170) REVERT: B 847 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7819 (mm-30) REVERT: B 861 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7516 (mmmm) REVERT: B 943 ASN cc_start: 0.8099 (m-40) cc_final: 0.7819 (p0) REVERT: B 999 PHE cc_start: 0.7718 (m-80) cc_final: 0.7360 (m-80) REVERT: B 1061 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8207 (p) REVERT: B 1067 PHE cc_start: 0.8040 (t80) cc_final: 0.7828 (t80) REVERT: B 1087 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7298 (tp30) REVERT: B 1098 ILE cc_start: 0.9039 (tt) cc_final: 0.8624 (tp) REVERT: B 1104 MET cc_start: 0.7978 (mmm) cc_final: 0.7758 (tpp) REVERT: B 1117 VAL cc_start: 0.8892 (t) cc_final: 0.8682 (t) REVERT: B 1134 PHE cc_start: 0.8224 (m-80) cc_final: 0.8013 (m-10) REVERT: B 1172 HIS cc_start: 0.7359 (t-90) cc_final: 0.7095 (t-90) outliers start: 69 outliers final: 46 residues processed: 540 average time/residue: 0.1262 time to fit residues: 100.9766 Evaluate side-chains 555 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 497 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 161 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 108 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN B 917 GLN ** B 959 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 = 0.3814 r_free = 0.3814 target = 0.137521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119463 restraints weight = 24474.375| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.17 r_work: 0.3430 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 16254 Z= 0.169 Angle : 0.809 59.189 22062 Z= 0.458 Chirality : 0.044 0.666 2660 Planarity : 0.004 0.063 2752 Dihedral : 5.011 57.888 2239 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.93 % Allowed : 26.76 % Favored : 69.31 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.19), residues: 2050 helix: 2.14 (0.14), residues: 1446 sheet: 1.21 (0.65), residues: 76 loop : -1.40 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 976 TYR 0.038 0.001 TYR A1178 PHE 0.052 0.002 PHE A 999 TRP 0.014 0.001 TRP A1112 HIS 0.020 0.001 HIS A1172 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (16254) covalent geometry : angle 0.80919 / 0.46 (22062) hydrogen bonds : bond 0.04098 / 2.79 ( 1198) hydrogen bonds : angle 3.86894 / 2.76 ( 3534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4228.57 seconds wall clock time: 73 minutes 8.95 seconds (4388.95 seconds total)