Starting phenix.real_space_refine on Sat Jun 14 09:14:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xpq_38559/06_2025/8xpq_38559.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xpq_38559/06_2025/8xpq_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_38559/06_2025/8xpq_38559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xpq_38559/06_2025/8xpq_38559.map" model { file = "/net/cci-nas-00/data/ceres_data/8xpq_38559/06_2025/8xpq_38559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xpq_38559/06_2025/8xpq_38559.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 107 Restraints were copied for chains: B Time building chain proxies: 18.99, per 1000 atoms: 1.19 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: 3.69 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.60 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: 5.13 Time building geometry restraints manager: 4.35 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: 0.09 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 45.580 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (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 TRP 0.022 0.002 TRP B 962 HIS 0.007 0.001 HIS A 908 PHE 0.015 0.002 PHE A 352 TYR 0.012 0.002 TYR B 102 ARG 0.005 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.11687 ( 1198) hydrogen bonds : angle 5.86608 ( 3534) covalent geometry : bond 0.00581 (16254) covalent geometry : angle 0.79876 (22062) *********************** 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 : 2.306 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 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: 0.7643 (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: 0.7366 (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: 0.7999 (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: 0.7332 (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: 0.7500 (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: 0.6916 (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: 0.6293 (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: 0.7722 (mm) REVERT: B 841 LYS cc_start: 0.7963 (mtpm) cc_final: 0.7730 (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: 0.7955 (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: 0.7958 (mt-10) REVERT: B 993 ASP cc_start: 0.8082 (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: 0.7906 (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: 0.7481 (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: 0.7546 (t-170) REVERT: B 1188 VAL cc_start: 0.8748 (m) cc_final: 0.8521 (p) outliers start: 88 outliers final: 32 residues processed: 622 average time/residue: 0.3022 time to fit residues: 275.9129 Evaluate side-chains 519 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 482 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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 173 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3989 r_free = 0.3989 target = 0.151692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.133177 restraints weight = 25451.760| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.34 r_work: 0.3625 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16254 Z= 0.169 Angle : 0.629 6.964 22062 Z= 0.330 Chirality : 0.042 0.160 2660 Planarity : 0.005 0.049 2752 Dihedral : 6.703 58.971 2281 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.24 % Allowed : 16.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2050 helix: 0.96 (0.13), residues: 1432 sheet: 0.09 (0.58), residues: 96 loop : -2.02 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 962 HIS 0.007 0.001 HIS B1172 PHE 0.019 0.002 PHE A 972 TYR 0.012 0.001 TYR B 837 ARG 0.007 0.001 ARG B 499 Details of bonding type rmsd hydrogen bonds : bond 0.04889 ( 1198) hydrogen bonds : angle 4.40616 ( 3534) covalent geometry : bond 0.00368 (16254) covalent geometry : angle 0.62932 (22062) *********************** 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 617 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 529 time to evaluate : 1.601 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: A 124 GLU cc_start: 0.6813 (tp30) cc_final: 0.6419 (tp30) REVERT: A 149 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 154 MET cc_start: 0.7803 (tpp) cc_final: 0.7413 (tpp) REVERT: A 155 ASP cc_start: 0.7495 (t70) cc_final: 0.7273 (t70) REVERT: A 160 MET cc_start: 0.7044 (mmt) cc_final: 0.6733 (mmm) REVERT: A 186 MET cc_start: 0.7351 (mtp) cc_final: 0.7123 (mmm) REVERT: A 187 ASN cc_start: 0.7178 (m-40) cc_final: 0.6832 (m110) REVERT: A 248 PHE cc_start: 0.7967 (m-80) cc_final: 0.7340 (m-80) REVERT: A 265 VAL cc_start: 0.8081 (t) cc_final: 0.7810 (p) REVERT: A 289 PHE cc_start: 0.7761 (t80) cc_final: 0.7394 (t80) REVERT: A 316 ASP cc_start: 0.7536 (t0) cc_final: 0.7336 (m-30) REVERT: A 337 GLU cc_start: 0.7637 (mp0) cc_final: 0.7321 (mp0) REVERT: A 355 MET cc_start: 0.8190 (ttp) cc_final: 0.7872 (ttp) REVERT: A 427 TRP cc_start: 0.8202 (t-100) cc_final: 0.7664 (t-100) REVERT: A 511 MET cc_start: 0.8380 (ttt) cc_final: 0.7997 (ttp) REVERT: A 534 ASP cc_start: 0.7367 (t70) cc_final: 0.7122 (t0) REVERT: A 536 TYR cc_start: 0.7799 (m-80) cc_final: 0.7336 (m-10) REVERT: A 552 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7443 (tt) REVERT: A 578 MET cc_start: 0.7214 (mtm) cc_final: 0.6898 (mtp) REVERT: A 823 LEU cc_start: 0.8244 (mp) cc_final: 0.7919 (mm) REVERT: A 845 ILE cc_start: 0.8650 (mt) cc_final: 0.8393 (mm) REVERT: A 849 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7778 (mm-30) REVERT: A 887 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7706 (ttt90) REVERT: A 926 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7302 (mm-30) REVERT: A 971 ASP cc_start: 0.8176 (m-30) cc_final: 0.7803 (m-30) REVERT: A 987 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8584 (m) REVERT: A 993 ASP cc_start: 0.7735 (p0) cc_final: 0.7400 (p0) REVERT: A 996 ASP cc_start: 0.7548 (p0) cc_final: 0.7261 (p0) REVERT: A 999 PHE cc_start: 0.7513 (m-80) cc_final: 0.6971 (m-10) REVERT: A 1002 VAL cc_start: 0.8387 (m) cc_final: 0.8155 (p) REVERT: A 1044 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7734 (mt-10) REVERT: A 1061 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8061 (p) REVERT: A 1073 MET cc_start: 0.8536 (mmm) cc_final: 0.8098 (mmm) REVERT: A 1098 ILE cc_start: 0.8985 (tt) cc_final: 0.8663 (tt) REVERT: A 1104 MET cc_start: 0.7857 (tpp) cc_final: 0.7478 (tpp) REVERT: A 1122 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7129 (mm-30) REVERT: A 1134 PHE cc_start: 0.7943 (m-80) cc_final: 0.7733 (m-10) REVERT: A 1190 ARG cc_start: 0.7141 (ttm-80) cc_final: 0.6877 (ttm-80) REVERT: B 124 GLU cc_start: 0.6508 (tp30) cc_final: 0.6188 (tp30) REVERT: B 140 GLN cc_start: 0.8000 (mm110) cc_final: 0.7703 (mp10) REVERT: B 154 MET cc_start: 0.7959 (tpp) cc_final: 0.7466 (tpp) REVERT: B 155 ASP cc_start: 0.7412 (t70) cc_final: 0.7195 (t70) REVERT: B 160 MET cc_start: 0.6965 (mmt) cc_final: 0.6646 (mmm) REVERT: B 176 VAL cc_start: 0.7893 (p) cc_final: 0.7682 (p) REVERT: B 231 GLU cc_start: 0.7132 (tt0) cc_final: 0.6791 (mt-10) REVERT: B 265 VAL cc_start: 0.7958 (t) cc_final: 0.7709 (p) REVERT: B 319 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7957 (mt) REVERT: B 333 ILE cc_start: 0.8010 (mt) cc_final: 0.7425 (mm) REVERT: B 337 GLU cc_start: 0.7650 (mp0) cc_final: 0.7135 (mp0) REVERT: B 368 VAL cc_start: 0.8351 (t) cc_final: 0.8085 (p) REVERT: B 375 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8234 (mtmm) REVERT: B 401 MET cc_start: 0.7304 (mmp) cc_final: 0.6990 (mtp) REVERT: B 404 SER cc_start: 0.7626 (m) cc_final: 0.7420 (p) REVERT: B 534 ASP cc_start: 0.7467 (t70) cc_final: 0.7142 (t0) REVERT: B 565 MET cc_start: 0.4606 (ppp) cc_final: 0.4372 (ppp) REVERT: B 569 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8087 (mp0) REVERT: B 578 MET cc_start: 0.7338 (mtt) cc_final: 0.7059 (mtp) REVERT: B 579 MET cc_start: 0.7166 (tpt) cc_final: 0.6860 (tpt) REVERT: B 595 TRP cc_start: 0.8257 (m100) cc_final: 0.7951 (m100) REVERT: B 624 GLN cc_start: 0.7468 (pt0) cc_final: 0.7213 (pt0) REVERT: B 820 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7664 (mmmt) REVERT: B 823 LEU cc_start: 0.8256 (mp) cc_final: 0.8007 (mm) REVERT: B 832 GLN cc_start: 0.8219 (tp40) cc_final: 0.7918 (tm-30) REVERT: B 841 LYS cc_start: 0.7825 (mtpm) cc_final: 0.7602 (mtpm) REVERT: B 847 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7144 (mm-30) REVERT: B 898 THR cc_start: 0.8286 (m) cc_final: 0.8079 (p) REVERT: B 926 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7303 (mm-30) REVERT: B 971 ASP cc_start: 0.8253 (m-30) cc_final: 0.7880 (m-30) REVERT: B 973 ILE cc_start: 0.8591 (mm) cc_final: 0.8202 (tt) REVERT: B 983 ASP cc_start: 0.8115 (p0) cc_final: 0.7824 (p0) REVERT: B 987 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8652 (m) REVERT: B 991 GLU cc_start: 0.7733 (tt0) cc_final: 0.7520 (tt0) REVERT: B 994 GLU cc_start: 0.7984 (mp0) cc_final: 0.7736 (mp0) REVERT: B 996 ASP cc_start: 0.7697 (p0) cc_final: 0.7458 (p0) REVERT: B 1002 VAL cc_start: 0.8390 (m) cc_final: 0.8158 (p) REVERT: B 1037 THR cc_start: 0.7963 (t) cc_final: 0.7749 (p) REVERT: B 1051 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8440 (mtpp) REVERT: B 1094 VAL cc_start: 0.8502 (m) cc_final: 0.8229 (p) REVERT: B 1098 ILE cc_start: 0.9008 (tt) cc_final: 0.8659 (tt) REVERT: B 1104 MET cc_start: 0.7812 (tpp) cc_final: 0.7422 (mmm) REVERT: B 1105 GLU cc_start: 0.7752 (tt0) cc_final: 0.7517 (tt0) REVERT: B 1110 GLN cc_start: 0.8337 (mp10) cc_final: 0.8011 (mp10) REVERT: B 1122 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7211 (mm-30) REVERT: B 1128 ASP cc_start: 0.7143 (t0) cc_final: 0.6897 (t70) REVERT: B 1134 PHE cc_start: 0.8049 (m-80) cc_final: 0.7777 (m-10) REVERT: B 1172 HIS cc_start: 0.7493 (t-170) cc_final: 0.7095 (t-170) REVERT: B 1188 VAL cc_start: 0.8644 (m) cc_final: 0.8297 (p) outliers start: 88 outliers final: 53 residues processed: 576 average time/residue: 0.2742 time to fit residues: 233.6722 Evaluate side-chains 540 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 481 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 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 935 GLU 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 82 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 96 optimal weight: 0.0970 chunk 111 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 140 GLN A 165 GLN A 374 GLN A 600 HIS A 614 HIS A 624 GLN A 943 ASN A1137 ASN A1172 HIS A1177 GLN B 165 GLN B 614 HIS ** B 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1137 ASN B1149 ASN B1177 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.142637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124155 restraints weight = 24826.614| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.28 r_work: 0.3498 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16254 Z= 0.175 Angle : 0.597 6.703 22062 Z= 0.317 Chirality : 0.042 0.182 2660 Planarity : 0.004 0.040 2752 Dihedral : 5.795 59.171 2254 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.42 % Allowed : 18.89 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 2050 helix: 1.45 (0.14), residues: 1434 sheet: 0.54 (0.59), residues: 96 loop : -1.85 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 962 HIS 0.005 0.001 HIS B 908 PHE 0.011 0.002 PHE A 517 TYR 0.012 0.001 TYR B1035 ARG 0.007 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04743 ( 1198) hydrogen bonds : angle 4.19766 ( 3534) covalent geometry : bond 0.00376 (16254) covalent geometry : angle 0.59691 (22062) *********************** 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 635 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 544 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8390 (t) REVERT: A 124 GLU cc_start: 0.7085 (tp30) cc_final: 0.6670 (tp30) REVERT: A 140 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8111 (mp10) REVERT: A 149 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 154 MET cc_start: 0.8265 (tpp) cc_final: 0.8015 (tpp) REVERT: A 155 ASP cc_start: 0.8008 (t70) cc_final: 0.7773 (t70) REVERT: A 166 VAL cc_start: 0.7673 (t) cc_final: 0.7436 (t) REVERT: A 180 LEU cc_start: 0.8375 (tt) cc_final: 0.8162 (tp) REVERT: A 186 MET cc_start: 0.7762 (mtp) cc_final: 0.7428 (mtp) REVERT: A 187 ASN cc_start: 0.7523 (m-40) cc_final: 0.7094 (m-40) REVERT: A 206 SER cc_start: 0.8259 (t) cc_final: 0.7986 (t) REVERT: A 265 VAL cc_start: 0.8338 (t) cc_final: 0.8110 (p) REVERT: A 289 PHE cc_start: 0.8183 (t80) cc_final: 0.7877 (t80) REVERT: A 337 GLU cc_start: 0.8063 (mp0) cc_final: 0.7609 (mp0) REVERT: A 346 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7795 (mt-10) REVERT: A 355 MET cc_start: 0.8436 (ttp) cc_final: 0.8126 (ttp) REVERT: A 427 TRP cc_start: 0.8673 (t-100) cc_final: 0.7772 (t-100) REVERT: A 451 ILE cc_start: 0.8558 (tt) cc_final: 0.7963 (tt) REVERT: A 534 ASP cc_start: 0.7869 (t70) cc_final: 0.7632 (t0) REVERT: A 552 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7579 (tt) REVERT: A 588 LYS cc_start: 0.8241 (tttm) cc_final: 0.8035 (tttm) REVERT: A 599 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: A 632 LYS cc_start: 0.8090 (mtpm) cc_final: 0.7818 (mtpp) REVERT: A 823 LEU cc_start: 0.8489 (mp) cc_final: 0.8113 (mm) REVERT: A 832 GLN cc_start: 0.8536 (tp40) cc_final: 0.8306 (tm-30) REVERT: A 845 ILE cc_start: 0.8668 (mt) cc_final: 0.8442 (mm) REVERT: A 958 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8300 (ttpp) REVERT: A 971 ASP cc_start: 0.8419 (m-30) cc_final: 0.8079 (m-30) REVERT: A 987 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8741 (m) REVERT: A 991 GLU cc_start: 0.7933 (tt0) cc_final: 0.7726 (tt0) REVERT: A 993 ASP cc_start: 0.8052 (p0) cc_final: 0.7761 (p0) REVERT: A 1044 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 1061 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8259 (p) REVERT: A 1067 PHE cc_start: 0.8072 (t80) cc_final: 0.7617 (t80) REVERT: A 1073 MET cc_start: 0.8572 (mmm) cc_final: 0.8137 (mmm) REVERT: A 1094 VAL cc_start: 0.8670 (m) cc_final: 0.8393 (p) REVERT: A 1098 ILE cc_start: 0.9111 (tt) cc_final: 0.8762 (tt) REVERT: A 1122 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7559 (tp30) REVERT: A 1127 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8322 (p) REVERT: A 1134 PHE cc_start: 0.8136 (m-80) cc_final: 0.7691 (m-10) REVERT: A 1190 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.7049 (ttm-80) REVERT: A 1202 ARG cc_start: 0.7044 (ttt-90) cc_final: 0.6650 (ttt-90) REVERT: B 79 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8422 (t) REVERT: B 93 SER cc_start: 0.8238 (m) cc_final: 0.7866 (p) REVERT: B 124 GLU cc_start: 0.6912 (tp30) cc_final: 0.6602 (tm-30) REVERT: B 140 GLN cc_start: 0.8151 (mm110) cc_final: 0.7907 (mp10) REVERT: B 149 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7560 (tp30) REVERT: B 154 MET cc_start: 0.8394 (tpp) cc_final: 0.8184 (tpp) REVERT: B 155 ASP cc_start: 0.7927 (t70) cc_final: 0.7707 (t70) REVERT: B 160 MET cc_start: 0.7491 (mmt) cc_final: 0.7120 (mmm) REVERT: B 166 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7539 (t) REVERT: B 206 SER cc_start: 0.8380 (t) cc_final: 0.8110 (t) REVERT: B 231 GLU cc_start: 0.7674 (tt0) cc_final: 0.7385 (mt-10) REVERT: B 233 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7218 (tt0) REVERT: B 289 PHE cc_start: 0.8144 (t80) cc_final: 0.7840 (t80) REVERT: B 319 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8154 (mt) REVERT: B 375 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8430 (ttpp) REVERT: B 401 MET cc_start: 0.7915 (mmp) cc_final: 0.7617 (mtp) REVERT: B 404 SER cc_start: 0.8179 (m) cc_final: 0.7951 (p) REVERT: B 451 ILE cc_start: 0.8625 (tt) cc_final: 0.7956 (tt) REVERT: B 477 LEU cc_start: 0.8411 (mm) cc_final: 0.8194 (mp) REVERT: B 478 LEU cc_start: 0.8168 (mt) cc_final: 0.7947 (mt) REVERT: B 520 ASP cc_start: 0.7952 (p0) cc_final: 0.7720 (p0) REVERT: B 534 ASP cc_start: 0.7927 (t70) cc_final: 0.7652 (t0) REVERT: B 565 MET cc_start: 0.5198 (ppp) cc_final: 0.4718 (ppp) REVERT: B 595 TRP cc_start: 0.8658 (m100) cc_final: 0.8281 (m100) REVERT: B 599 GLU cc_start: 0.8032 (tp30) cc_final: 0.7828 (mm-30) REVERT: B 600 HIS cc_start: 0.8389 (m90) cc_final: 0.8158 (m-70) REVERT: B 820 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7929 (mmmt) REVERT: B 823 LEU cc_start: 0.8436 (mp) cc_final: 0.8200 (mm) REVERT: B 832 GLN cc_start: 0.8498 (tp40) cc_final: 0.8186 (tm-30) REVERT: B 884 LEU cc_start: 0.8668 (mp) cc_final: 0.8465 (mm) REVERT: B 897 LYS cc_start: 0.8564 (mmtp) cc_final: 0.8310 (mttp) REVERT: B 926 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7086 (mm-30) REVERT: B 929 LYS cc_start: 0.8271 (ttmt) cc_final: 0.8061 (ttmt) REVERT: B 971 ASP cc_start: 0.8428 (m-30) cc_final: 0.8098 (m-30) REVERT: B 972 PHE cc_start: 0.8318 (t80) cc_final: 0.8045 (t80) REVERT: B 987 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8854 (m) REVERT: B 1061 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8225 (p) REVERT: B 1067 PHE cc_start: 0.8021 (t80) cc_final: 0.7540 (t80) REVERT: B 1094 VAL cc_start: 0.8646 (m) cc_final: 0.8392 (p) REVERT: B 1098 ILE cc_start: 0.9133 (tt) cc_final: 0.8727 (tt) REVERT: B 1104 MET cc_start: 0.7989 (tpp) cc_final: 0.7610 (tpp) REVERT: B 1110 GLN cc_start: 0.8477 (mp10) cc_final: 0.8182 (mp10) REVERT: B 1117 VAL cc_start: 0.8968 (t) cc_final: 0.8644 (t) REVERT: B 1127 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8220 (m) REVERT: B 1128 ASP cc_start: 0.7501 (t0) cc_final: 0.7284 (t0) REVERT: B 1134 PHE cc_start: 0.8230 (m-80) cc_final: 0.7766 (m-10) REVERT: B 1141 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 1172 HIS cc_start: 0.7718 (t-170) cc_final: 0.7409 (t-170) REVERT: B 1214 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.6913 (mm) outliers start: 91 outliers final: 51 residues processed: 580 average time/residue: 0.3083 time to fit residues: 260.3254 Evaluate side-chains 572 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 506 time to evaluate : 1.791 ------------------------------------------------------------------------------- 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 624 GLN Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 821 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 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 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 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 166 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 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 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 140 optimal weight: 0.0670 chunk 46 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 614 HIS ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.141215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122686 restraints weight = 24668.178| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.26 r_work: 0.3480 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16254 Z= 0.141 Angle : 0.569 7.101 22062 Z= 0.300 Chirality : 0.041 0.185 2660 Planarity : 0.004 0.042 2752 Dihedral : 5.541 57.802 2248 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.48 % Allowed : 20.80 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.19), residues: 2050 helix: 1.77 (0.14), residues: 1442 sheet: 0.66 (0.58), residues: 96 loop : -1.70 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1112 HIS 0.005 0.001 HIS A 908 PHE 0.027 0.001 PHE B 248 TYR 0.011 0.001 TYR B1125 ARG 0.005 0.001 ARG A 887 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 1198) hydrogen bonds : angle 4.07899 ( 3534) covalent geometry : bond 0.00300 (16254) covalent geometry : angle 0.56853 (22062) *********************** 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 594 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 502 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8359 (t) REVERT: A 124 GLU cc_start: 0.7105 (tp30) cc_final: 0.6733 (tp30) REVERT: A 129 ASP cc_start: 0.6310 (OUTLIER) cc_final: 0.6049 (p0) REVERT: A 149 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7468 (tm-30) REVERT: A 154 MET cc_start: 0.8317 (tpp) cc_final: 0.7849 (ttm) REVERT: A 155 ASP cc_start: 0.7979 (t70) cc_final: 0.7696 (t70) REVERT: A 180 LEU cc_start: 0.8334 (tt) cc_final: 0.8023 (tp) REVERT: A 183 VAL cc_start: 0.7776 (t) cc_final: 0.7475 (p) REVERT: A 184 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7907 (tp) REVERT: A 186 MET cc_start: 0.7805 (mtp) cc_final: 0.7466 (mtp) REVERT: A 187 ASN cc_start: 0.7632 (m-40) cc_final: 0.7194 (m-40) REVERT: A 206 SER cc_start: 0.8476 (t) cc_final: 0.8207 (t) REVERT: A 289 PHE cc_start: 0.8285 (t80) cc_final: 0.8003 (t80) REVERT: A 319 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8122 (mt) REVERT: A 337 GLU cc_start: 0.8046 (mp0) cc_final: 0.7594 (mp0) REVERT: A 346 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7784 (mt-10) REVERT: A 355 MET cc_start: 0.8453 (ttp) cc_final: 0.8124 (ttp) REVERT: A 363 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 383 MET cc_start: 0.7065 (mmp) cc_final: 0.6713 (mmm) REVERT: A 427 TRP cc_start: 0.8746 (t-100) cc_final: 0.7783 (t-100) REVERT: A 534 ASP cc_start: 0.7927 (t70) cc_final: 0.7710 (t0) REVERT: A 599 GLU cc_start: 0.8145 (tp30) cc_final: 0.7707 (mp0) REVERT: A 624 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7282 (pp30) REVERT: A 632 LYS cc_start: 0.8182 (mtpm) cc_final: 0.7806 (mtpp) REVERT: A 832 GLN cc_start: 0.8601 (tp40) cc_final: 0.8263 (tt0) REVERT: A 845 ILE cc_start: 0.8735 (mt) cc_final: 0.8517 (mm) REVERT: A 958 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8254 (ttpp) REVERT: A 971 ASP cc_start: 0.8491 (m-30) cc_final: 0.8152 (m-30) REVERT: A 987 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8727 (m) REVERT: A 999 PHE cc_start: 0.7662 (m-80) cc_final: 0.7032 (m-80) REVERT: A 1044 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8067 (mt-10) REVERT: A 1060 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7431 (mm-30) REVERT: A 1061 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8300 (p) REVERT: A 1067 PHE cc_start: 0.8140 (t80) cc_final: 0.7670 (t80) REVERT: A 1073 MET cc_start: 0.8540 (mmm) cc_final: 0.8089 (mmm) REVERT: A 1094 VAL cc_start: 0.8685 (m) cc_final: 0.8379 (p) REVERT: A 1098 ILE cc_start: 0.9096 (tt) cc_final: 0.8747 (tt) REVERT: A 1127 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8440 (p) REVERT: A 1134 PHE cc_start: 0.8213 (m-80) cc_final: 0.7979 (m-80) REVERT: B 79 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8393 (t) REVERT: B 93 SER cc_start: 0.8297 (m) cc_final: 0.7907 (p) REVERT: B 107 LEU cc_start: 0.8289 (tt) cc_final: 0.8064 (tp) REVERT: B 124 GLU cc_start: 0.6920 (tp30) cc_final: 0.6603 (tm-30) REVERT: B 140 GLN cc_start: 0.8102 (mm110) cc_final: 0.7840 (mp10) REVERT: B 149 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7601 (tp30) REVERT: B 154 MET cc_start: 0.8417 (tpp) cc_final: 0.8216 (tpp) REVERT: B 160 MET cc_start: 0.7535 (mmt) cc_final: 0.7150 (mmm) REVERT: B 166 VAL cc_start: 0.7859 (t) cc_final: 0.7520 (t) REVERT: B 206 SER cc_start: 0.8542 (t) cc_final: 0.8264 (t) REVERT: B 231 GLU cc_start: 0.7777 (tt0) cc_final: 0.7481 (mt-10) REVERT: B 233 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7303 (tt0) REVERT: B 289 PHE cc_start: 0.8192 (t80) cc_final: 0.7957 (t80) REVERT: B 319 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8086 (mt) REVERT: B 401 MET cc_start: 0.7960 (mmp) cc_final: 0.7741 (mtp) REVERT: B 477 LEU cc_start: 0.8485 (mm) cc_final: 0.8277 (mp) REVERT: B 534 ASP cc_start: 0.7902 (t70) cc_final: 0.7699 (t0) REVERT: B 565 MET cc_start: 0.5126 (ppp) cc_final: 0.4631 (ppp) REVERT: B 579 MET cc_start: 0.7827 (tpt) cc_final: 0.7476 (tpt) REVERT: B 595 TRP cc_start: 0.8727 (m100) cc_final: 0.8385 (m100) REVERT: B 600 HIS cc_start: 0.8275 (m90) cc_final: 0.8026 (m-70) REVERT: B 606 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8006 (pm20) REVERT: B 818 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7498 (tp) REVERT: B 823 LEU cc_start: 0.8502 (mp) cc_final: 0.8204 (mm) REVERT: B 832 GLN cc_start: 0.8550 (tp40) cc_final: 0.8177 (tt0) REVERT: B 940 ARG cc_start: 0.8564 (tpp80) cc_final: 0.8287 (ttm-80) REVERT: B 971 ASP cc_start: 0.8447 (m-30) cc_final: 0.8117 (m-30) REVERT: B 972 PHE cc_start: 0.8279 (t80) cc_final: 0.8027 (t80) REVERT: B 987 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8878 (m) REVERT: B 1051 LYS cc_start: 0.8817 (mtpp) cc_final: 0.8575 (mtpp) REVERT: B 1061 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8232 (p) REVERT: B 1067 PHE cc_start: 0.8102 (t80) cc_final: 0.7737 (t80) REVERT: B 1072 ASP cc_start: 0.7903 (m-30) cc_final: 0.7515 (m-30) REVERT: B 1094 VAL cc_start: 0.8585 (m) cc_final: 0.8382 (p) REVERT: B 1098 ILE cc_start: 0.9111 (tt) cc_final: 0.8712 (tt) REVERT: B 1104 MET cc_start: 0.7898 (tpp) cc_final: 0.7519 (tpp) REVERT: B 1117 VAL cc_start: 0.8992 (t) cc_final: 0.8622 (t) REVERT: B 1127 VAL cc_start: 0.8555 (t) cc_final: 0.8292 (m) REVERT: B 1134 PHE cc_start: 0.8263 (m-80) cc_final: 0.7844 (m-10) REVERT: B 1141 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8264 (p) REVERT: B 1172 HIS cc_start: 0.7671 (t-90) cc_final: 0.7416 (t-170) REVERT: B 1214 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.6951 (mm) REVERT: B 1221 MET cc_start: 0.7563 (mmm) cc_final: 0.6320 (mmm) outliers start: 92 outliers final: 53 residues processed: 553 average time/residue: 0.2918 time to fit residues: 237.5493 Evaluate side-chains 558 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 487 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 129 ASP 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 319 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 603 LEU 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 821 LEU 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 1038 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 1165 CYS 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 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 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 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 961 SER Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 987 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 1114 GLN Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1165 CYS 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 99 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 172 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A 614 HIS A 624 GLN A 886 GLN A 943 ASN B 917 GLN B 955 ASN B1154 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120858 restraints weight = 24810.369| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.23 r_work: 0.3455 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16254 Z= 0.141 Angle : 0.569 7.661 22062 Z= 0.298 Chirality : 0.041 0.164 2660 Planarity : 0.004 0.035 2752 Dihedral : 5.397 57.906 2246 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 6.20 % Allowed : 21.81 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.19), residues: 2050 helix: 1.93 (0.14), residues: 1448 sheet: 0.97 (0.59), residues: 96 loop : -1.62 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 643 HIS 0.004 0.001 HIS A 908 PHE 0.020 0.001 PHE B 248 TYR 0.011 0.001 TYR B1125 ARG 0.007 0.001 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.04399 ( 1198) hydrogen bonds : angle 3.99067 ( 3534) covalent geometry : bond 0.00301 (16254) covalent geometry : angle 0.56949 (22062) *********************** 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 618 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 514 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8394 (t) REVERT: A 112 ILE cc_start: 0.8549 (mt) cc_final: 0.8231 (mm) REVERT: A 124 GLU cc_start: 0.7146 (tp30) cc_final: 0.6794 (tp30) REVERT: A 129 ASP cc_start: 0.6325 (OUTLIER) cc_final: 0.6079 (p0) REVERT: A 149 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 154 MET cc_start: 0.8342 (tpp) cc_final: 0.7944 (ttm) REVERT: A 160 MET cc_start: 0.8095 (mmt) cc_final: 0.7732 (mmm) REVERT: A 184 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7957 (tp) REVERT: A 187 ASN cc_start: 0.7765 (m-40) cc_final: 0.7388 (m-40) REVERT: A 206 SER cc_start: 0.8576 (t) cc_final: 0.7977 (t) REVERT: A 233 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7462 (tm-30) REVERT: A 289 PHE cc_start: 0.8339 (t80) cc_final: 0.8089 (t80) REVERT: A 319 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8070 (mt) REVERT: A 337 GLU cc_start: 0.8056 (mp0) cc_final: 0.7580 (mp0) REVERT: A 346 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7752 (mt-10) REVERT: A 355 MET cc_start: 0.8455 (ttp) cc_final: 0.8118 (ttp) REVERT: A 383 MET cc_start: 0.7163 (mmp) cc_final: 0.6768 (mmm) REVERT: A 398 ILE cc_start: 0.8641 (mt) cc_final: 0.8430 (mt) REVERT: A 427 TRP cc_start: 0.8848 (t-100) cc_final: 0.7732 (t-100) REVERT: A 522 ASP cc_start: 0.8160 (m-30) cc_final: 0.7936 (t0) REVERT: A 552 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7705 (tt) REVERT: A 599 GLU cc_start: 0.8159 (tp30) cc_final: 0.7718 (mp0) REVERT: A 622 LYS cc_start: 0.8782 (tppt) cc_final: 0.8456 (tppt) REVERT: A 632 LYS cc_start: 0.8321 (mtpm) cc_final: 0.8107 (mtpp) REVERT: A 845 ILE cc_start: 0.8799 (mt) cc_final: 0.8582 (mm) REVERT: A 881 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8132 (tp30) REVERT: A 958 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8196 (ttpp) REVERT: A 971 ASP cc_start: 0.8547 (m-30) cc_final: 0.8204 (m-30) REVERT: A 987 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8741 (m) REVERT: A 999 PHE cc_start: 0.7601 (m-80) cc_final: 0.7006 (m-80) REVERT: A 1044 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8133 (mt-10) REVERT: A 1060 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 1061 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8309 (p) REVERT: A 1067 PHE cc_start: 0.8116 (t80) cc_final: 0.7641 (t80) REVERT: A 1073 MET cc_start: 0.8524 (mmm) cc_final: 0.8083 (mmm) REVERT: A 1098 ILE cc_start: 0.9094 (tt) cc_final: 0.8839 (tt) REVERT: A 1104 MET cc_start: 0.8096 (tpt) cc_final: 0.7799 (mmm) REVERT: A 1115 GLU cc_start: 0.8108 (tt0) cc_final: 0.7844 (tp30) REVERT: A 1122 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7665 (mm-30) REVERT: A 1134 PHE cc_start: 0.8210 (m-80) cc_final: 0.7861 (m-10) REVERT: A 1170 THR cc_start: 0.8845 (p) cc_final: 0.8583 (t) REVERT: A 1190 ARG cc_start: 0.7310 (ttm-80) cc_final: 0.7091 (mtt-85) REVERT: A 1202 ARG cc_start: 0.6901 (ttt-90) cc_final: 0.6570 (ttt-90) REVERT: B 79 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8400 (t) REVERT: B 140 GLN cc_start: 0.8094 (mm110) cc_final: 0.7823 (mp10) REVERT: B 149 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7613 (tp30) REVERT: B 154 MET cc_start: 0.8342 (tpp) cc_final: 0.7931 (ttm) REVERT: B 155 ASP cc_start: 0.8135 (p0) cc_final: 0.7841 (p0) REVERT: B 160 MET cc_start: 0.7629 (mmt) cc_final: 0.7272 (mmm) REVERT: B 206 SER cc_start: 0.8703 (t) cc_final: 0.8463 (t) REVERT: B 233 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7399 (tm-30) REVERT: B 289 PHE cc_start: 0.8256 (t80) cc_final: 0.7958 (t80) REVERT: B 319 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8100 (mt) REVERT: B 387 TYR cc_start: 0.8163 (m-10) cc_final: 0.7779 (m-10) REVERT: B 579 MET cc_start: 0.7901 (tpt) cc_final: 0.7574 (tpt) REVERT: B 595 TRP cc_start: 0.8729 (m100) cc_final: 0.8275 (m100) REVERT: B 606 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: B 643 TRP cc_start: 0.6288 (t-100) cc_final: 0.6081 (t-100) REVERT: B 646 ARG cc_start: 0.6772 (ptp-170) cc_final: 0.6470 (ptp-170) REVERT: B 818 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7681 (tp) REVERT: B 823 LEU cc_start: 0.8550 (mp) cc_final: 0.8210 (mm) REVERT: B 832 GLN cc_start: 0.8572 (tp40) cc_final: 0.8235 (tt0) REVERT: B 940 ARG cc_start: 0.8564 (tpp80) cc_final: 0.8298 (ttm-80) REVERT: B 958 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8499 (ttpp) REVERT: B 971 ASP cc_start: 0.8413 (m-30) cc_final: 0.8116 (m-30) REVERT: B 976 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7395 (ttm170) REVERT: B 987 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8888 (m) REVERT: B 1051 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8547 (mtpp) REVERT: B 1060 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7738 (mm-30) REVERT: B 1061 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8302 (p) REVERT: B 1067 PHE cc_start: 0.8164 (t80) cc_final: 0.7820 (t80) REVERT: B 1072 ASP cc_start: 0.7849 (m-30) cc_final: 0.7120 (m-30) REVERT: B 1094 VAL cc_start: 0.8574 (m) cc_final: 0.8352 (p) REVERT: B 1098 ILE cc_start: 0.9123 (tt) cc_final: 0.8707 (tt) REVERT: B 1117 VAL cc_start: 0.8948 (t) cc_final: 0.8725 (t) REVERT: B 1131 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7216 (tp30) REVERT: B 1134 PHE cc_start: 0.8268 (m-80) cc_final: 0.7834 (m-80) REVERT: B 1141 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8335 (p) REVERT: B 1214 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.6937 (mm) REVERT: B 1221 MET cc_start: 0.7557 (mmm) cc_final: 0.6385 (mmm) outliers start: 104 outliers final: 58 residues processed: 568 average time/residue: 0.2987 time to fit residues: 248.2425 Evaluate side-chains 562 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 488 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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 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 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 418 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 477 LEU 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 603 LEU Chi-restraints excluded: chain A residue 610 LEU 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 1038 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 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 156 VAL 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 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 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 849 GLU Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 917 GLN 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 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 1114 GLN Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1149 ASN Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1189 VAL 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 7 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN B 600 HIS B 614 HIS B1114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.137293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118885 restraints weight = 24449.025| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.18 r_work: 0.3421 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16254 Z= 0.154 Angle : 0.583 8.371 22062 Z= 0.304 Chirality : 0.041 0.150 2660 Planarity : 0.004 0.035 2752 Dihedral : 5.362 58.501 2244 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 6.26 % Allowed : 22.41 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.19), residues: 2050 helix: 1.99 (0.14), residues: 1438 sheet: 0.90 (0.59), residues: 96 loop : -1.60 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 643 HIS 0.005 0.001 HIS A 908 PHE 0.020 0.001 PHE B 248 TYR 0.010 0.001 TYR B1125 ARG 0.008 0.001 ARG B 605 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 1198) hydrogen bonds : angle 3.98631 ( 3534) covalent geometry : bond 0.00333 (16254) covalent geometry : angle 0.58340 (22062) *********************** 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 605 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 500 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8433 (t) REVERT: A 112 ILE cc_start: 0.8546 (mt) cc_final: 0.8208 (mm) REVERT: A 124 GLU cc_start: 0.7146 (tp30) cc_final: 0.6826 (tm-30) REVERT: A 129 ASP cc_start: 0.6306 (OUTLIER) cc_final: 0.6024 (p0) REVERT: A 149 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7423 (tm-30) REVERT: A 154 MET cc_start: 0.8305 (tpp) cc_final: 0.8024 (tpp) REVERT: A 155 ASP cc_start: 0.7907 (p0) cc_final: 0.7495 (p0) REVERT: A 160 MET cc_start: 0.8145 (mmt) cc_final: 0.7824 (mmm) REVERT: A 180 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8147 (mt) REVERT: A 184 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7899 (tp) REVERT: A 186 MET cc_start: 0.7873 (mtp) cc_final: 0.7565 (mtp) REVERT: A 191 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: A 199 MET cc_start: 0.8267 (mmm) cc_final: 0.7332 (tpp) REVERT: A 233 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7572 (tm-30) REVERT: A 289 PHE cc_start: 0.8367 (t80) cc_final: 0.8136 (t80) REVERT: A 319 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8101 (mt) REVERT: A 337 GLU cc_start: 0.8053 (mp0) cc_final: 0.7601 (mp0) REVERT: A 346 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 355 MET cc_start: 0.8441 (ttp) cc_final: 0.8098 (ttp) REVERT: A 363 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8354 (mt) REVERT: A 377 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 383 MET cc_start: 0.7200 (mmp) cc_final: 0.5903 (mmm) REVERT: A 387 TYR cc_start: 0.8134 (m-10) cc_final: 0.7549 (m-10) REVERT: A 398 ILE cc_start: 0.8632 (mt) cc_final: 0.8344 (mt) REVERT: A 522 ASP cc_start: 0.8167 (m-30) cc_final: 0.7962 (t0) REVERT: A 552 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7715 (tt) REVERT: A 574 GLU cc_start: 0.6852 (pt0) cc_final: 0.6645 (pt0) REVERT: A 580 GLU cc_start: 0.7435 (tp30) cc_final: 0.7111 (tp30) REVERT: A 599 GLU cc_start: 0.8177 (tp30) cc_final: 0.7719 (mp0) REVERT: A 622 LYS cc_start: 0.8758 (tppt) cc_final: 0.8523 (tppt) REVERT: A 632 LYS cc_start: 0.8490 (mtpm) cc_final: 0.8246 (mtpp) REVERT: A 881 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8125 (tp30) REVERT: A 958 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8265 (ttpp) REVERT: A 971 ASP cc_start: 0.8440 (m-30) cc_final: 0.8107 (m-30) REVERT: A 976 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7725 (mtm-85) REVERT: A 983 ASP cc_start: 0.8136 (p0) cc_final: 0.7811 (p0) REVERT: A 986 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7765 (mt-10) REVERT: A 987 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8863 (m) REVERT: A 999 PHE cc_start: 0.7543 (m-80) cc_final: 0.7017 (m-80) REVERT: A 1044 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8159 (mt-10) REVERT: A 1060 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7507 (mm-30) REVERT: A 1061 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8347 (p) REVERT: A 1067 PHE cc_start: 0.8158 (t80) cc_final: 0.7803 (t80) REVERT: A 1087 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7358 (mm-30) REVERT: A 1098 ILE cc_start: 0.9074 (tt) cc_final: 0.8823 (tt) REVERT: A 1104 MET cc_start: 0.8106 (tpt) cc_final: 0.7810 (mmm) REVERT: A 1115 GLU cc_start: 0.8152 (tt0) cc_final: 0.7899 (tp30) REVERT: A 1122 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 1134 PHE cc_start: 0.8262 (m-80) cc_final: 0.7896 (m-80) REVERT: A 1190 ARG cc_start: 0.7467 (ttm-80) cc_final: 0.7093 (mtt-85) REVERT: A 1202 ARG cc_start: 0.6892 (ttt-90) cc_final: 0.6592 (ttt-90) REVERT: B 79 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8357 (p) REVERT: B 124 GLU cc_start: 0.7355 (tp30) cc_final: 0.7098 (tp30) REVERT: B 149 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7628 (tp30) REVERT: B 154 MET cc_start: 0.8355 (tpp) cc_final: 0.7926 (ttm) REVERT: B 155 ASP cc_start: 0.8086 (p0) cc_final: 0.7785 (p0) REVERT: B 160 MET cc_start: 0.7707 (mmt) cc_final: 0.7371 (mmm) REVERT: B 231 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: B 233 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7386 (tm-30) REVERT: B 289 PHE cc_start: 0.8345 (t80) cc_final: 0.8115 (t80) REVERT: B 319 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8087 (mt) REVERT: B 387 TYR cc_start: 0.8246 (m-10) cc_final: 0.7690 (m-10) REVERT: B 588 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8025 (ttpm) REVERT: B 595 TRP cc_start: 0.8769 (m100) cc_final: 0.8359 (m100) REVERT: B 606 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: B 643 TRP cc_start: 0.6510 (t-100) cc_final: 0.6267 (t-100) REVERT: B 646 ARG cc_start: 0.6919 (ptp-170) cc_final: 0.6587 (ptp-170) REVERT: B 832 GLN cc_start: 0.8592 (tp40) cc_final: 0.8305 (tt0) REVERT: B 958 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8444 (ttpp) REVERT: B 967 MET cc_start: 0.8253 (mmp) cc_final: 0.7866 (mmp) REVERT: B 971 ASP cc_start: 0.8336 (m-30) cc_final: 0.8050 (m-30) REVERT: B 972 PHE cc_start: 0.8315 (t80) cc_final: 0.8095 (t80) REVERT: B 976 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7618 (ttm170) REVERT: B 1060 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 1061 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8234 (p) REVERT: B 1067 PHE cc_start: 0.8140 (t80) cc_final: 0.7793 (t80) REVERT: B 1072 ASP cc_start: 0.7888 (m-30) cc_final: 0.7515 (m-30) REVERT: B 1087 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7338 (tp30) REVERT: B 1094 VAL cc_start: 0.8589 (m) cc_final: 0.8348 (p) REVERT: B 1098 ILE cc_start: 0.9130 (tt) cc_final: 0.8710 (tt) REVERT: B 1104 MET cc_start: 0.7954 (tpp) cc_final: 0.7693 (tpp) REVERT: B 1117 VAL cc_start: 0.8931 (t) cc_final: 0.8620 (t) REVERT: B 1134 PHE cc_start: 0.8316 (m-80) cc_final: 0.7895 (m-80) REVERT: B 1141 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8242 (p) REVERT: B 1214 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6837 (mm) REVERT: B 1220 ASN cc_start: 0.7916 (m-40) cc_final: 0.7680 (m-40) REVERT: B 1221 MET cc_start: 0.7659 (mmm) cc_final: 0.6553 (mmm) outliers start: 105 outliers final: 67 residues processed: 549 average time/residue: 0.4098 time to fit residues: 334.1477 Evaluate side-chains 571 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 484 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 175 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 298 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 477 LEU 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 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 855 ASP Chi-restraints excluded: chain A residue 917 GLN 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 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 1127 VAL Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1175 THR 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 133 MET Chi-restraints excluded: chain B residue 156 VAL 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 372 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 483 MET 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 647 LYS Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 884 LEU 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 1061 THR Chi-restraints excluded: chain B residue 1066 TYR 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 1142 LEU Chi-restraints excluded: chain B residue 1147 LEU Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1189 VAL 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 175 optimal weight: 0.6980 chunk 170 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 205 optimal weight: 30.0000 chunk 79 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 ASN B 943 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118363 restraints weight = 24693.583| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.19 r_work: 0.3414 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16254 Z= 0.151 Angle : 0.593 10.524 22062 Z= 0.306 Chirality : 0.041 0.160 2660 Planarity : 0.004 0.032 2752 Dihedral : 5.337 59.094 2243 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 6.38 % Allowed : 22.71 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.19), residues: 2050 helix: 1.99 (0.14), residues: 1446 sheet: 0.92 (0.59), residues: 96 loop : -1.58 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 643 HIS 0.004 0.001 HIS A 908 PHE 0.021 0.001 PHE B 253 TYR 0.010 0.001 TYR B1125 ARG 0.008 0.000 ARG B 605 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 1198) hydrogen bonds : angle 3.97183 ( 3534) covalent geometry : bond 0.00321 (16254) covalent geometry : angle 0.59337 (22062) *********************** 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 604 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 497 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8428 (t) REVERT: A 112 ILE cc_start: 0.8497 (mt) cc_final: 0.8166 (mm) REVERT: A 124 GLU cc_start: 0.7174 (tp30) cc_final: 0.6849 (tm-30) REVERT: A 129 ASP cc_start: 0.6295 (OUTLIER) cc_final: 0.6014 (p0) REVERT: A 149 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7455 (tm-30) REVERT: A 154 MET cc_start: 0.8352 (tpp) cc_final: 0.7997 (ttm) REVERT: A 160 MET cc_start: 0.8231 (mmt) cc_final: 0.7895 (mmm) REVERT: A 180 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8149 (mt) REVERT: A 184 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7951 (tp) REVERT: A 186 MET cc_start: 0.7836 (mtp) cc_final: 0.7567 (mtt) REVERT: A 191 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: A 217 LEU cc_start: 0.8503 (mt) cc_final: 0.8237 (mm) REVERT: A 233 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 289 PHE cc_start: 0.8369 (t80) cc_final: 0.8137 (t80) REVERT: A 319 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7943 (mp) REVERT: A 337 GLU cc_start: 0.8046 (mp0) cc_final: 0.7585 (mp0) REVERT: A 346 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7737 (mt-10) REVERT: A 355 MET cc_start: 0.8412 (ttp) cc_final: 0.8066 (ttp) REVERT: A 363 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8353 (mt) REVERT: A 372 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8540 (p) REVERT: A 377 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8477 (mp) REVERT: A 383 MET cc_start: 0.7244 (mmp) cc_final: 0.5936 (mmm) REVERT: A 387 TYR cc_start: 0.8224 (m-10) cc_final: 0.7573 (m-10) REVERT: A 398 ILE cc_start: 0.8674 (mt) cc_final: 0.8385 (mt) REVERT: A 484 SER cc_start: 0.8695 (p) cc_final: 0.8392 (t) REVERT: A 522 ASP cc_start: 0.8201 (m-30) cc_final: 0.7993 (t0) REVERT: A 552 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7714 (tt) REVERT: A 580 GLU cc_start: 0.7516 (tp30) cc_final: 0.7186 (tp30) REVERT: A 588 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7937 (tttt) REVERT: A 599 GLU cc_start: 0.8199 (tp30) cc_final: 0.7742 (mp0) REVERT: A 622 LYS cc_start: 0.8714 (tppt) cc_final: 0.8429 (tppt) REVERT: A 630 ASP cc_start: 0.7393 (p0) cc_final: 0.7085 (p0) REVERT: A 632 LYS cc_start: 0.8541 (mtpm) cc_final: 0.8257 (mtpp) REVERT: A 881 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8058 (tp30) REVERT: A 986 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7854 (mt-10) REVERT: A 987 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8883 (m) REVERT: A 999 PHE cc_start: 0.7526 (m-80) cc_final: 0.6983 (m-80) REVERT: A 1044 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8165 (mt-10) REVERT: A 1060 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 1061 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8339 (p) REVERT: A 1067 PHE cc_start: 0.8176 (t80) cc_final: 0.7730 (t80) REVERT: A 1087 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 1098 ILE cc_start: 0.9049 (tt) cc_final: 0.8800 (tt) REVERT: A 1104 MET cc_start: 0.8091 (tpt) cc_final: 0.7807 (mmm) REVERT: A 1115 GLU cc_start: 0.8136 (tt0) cc_final: 0.7899 (tp30) REVERT: A 1122 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7643 (mm-30) REVERT: A 1134 PHE cc_start: 0.8249 (m-80) cc_final: 0.7891 (m-80) REVERT: A 1202 ARG cc_start: 0.6874 (ttt-90) cc_final: 0.6583 (ttt-90) REVERT: B 79 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8357 (p) REVERT: B 93 SER cc_start: 0.8336 (m) cc_final: 0.7952 (p) REVERT: B 124 GLU cc_start: 0.7356 (tp30) cc_final: 0.7091 (tp30) REVERT: B 133 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7554 (mtm) REVERT: B 149 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7668 (tp30) REVERT: B 154 MET cc_start: 0.8358 (tpp) cc_final: 0.7952 (ttm) REVERT: B 155 ASP cc_start: 0.8101 (p0) cc_final: 0.7831 (p0) REVERT: B 160 MET cc_start: 0.7931 (mmt) cc_final: 0.7599 (mmm) REVERT: B 179 VAL cc_start: 0.8331 (t) cc_final: 0.8116 (t) REVERT: B 197 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7584 (mt-10) REVERT: B 231 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: B 233 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7652 (tt0) REVERT: B 253 PHE cc_start: 0.8169 (m-10) cc_final: 0.7860 (m-80) REVERT: B 289 PHE cc_start: 0.8387 (t80) cc_final: 0.8160 (t80) REVERT: B 319 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7780 (mt) REVERT: B 387 TYR cc_start: 0.8297 (m-10) cc_final: 0.7704 (m-10) REVERT: B 484 SER cc_start: 0.8692 (p) cc_final: 0.8448 (t) REVERT: B 588 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8022 (ttpm) REVERT: B 595 TRP cc_start: 0.8781 (m100) cc_final: 0.8390 (m100) REVERT: B 643 TRP cc_start: 0.6697 (t-100) cc_final: 0.6416 (t-100) REVERT: B 646 ARG cc_start: 0.7036 (ptp-170) cc_final: 0.6735 (ptp-170) REVERT: B 832 GLN cc_start: 0.8531 (tp40) cc_final: 0.8331 (tt0) REVERT: B 958 LYS cc_start: 0.8680 (ttpp) cc_final: 0.8466 (ttpp) REVERT: B 967 MET cc_start: 0.8104 (mmp) cc_final: 0.7731 (mmp) REVERT: B 971 ASP cc_start: 0.8325 (m-30) cc_final: 0.7996 (m-30) REVERT: B 976 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7461 (ttm-80) REVERT: B 1060 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7764 (mm-30) REVERT: B 1061 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8221 (p) REVERT: B 1067 PHE cc_start: 0.8207 (t80) cc_final: 0.7878 (t80) REVERT: B 1072 ASP cc_start: 0.7881 (m-30) cc_final: 0.7181 (m-30) REVERT: B 1087 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7296 (tp30) REVERT: B 1094 VAL cc_start: 0.8663 (m) cc_final: 0.8435 (p) REVERT: B 1098 ILE cc_start: 0.9133 (tt) cc_final: 0.8715 (tp) REVERT: B 1117 VAL cc_start: 0.8913 (t) cc_final: 0.8589 (t) REVERT: B 1122 GLU cc_start: 0.8117 (tp30) cc_final: 0.7910 (tp30) REVERT: B 1131 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7366 (tm-30) REVERT: B 1141 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8247 (p) REVERT: B 1172 HIS cc_start: 0.7566 (t-170) cc_final: 0.7310 (t-170) REVERT: B 1214 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.6837 (mm) REVERT: B 1220 ASN cc_start: 0.7945 (m-40) cc_final: 0.7728 (m-40) REVERT: B 1221 MET cc_start: 0.7701 (mmm) cc_final: 0.6630 (mmm) outliers start: 107 outliers final: 68 residues processed: 539 average time/residue: 0.2880 time to fit residues: 226.8810 Evaluate side-chains 584 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 495 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 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 298 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 503 GLU 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 606 GLU 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 822 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 961 SER 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 1127 VAL 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 156 VAL 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 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 450 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 483 MET 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 559 CYS 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 855 ASP Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 884 LEU 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 1147 LEU Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1189 VAL 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 194 optimal weight: 0.0010 chunk 65 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 917 GLN ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118621 restraints weight = 24445.479| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.16 r_work: 0.3421 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5950 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= 0.133 Angle : 0.599 11.140 22062 Z= 0.307 Chirality : 0.041 0.182 2660 Planarity : 0.004 0.036 2752 Dihedral : 5.295 59.876 2243 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.54 % Allowed : 23.66 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 2050 helix: 2.10 (0.14), residues: 1440 sheet: 0.91 (0.59), residues: 96 loop : -1.56 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 643 HIS 0.004 0.001 HIS A 908 PHE 0.024 0.001 PHE B 972 TYR 0.013 0.001 TYR B1178 ARG 0.007 0.000 ARG B 605 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 1198) hydrogen bonds : angle 3.91684 ( 3534) covalent geometry : bond 0.00280 (16254) covalent geometry : angle 0.59856 (22062) *********************** 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 597 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 504 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8350 (p) REVERT: A 112 ILE cc_start: 0.8440 (mt) cc_final: 0.8105 (mm) REVERT: A 124 GLU cc_start: 0.7130 (tp30) cc_final: 0.6793 (tp30) REVERT: A 129 ASP cc_start: 0.6194 (OUTLIER) cc_final: 0.5952 (p0) REVERT: A 133 MET cc_start: 0.8146 (ttm) cc_final: 0.7344 (mtm) REVERT: A 137 VAL cc_start: 0.8108 (p) cc_final: 0.7837 (m) REVERT: A 149 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7436 (tm-30) REVERT: A 154 MET cc_start: 0.8329 (tpp) cc_final: 0.7981 (ttm) REVERT: A 160 MET cc_start: 0.8262 (mmt) cc_final: 0.7958 (mmm) REVERT: A 184 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7886 (tp) REVERT: A 186 MET cc_start: 0.7855 (mtp) cc_final: 0.7598 (mtt) REVERT: A 191 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: A 217 LEU cc_start: 0.8532 (mt) cc_final: 0.8273 (mm) REVERT: A 233 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7400 (tm-30) REVERT: A 249 MET cc_start: 0.8335 (ttm) cc_final: 0.8123 (ttp) REVERT: A 266 LEU cc_start: 0.8141 (tp) cc_final: 0.7849 (tp) REVERT: A 289 PHE cc_start: 0.8393 (t80) cc_final: 0.8124 (t80) REVERT: A 319 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7808 (mt) REVERT: A 337 GLU cc_start: 0.8062 (mp0) cc_final: 0.7611 (mp0) REVERT: A 355 MET cc_start: 0.8436 (ttp) cc_final: 0.8081 (ttp) REVERT: A 363 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8392 (mt) REVERT: A 372 VAL cc_start: 0.8793 (p) cc_final: 0.8521 (p) REVERT: A 377 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8478 (mp) REVERT: A 383 MET cc_start: 0.7160 (mmp) cc_final: 0.5995 (mmm) REVERT: A 387 TYR cc_start: 0.8183 (m-10) cc_final: 0.7410 (m-10) REVERT: A 398 ILE cc_start: 0.8675 (mt) cc_final: 0.8375 (mt) REVERT: A 427 TRP cc_start: 0.8846 (t-100) cc_final: 0.8415 (t-100) REVERT: A 484 SER cc_start: 0.8696 (p) cc_final: 0.8432 (t) REVERT: A 522 ASP cc_start: 0.8156 (m-30) cc_final: 0.7933 (t0) REVERT: A 552 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7755 (tt) REVERT: A 580 GLU cc_start: 0.7564 (tp30) cc_final: 0.7230 (tp30) REVERT: A 588 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8023 (tttm) REVERT: A 599 GLU cc_start: 0.8127 (tp30) cc_final: 0.7619 (mp0) REVERT: A 622 LYS cc_start: 0.8661 (tppt) cc_final: 0.8376 (tppt) REVERT: A 630 ASP cc_start: 0.7419 (p0) cc_final: 0.7111 (p0) REVERT: A 632 LYS cc_start: 0.8539 (mtpm) cc_final: 0.8249 (mtpp) REVERT: A 646 ARG cc_start: 0.6794 (ptp90) cc_final: 0.6589 (ptp90) REVERT: A 881 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8067 (tp30) REVERT: A 957 LEU cc_start: 0.8699 (tp) cc_final: 0.8303 (mp) REVERT: A 987 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8852 (m) REVERT: A 999 PHE cc_start: 0.7486 (m-80) cc_final: 0.6992 (m-80) REVERT: A 1060 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7445 (mm-30) REVERT: A 1061 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 1067 PHE cc_start: 0.8269 (t80) cc_final: 0.7866 (t80) REVERT: A 1087 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 1098 ILE cc_start: 0.9067 (tt) cc_final: 0.8827 (tt) REVERT: A 1104 MET cc_start: 0.8062 (tpt) cc_final: 0.7799 (mmm) REVERT: A 1115 GLU cc_start: 0.8150 (tt0) cc_final: 0.7913 (tp30) REVERT: A 1122 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7579 (mm-30) REVERT: A 1134 PHE cc_start: 0.8287 (m-80) cc_final: 0.7929 (m-80) REVERT: A 1190 ARG cc_start: 0.7342 (ttm-80) cc_final: 0.7016 (mtt-85) REVERT: A 1202 ARG cc_start: 0.6778 (ttt-90) cc_final: 0.6505 (ttt-90) REVERT: B 79 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8331 (p) REVERT: B 93 SER cc_start: 0.8188 (m) cc_final: 0.7809 (p) REVERT: B 124 GLU cc_start: 0.7311 (tp30) cc_final: 0.7031 (tp30) REVERT: B 133 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7613 (mtm) REVERT: B 154 MET cc_start: 0.8338 (tpp) cc_final: 0.7923 (ttm) REVERT: B 155 ASP cc_start: 0.8132 (p0) cc_final: 0.7847 (p0) REVERT: B 160 MET cc_start: 0.7949 (mmt) cc_final: 0.7673 (mmm) REVERT: B 231 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: B 233 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7434 (tm-30) REVERT: B 253 PHE cc_start: 0.8125 (m-10) cc_final: 0.7810 (m-80) REVERT: B 289 PHE cc_start: 0.8378 (t80) cc_final: 0.8107 (t80) REVERT: B 319 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7824 (mt) REVERT: B 386 PHE cc_start: 0.8330 (t80) cc_final: 0.8124 (t80) REVERT: B 387 TYR cc_start: 0.8256 (m-10) cc_final: 0.7644 (m-10) REVERT: B 484 SER cc_start: 0.8672 (p) cc_final: 0.8420 (t) REVERT: B 588 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7974 (ttpm) REVERT: B 595 TRP cc_start: 0.8795 (m100) cc_final: 0.8402 (m100) REVERT: B 643 TRP cc_start: 0.6738 (t-100) cc_final: 0.6439 (t-100) REVERT: B 646 ARG cc_start: 0.7097 (ptp-170) cc_final: 0.6823 (ptp-170) REVERT: B 847 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 871 SER cc_start: 0.8358 (p) cc_final: 0.8046 (t) REVERT: B 958 LYS cc_start: 0.8667 (ttpp) cc_final: 0.8457 (ttpp) REVERT: B 967 MET cc_start: 0.8107 (mmp) cc_final: 0.7762 (mmp) REVERT: B 971 ASP cc_start: 0.8201 (m-30) cc_final: 0.7873 (m-30) REVERT: B 976 ARG cc_start: 0.7927 (mtt90) cc_final: 0.7618 (ttm170) REVERT: B 986 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7724 (mt-10) REVERT: B 999 PHE cc_start: 0.7650 (m-80) cc_final: 0.7147 (m-80) REVERT: B 1060 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7849 (mm-30) REVERT: B 1061 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8209 (p) REVERT: B 1067 PHE cc_start: 0.8204 (t80) cc_final: 0.7761 (t80) REVERT: B 1072 ASP cc_start: 0.7816 (m-30) cc_final: 0.7397 (m-30) REVERT: B 1094 VAL cc_start: 0.8652 (m) cc_final: 0.8441 (p) REVERT: B 1098 ILE cc_start: 0.9095 (tt) cc_final: 0.8661 (tp) REVERT: B 1104 MET cc_start: 0.7779 (tpp) cc_final: 0.7485 (mmm) REVERT: B 1122 GLU cc_start: 0.8074 (tp30) cc_final: 0.7567 (mm-30) REVERT: B 1134 PHE cc_start: 0.8194 (m-80) cc_final: 0.7986 (m-80) REVERT: B 1141 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8248 (p) REVERT: B 1214 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6798 (mm) REVERT: B 1221 MET cc_start: 0.7681 (mmm) cc_final: 0.6646 (mmm) outliers start: 93 outliers final: 59 residues processed: 538 average time/residue: 0.3115 time to fit residues: 247.2199 Evaluate side-chains 568 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 490 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 270 GLN 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 363 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 477 LEU 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 588 LYS Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 850 VAL 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 1127 VAL 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 184 LEU 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 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 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 862 LYS Chi-restraints excluded: chain B residue 884 LEU 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 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 1147 LEU Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1161 ILE 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 148 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 0.0270 chunk 191 optimal weight: 3.9990 chunk 168 optimal weight: 0.4980 chunk 193 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.136803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118572 restraints weight = 24552.289| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.16 r_work: 0.3421 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16254 Z= 0.139 Angle : 0.614 10.712 22062 Z= 0.314 Chirality : 0.041 0.213 2660 Planarity : 0.004 0.030 2752 Dihedral : 5.184 59.559 2241 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.54 % Allowed : 24.37 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.19), residues: 2050 helix: 2.11 (0.14), residues: 1440 sheet: 0.94 (0.59), residues: 96 loop : -1.53 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.005 0.001 HIS B1120 PHE 0.026 0.001 PHE A 972 TYR 0.013 0.001 TYR B 280 ARG 0.007 0.000 ARG B 605 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 1198) hydrogen bonds : angle 3.90022 ( 3534) covalent geometry : bond 0.00296 (16254) covalent geometry : angle 0.61407 (22062) *********************** 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 587 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 494 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8342 (p) REVERT: A 112 ILE cc_start: 0.8421 (mt) cc_final: 0.8087 (mm) REVERT: A 124 GLU cc_start: 0.7150 (tp30) cc_final: 0.6818 (tm-30) REVERT: A 129 ASP cc_start: 0.6190 (OUTLIER) cc_final: 0.5928 (p0) REVERT: A 137 VAL cc_start: 0.8113 (p) cc_final: 0.7883 (m) REVERT: A 149 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7609 (tp30) REVERT: A 154 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7928 (ttm) REVERT: A 155 ASP cc_start: 0.8034 (p0) cc_final: 0.7658 (p0) REVERT: A 160 MET cc_start: 0.8295 (mmt) cc_final: 0.7941 (mmm) REVERT: A 184 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7919 (tp) REVERT: A 186 MET cc_start: 0.7897 (mtp) cc_final: 0.7638 (mtt) REVERT: A 217 LEU cc_start: 0.8560 (mt) cc_final: 0.8299 (mm) REVERT: A 233 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 249 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8107 (ttp) REVERT: A 266 LEU cc_start: 0.8169 (tp) cc_final: 0.7881 (tp) REVERT: A 289 PHE cc_start: 0.8387 (t80) cc_final: 0.8120 (t80) REVERT: A 319 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7715 (mt) REVERT: A 337 GLU cc_start: 0.8002 (mp0) cc_final: 0.7586 (mp0) REVERT: A 355 MET cc_start: 0.8433 (ttp) cc_final: 0.8087 (ttp) REVERT: A 363 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8398 (mt) REVERT: A 372 VAL cc_start: 0.8825 (p) cc_final: 0.8559 (p) REVERT: A 377 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8474 (mp) REVERT: A 383 MET cc_start: 0.7168 (mmp) cc_final: 0.6004 (mmm) REVERT: A 387 TYR cc_start: 0.8197 (m-10) cc_final: 0.7389 (m-10) REVERT: A 398 ILE cc_start: 0.8682 (mt) cc_final: 0.8380 (mt) REVERT: A 427 TRP cc_start: 0.8851 (t-100) cc_final: 0.8385 (t-100) REVERT: A 484 SER cc_start: 0.8744 (p) cc_final: 0.8458 (t) REVERT: A 522 ASP cc_start: 0.8155 (m-30) cc_final: 0.7951 (t0) REVERT: A 580 GLU cc_start: 0.7577 (tp30) cc_final: 0.7281 (tp30) REVERT: A 588 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8063 (tttm) REVERT: A 622 LYS cc_start: 0.8628 (tppt) cc_final: 0.8348 (tppt) REVERT: A 630 ASP cc_start: 0.7472 (p0) cc_final: 0.7140 (p0) REVERT: A 632 LYS cc_start: 0.8583 (mtpm) cc_final: 0.8222 (mtpp) REVERT: A 646 ARG cc_start: 0.6888 (ptp90) cc_final: 0.6487 (ptp90) REVERT: A 847 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7903 (mm-30) REVERT: A 861 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7489 (mmtm) REVERT: A 957 LEU cc_start: 0.8677 (tp) cc_final: 0.8272 (mp) REVERT: A 986 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7800 (mt-10) REVERT: A 987 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8871 (m) REVERT: A 1060 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7477 (mm-30) REVERT: A 1061 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 1067 PHE cc_start: 0.8283 (t80) cc_final: 0.8034 (t80) REVERT: A 1087 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7449 (tp30) REVERT: A 1098 ILE cc_start: 0.9075 (tt) cc_final: 0.8835 (tt) REVERT: A 1104 MET cc_start: 0.8057 (tpt) cc_final: 0.7813 (mmm) REVERT: A 1115 GLU cc_start: 0.8137 (tt0) cc_final: 0.7897 (tp30) REVERT: A 1134 PHE cc_start: 0.8299 (m-80) cc_final: 0.7921 (m-80) REVERT: A 1173 LYS cc_start: 0.7513 (tppt) cc_final: 0.7185 (tppt) REVERT: A 1190 ARG cc_start: 0.7393 (ttm-80) cc_final: 0.7064 (mtt-85) REVERT: A 1202 ARG cc_start: 0.6777 (ttt-90) cc_final: 0.6509 (ttt-90) REVERT: B 79 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8326 (p) REVERT: B 93 SER cc_start: 0.8197 (m) cc_final: 0.7796 (p) REVERT: B 133 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7656 (mtm) REVERT: B 154 MET cc_start: 0.8358 (tpp) cc_final: 0.7944 (ttm) REVERT: B 155 ASP cc_start: 0.8110 (p0) cc_final: 0.7812 (p0) REVERT: B 160 MET cc_start: 0.8264 (mmt) cc_final: 0.7995 (mmm) REVERT: B 231 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: B 233 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7505 (tm-30) REVERT: B 253 PHE cc_start: 0.8079 (m-10) cc_final: 0.7785 (m-80) REVERT: B 289 PHE cc_start: 0.8380 (t80) cc_final: 0.8117 (t80) REVERT: B 300 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7776 (mt-10) REVERT: B 319 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7807 (mt) REVERT: B 386 PHE cc_start: 0.8335 (t80) cc_final: 0.8111 (t80) REVERT: B 387 TYR cc_start: 0.8283 (m-10) cc_final: 0.7637 (m-10) REVERT: B 484 SER cc_start: 0.8673 (p) cc_final: 0.8442 (t) REVERT: B 577 ASP cc_start: 0.7709 (m-30) cc_final: 0.7494 (m-30) REVERT: B 588 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7973 (ttpm) REVERT: B 595 TRP cc_start: 0.8812 (m100) cc_final: 0.8398 (m100) REVERT: B 643 TRP cc_start: 0.6877 (t-100) cc_final: 0.6548 (t-100) REVERT: B 646 ARG cc_start: 0.7168 (ptp-170) cc_final: 0.6889 (ptp-170) REVERT: B 828 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8454 (mmmt) REVERT: B 847 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7661 (mm-30) REVERT: B 871 SER cc_start: 0.8359 (p) cc_final: 0.8146 (t) REVERT: B 958 LYS cc_start: 0.8663 (ttpp) cc_final: 0.8440 (ttpp) REVERT: B 967 MET cc_start: 0.8125 (mmp) cc_final: 0.7784 (mmp) REVERT: B 971 ASP cc_start: 0.8208 (m-30) cc_final: 0.7861 (m-30) REVERT: B 976 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7565 (ttm170) REVERT: B 986 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7703 (mt-10) REVERT: B 999 PHE cc_start: 0.7649 (m-80) cc_final: 0.7136 (m-80) REVERT: B 1060 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7854 (mm-30) REVERT: B 1061 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8234 (p) REVERT: B 1067 PHE cc_start: 0.8210 (t80) cc_final: 0.7795 (t80) REVERT: B 1072 ASP cc_start: 0.7808 (m-30) cc_final: 0.7365 (m-30) REVERT: B 1094 VAL cc_start: 0.8664 (m) cc_final: 0.8420 (p) REVERT: B 1098 ILE cc_start: 0.9089 (tt) cc_final: 0.8653 (tp) REVERT: B 1104 MET cc_start: 0.7739 (tpp) cc_final: 0.7477 (mmm) REVERT: B 1122 GLU cc_start: 0.8087 (tp30) cc_final: 0.7566 (mm-30) REVERT: B 1134 PHE cc_start: 0.8226 (m-80) cc_final: 0.8011 (m-80) REVERT: B 1141 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8248 (p) REVERT: B 1214 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6807 (mm) REVERT: B 1221 MET cc_start: 0.7708 (mmm) cc_final: 0.6706 (mmm) outliers start: 93 outliers final: 59 residues processed: 529 average time/residue: 0.2926 time to fit residues: 226.5603 Evaluate side-chains 564 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 486 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 154 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 249 MET 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 363 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 477 LEU 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 603 LEU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 850 VAL 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 1066 TYR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1217 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 231 GLU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 270 GLN 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 448 ASN 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 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 872 GLU Chi-restraints excluded: chain B residue 884 LEU 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 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 1147 LEU Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1212 ILE Chi-restraints excluded: chain B residue 1214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 192 optimal weight: 0.4980 chunk 98 optimal weight: 0.0000 chunk 21 optimal weight: 2.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 917 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.136261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118080 restraints weight = 24642.782| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.17 r_work: 0.3415 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.6285 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= 0.141 Angle : 0.610 9.870 22062 Z= 0.312 Chirality : 0.041 0.204 2660 Planarity : 0.004 0.062 2752 Dihedral : 5.099 59.063 2239 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.01 % Allowed : 24.97 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 2050 helix: 2.11 (0.14), residues: 1444 sheet: 0.93 (0.59), residues: 96 loop : -1.53 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.005 0.001 HIS A 908 PHE 0.018 0.001 PHE B 248 TYR 0.014 0.001 TYR B 280 ARG 0.008 0.000 ARG B 605 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 1198) hydrogen bonds : angle 3.89405 ( 3534) covalent geometry : bond 0.00302 (16254) covalent geometry : angle 0.60972 (22062) ********************** 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 579 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 495 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8360 (p) REVERT: A 112 ILE cc_start: 0.8432 (mt) cc_final: 0.8108 (mm) REVERT: A 124 GLU cc_start: 0.7148 (tp30) cc_final: 0.6820 (tm-30) REVERT: A 129 ASP cc_start: 0.6207 (OUTLIER) cc_final: 0.5943 (p0) REVERT: A 137 VAL cc_start: 0.8122 (p) cc_final: 0.7893 (m) REVERT: A 149 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7613 (tp30) REVERT: A 154 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7949 (ttm) REVERT: A 155 ASP cc_start: 0.8039 (p0) cc_final: 0.7661 (p0) REVERT: A 160 MET cc_start: 0.8364 (mmt) cc_final: 0.8035 (mmm) REVERT: A 184 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7918 (tp) REVERT: A 186 MET cc_start: 0.7914 (mtp) cc_final: 0.7667 (mtt) REVERT: A 199 MET cc_start: 0.8082 (mmm) cc_final: 0.7116 (tpp) REVERT: A 217 LEU cc_start: 0.8569 (mt) cc_final: 0.8302 (mm) REVERT: A 233 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 249 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8135 (ttp) REVERT: A 266 LEU cc_start: 0.8257 (tp) cc_final: 0.7961 (tp) REVERT: A 289 PHE cc_start: 0.8470 (t80) cc_final: 0.8211 (t80) REVERT: A 319 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7472 (mp) REVERT: A 337 GLU cc_start: 0.7992 (mp0) cc_final: 0.7549 (mp0) REVERT: A 355 MET cc_start: 0.8449 (ttp) cc_final: 0.8105 (ttp) REVERT: A 363 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8392 (mt) REVERT: A 372 VAL cc_start: 0.8847 (p) cc_final: 0.8586 (p) REVERT: A 377 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8466 (mp) REVERT: A 383 MET cc_start: 0.7178 (mmp) cc_final: 0.5884 (mmm) REVERT: A 387 TYR cc_start: 0.8223 (m-10) cc_final: 0.7312 (m-10) REVERT: A 398 ILE cc_start: 0.8700 (mt) cc_final: 0.8378 (mt) REVERT: A 427 TRP cc_start: 0.8849 (t-100) cc_final: 0.8401 (t-100) REVERT: A 484 SER cc_start: 0.8712 (p) cc_final: 0.8431 (t) REVERT: A 552 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7858 (tt) REVERT: A 580 GLU cc_start: 0.7616 (tp30) cc_final: 0.7307 (tp30) REVERT: A 588 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8032 (tttm) REVERT: A 622 LYS cc_start: 0.8599 (tppt) cc_final: 0.8335 (tppt) REVERT: A 630 ASP cc_start: 0.7533 (p0) cc_final: 0.7223 (p0) REVERT: A 632 LYS cc_start: 0.8614 (mtpm) cc_final: 0.8254 (mtpp) REVERT: A 646 ARG cc_start: 0.6905 (ptp90) cc_final: 0.6657 (ptp90) REVERT: A 861 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7678 (mmtp) REVERT: A 957 LEU cc_start: 0.8663 (tp) cc_final: 0.8241 (mp) REVERT: A 986 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7786 (mt-10) REVERT: A 987 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8874 (m) REVERT: A 1060 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7581 (mm-30) REVERT: A 1061 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8451 (p) REVERT: A 1067 PHE cc_start: 0.8286 (t80) cc_final: 0.8062 (t80) REVERT: A 1098 ILE cc_start: 0.9082 (tt) cc_final: 0.8838 (tt) REVERT: A 1115 GLU cc_start: 0.8127 (tt0) cc_final: 0.7899 (tp30) REVERT: A 1134 PHE cc_start: 0.8269 (m-80) cc_final: 0.7935 (m-80) REVERT: A 1173 LYS cc_start: 0.7548 (tppt) cc_final: 0.7111 (mmmm) REVERT: A 1202 ARG cc_start: 0.6759 (ttt-90) cc_final: 0.6504 (ttt-90) REVERT: B 79 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8327 (p) REVERT: B 93 SER cc_start: 0.8205 (m) cc_final: 0.7796 (p) REVERT: B 133 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7699 (mtm) REVERT: B 154 MET cc_start: 0.8355 (tpp) cc_final: 0.7936 (ttm) REVERT: B 155 ASP cc_start: 0.8090 (p0) cc_final: 0.7787 (p0) REVERT: B 160 MET cc_start: 0.8269 (mmt) cc_final: 0.8014 (mmm) REVERT: B 161 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7702 (mtm-85) REVERT: B 231 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: B 233 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7401 (tm-30) REVERT: B 253 PHE cc_start: 0.8124 (m-10) cc_final: 0.7821 (m-80) REVERT: B 265 VAL cc_start: 0.8657 (p) cc_final: 0.8456 (p) REVERT: B 266 LEU cc_start: 0.8328 (tp) cc_final: 0.8016 (tp) REVERT: B 289 PHE cc_start: 0.8391 (t80) cc_final: 0.8125 (t80) REVERT: B 300 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 319 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7669 (mt) REVERT: B 386 PHE cc_start: 0.8329 (t80) cc_final: 0.8104 (t80) REVERT: B 387 TYR cc_start: 0.8302 (m-10) cc_final: 0.7603 (m-10) REVERT: B 484 SER cc_start: 0.8645 (p) cc_final: 0.8377 (t) REVERT: B 577 ASP cc_start: 0.7721 (m-30) cc_final: 0.7485 (m-30) REVERT: B 588 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7866 (ttpm) REVERT: B 595 TRP cc_start: 0.8814 (m100) cc_final: 0.8408 (m100) REVERT: B 643 TRP cc_start: 0.7017 (t-100) cc_final: 0.6629 (t-100) REVERT: B 646 ARG cc_start: 0.7283 (ptp-170) cc_final: 0.6988 (ptp-170) REVERT: B 847 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7735 (mm-30) REVERT: B 871 SER cc_start: 0.8385 (p) cc_final: 0.8179 (t) REVERT: B 943 ASN cc_start: 0.8217 (m-40) cc_final: 0.7889 (p0) REVERT: B 958 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8430 (ttpp) REVERT: B 967 MET cc_start: 0.8096 (mmp) cc_final: 0.7764 (mmp) REVERT: B 971 ASP cc_start: 0.8130 (m-30) cc_final: 0.7780 (m-30) REVERT: B 976 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7466 (ttm170) REVERT: B 986 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7637 (mt-10) REVERT: B 1061 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8233 (p) REVERT: B 1072 ASP cc_start: 0.7778 (m-30) cc_final: 0.7319 (m-30) REVERT: B 1094 VAL cc_start: 0.8664 (m) cc_final: 0.8430 (p) REVERT: B 1098 ILE cc_start: 0.9080 (tt) cc_final: 0.8653 (tp) REVERT: B 1104 MET cc_start: 0.7739 (tpp) cc_final: 0.7521 (mmm) REVERT: B 1122 GLU cc_start: 0.8063 (tp30) cc_final: 0.7540 (mm-30) REVERT: B 1141 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8247 (p) REVERT: B 1214 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6819 (mm) REVERT: B 1221 MET cc_start: 0.7847 (mmm) cc_final: 0.6856 (mmm) outliers start: 84 outliers final: 59 residues processed: 528 average time/residue: 0.3667 time to fit residues: 285.2173 Evaluate side-chains 566 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 487 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 154 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 249 MET 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 363 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 418 THR 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 588 LYS 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 837 TYR Chi-restraints excluded: chain A residue 850 VAL 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 1050 LYS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1217 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 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 448 ASN 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 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 855 ASP Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 917 GLN 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 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 1147 LEU Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1212 ILE Chi-restraints excluded: chain B residue 1214 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 179 optimal weight: 0.3980 chunk 102 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 181 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.117980 restraints weight = 24398.242| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.16 r_work: 0.3414 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16254 Z= 0.145 Angle : 0.619 9.828 22062 Z= 0.315 Chirality : 0.041 0.167 2660 Planarity : 0.004 0.045 2752 Dihedral : 5.093 58.869 2239 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.95 % Allowed : 25.45 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 2050 helix: 2.10 (0.14), residues: 1444 sheet: 0.90 (0.59), residues: 96 loop : -1.51 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 643 HIS 0.004 0.001 HIS A 908 PHE 0.028 0.002 PHE B 999 TYR 0.021 0.001 TYR B1178 ARG 0.008 0.000 ARG B 605 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 1198) hydrogen bonds : angle 3.89806 ( 3534) covalent geometry : bond 0.00315 (16254) covalent geometry : angle 0.61929 (22062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10238.73 seconds wall clock time: 181 minutes 36.85 seconds (10896.85 seconds total)