Starting phenix.real_space_refine on Tue Aug 6 09:13:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xpq_38559/08_2024/8xpq_38559.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xpq_38559/08_2024/8xpq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xpq_38559/08_2024/8xpq_38559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xpq_38559/08_2024/8xpq_38559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xpq_38559/08_2024/8xpq_38559.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xpq_38559/08_2024/8xpq_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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15966 Number of models: 1 Model: "" Number of chains: 2 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 Chain: "B" 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 Time building chain proxies: 8.00, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 5.83 Conformation dependent library (CDL) restraints added in 2.9 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: 1.95 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: 5.62 Time building geometry restraints manager: 6.45 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: 99.92 - 106.75: 416 106.75 - 113.58: 9331 113.58 - 120.41: 6343 120.41 - 127.23: 5816 127.23 - 134.06: 156 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 43.560 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.310 ------------------------------------------------------------------------------- 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= 0.372 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 *********************** 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 fitting. rotamer outliers: 88 poor density : 561 time to evaluate : 2.184 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: 0.2764 time to fit residues: 251.0240 Evaluate side-chains 519 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 482 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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= 0.236 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 *********************** 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 fitting. rotamer outliers: 88 poor density : 529 time to evaluate : 1.778 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: 0.7072 (tp30) cc_final: 0.6659 (tp30) REVERT: A 149 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7342 (tm-30) REVERT: A 154 MET cc_start: 0.7869 (tpp) cc_final: 0.7420 (tpp) REVERT: A 155 ASP cc_start: 0.7617 (t70) cc_final: 0.7400 (t70) REVERT: A 160 MET cc_start: 0.7226 (mmt) cc_final: 0.6898 (mmm) REVERT: A 186 MET cc_start: 0.7218 (mtp) cc_final: 0.6978 (mmm) REVERT: A 187 ASN cc_start: 0.7243 (m-40) cc_final: 0.6920 (m110) REVERT: A 248 PHE cc_start: 0.8035 (m-80) cc_final: 0.7432 (m-80) REVERT: A 265 VAL cc_start: 0.8110 (t) cc_final: 0.7837 (p) REVERT: A 289 PHE cc_start: 0.7911 (t80) cc_final: 0.7522 (t80) REVERT: A 337 GLU cc_start: 0.7859 (mp0) cc_final: 0.7523 (mp0) REVERT: A 355 MET cc_start: 0.8390 (ttp) cc_final: 0.8086 (ttp) REVERT: A 427 TRP cc_start: 0.8191 (t-100) cc_final: 0.7758 (t-100) REVERT: A 511 MET cc_start: 0.8595 (ttt) cc_final: 0.8180 (ttp) REVERT: A 534 ASP cc_start: 0.7452 (t70) cc_final: 0.7215 (t0) REVERT: A 536 TYR cc_start: 0.7813 (m-80) cc_final: 0.7384 (m-10) REVERT: A 552 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7450 (tt) REVERT: A 578 MET cc_start: 0.7341 (mtm) cc_final: 0.7067 (mtp) REVERT: A 823 LEU cc_start: 0.8299 (mp) cc_final: 0.7970 (mm) REVERT: A 845 ILE cc_start: 0.8801 (mt) cc_final: 0.8554 (mm) REVERT: A 849 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7931 (mm-30) REVERT: A 887 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7834 (ttt90) REVERT: A 926 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7548 (mm-30) REVERT: A 971 ASP cc_start: 0.8333 (m-30) cc_final: 0.7982 (m-30) REVERT: A 987 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8603 (m) REVERT: A 993 ASP cc_start: 0.7996 (p0) cc_final: 0.7664 (p0) REVERT: A 996 ASP cc_start: 0.7705 (p0) cc_final: 0.7428 (p0) REVERT: A 999 PHE cc_start: 0.7733 (m-80) cc_final: 0.7107 (m-10) REVERT: A 1002 VAL cc_start: 0.8430 (m) cc_final: 0.8170 (p) REVERT: A 1044 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8071 (mt-10) REVERT: A 1061 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8072 (p) REVERT: A 1073 MET cc_start: 0.8618 (mmm) cc_final: 0.8216 (mmm) REVERT: A 1098 ILE cc_start: 0.8982 (tt) cc_final: 0.8680 (tt) REVERT: A 1104 MET cc_start: 0.7734 (tpp) cc_final: 0.7382 (tpp) REVERT: A 1122 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7548 (mm-30) REVERT: A 1134 PHE cc_start: 0.8271 (m-80) cc_final: 0.7976 (m-10) REVERT: A 1190 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.7387 (ttm-80) REVERT: B 124 GLU cc_start: 0.6829 (tp30) cc_final: 0.6460 (tp30) REVERT: B 140 GLN cc_start: 0.8201 (mm110) cc_final: 0.7871 (mp10) REVERT: B 154 MET cc_start: 0.8021 (tpp) cc_final: 0.7488 (tpp) REVERT: B 155 ASP cc_start: 0.7540 (t70) cc_final: 0.7310 (t70) REVERT: B 160 MET cc_start: 0.7166 (mmt) cc_final: 0.6826 (mmm) REVERT: B 231 GLU cc_start: 0.7458 (tt0) cc_final: 0.7110 (mt-10) REVERT: B 265 VAL cc_start: 0.7964 (t) cc_final: 0.7749 (p) REVERT: B 319 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8097 (mt) REVERT: B 333 ILE cc_start: 0.8067 (mt) cc_final: 0.7618 (mm) REVERT: B 337 GLU cc_start: 0.7977 (mp0) cc_final: 0.7430 (mp0) REVERT: B 368 VAL cc_start: 0.8432 (t) cc_final: 0.8171 (p) REVERT: B 375 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8297 (mtmm) REVERT: B 401 MET cc_start: 0.7425 (mmp) cc_final: 0.7138 (mtp) REVERT: B 534 ASP cc_start: 0.7553 (t70) cc_final: 0.7220 (t0) REVERT: B 565 MET cc_start: 0.4502 (ppp) cc_final: 0.4269 (ppp) REVERT: B 569 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8192 (mp0) REVERT: B 578 MET cc_start: 0.7487 (mtt) cc_final: 0.7231 (mtp) REVERT: B 579 MET cc_start: 0.7322 (tpt) cc_final: 0.7087 (tpt) REVERT: B 595 TRP cc_start: 0.8321 (m100) cc_final: 0.8095 (m100) REVERT: B 624 GLN cc_start: 0.7361 (pt0) cc_final: 0.7134 (pt0) REVERT: B 820 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7846 (mmmt) REVERT: B 823 LEU cc_start: 0.8313 (mp) cc_final: 0.8063 (mm) REVERT: B 832 GLN cc_start: 0.8403 (tp40) cc_final: 0.8103 (tm-30) REVERT: B 841 LYS cc_start: 0.8102 (mtpm) cc_final: 0.7900 (mtpm) REVERT: B 847 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7400 (mm-30) REVERT: B 898 THR cc_start: 0.8412 (m) cc_final: 0.8202 (p) REVERT: B 926 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7481 (mm-30) REVERT: B 971 ASP cc_start: 0.8381 (m-30) cc_final: 0.8045 (m-30) REVERT: B 973 ILE cc_start: 0.8606 (mm) cc_final: 0.8237 (tt) REVERT: B 983 ASP cc_start: 0.8391 (p0) cc_final: 0.8083 (p0) REVERT: B 986 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7966 (mt-10) REVERT: B 987 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8664 (m) REVERT: B 991 GLU cc_start: 0.7843 (tt0) cc_final: 0.7593 (tt0) REVERT: B 994 GLU cc_start: 0.8116 (mp0) cc_final: 0.7815 (mp0) REVERT: B 996 ASP cc_start: 0.7831 (p0) cc_final: 0.7583 (p0) REVERT: B 1002 VAL cc_start: 0.8415 (m) cc_final: 0.8170 (p) REVERT: B 1051 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8476 (mtpp) REVERT: B 1094 VAL cc_start: 0.8561 (m) cc_final: 0.8310 (p) REVERT: B 1098 ILE cc_start: 0.9013 (tt) cc_final: 0.8683 (tt) REVERT: B 1104 MET cc_start: 0.7684 (tpp) cc_final: 0.7339 (mmm) REVERT: B 1105 GLU cc_start: 0.7937 (tt0) cc_final: 0.7699 (tt0) REVERT: B 1110 GLN cc_start: 0.8469 (mp10) cc_final: 0.8151 (mp10) REVERT: B 1122 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7609 (mm-30) REVERT: B 1128 ASP cc_start: 0.7325 (t0) cc_final: 0.7081 (t70) REVERT: B 1134 PHE cc_start: 0.8329 (m-80) cc_final: 0.8020 (m-10) REVERT: B 1172 HIS cc_start: 0.7934 (t-170) cc_final: 0.7532 (t-170) REVERT: B 1183 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: B 1188 VAL cc_start: 0.8749 (m) cc_final: 0.8448 (p) outliers start: 88 outliers final: 53 residues processed: 576 average time/residue: 0.2661 time to fit residues: 226.6683 Evaluate side-chains 541 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 481 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 1183 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 185 optimal weight: 0.0070 chunk 63 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16254 Z= 0.254 Angle : 0.611 7.708 22062 Z= 0.324 Chirality : 0.042 0.184 2660 Planarity : 0.004 0.040 2752 Dihedral : 5.821 59.286 2254 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.96 % Allowed : 18.30 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.19), residues: 2050 helix: 1.42 (0.14), residues: 1434 sheet: 0.52 (0.58), residues: 96 loop : -1.85 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 962 HIS 0.005 0.001 HIS A 908 PHE 0.014 0.002 PHE A 999 TYR 0.012 0.001 TYR B1035 ARG 0.007 0.001 ARG A 161 *********************** 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 645 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 545 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7263 (tp30) cc_final: 0.6840 (tp30) REVERT: A 140 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8144 (mp10) REVERT: A 149 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7326 (tm-30) REVERT: A 154 MET cc_start: 0.8194 (tpp) cc_final: 0.7708 (ttm) REVERT: A 155 ASP cc_start: 0.7911 (t70) cc_final: 0.7617 (t70) REVERT: A 180 LEU cc_start: 0.8480 (tt) cc_final: 0.8253 (tp) REVERT: A 186 MET cc_start: 0.7419 (mtp) cc_final: 0.7078 (mtp) REVERT: A 187 ASN cc_start: 0.7528 (m-40) cc_final: 0.7115 (m-40) REVERT: A 206 SER cc_start: 0.8305 (t) cc_final: 0.8002 (t) REVERT: A 265 VAL cc_start: 0.8350 (t) cc_final: 0.8121 (p) REVERT: A 289 PHE cc_start: 0.8213 (t80) cc_final: 0.7891 (t80) REVERT: A 337 GLU cc_start: 0.7960 (mp0) cc_final: 0.7532 (mp0) REVERT: A 346 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 355 MET cc_start: 0.8434 (ttp) cc_final: 0.8112 (ttp) REVERT: A 427 TRP cc_start: 0.8714 (t-100) cc_final: 0.7972 (t-100) REVERT: A 451 ILE cc_start: 0.8559 (tt) cc_final: 0.7929 (tt) REVERT: A 477 LEU cc_start: 0.8391 (mm) cc_final: 0.8189 (mp) REVERT: A 511 MET cc_start: 0.8609 (ttt) cc_final: 0.8400 (ttt) REVERT: A 534 ASP cc_start: 0.7867 (t70) cc_final: 0.7642 (t0) REVERT: A 552 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7569 (tt) REVERT: A 599 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: A 605 ARG cc_start: 0.8531 (tpp80) cc_final: 0.8290 (tpp80) REVERT: A 606 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7829 (pm20) REVERT: A 632 LYS cc_start: 0.8068 (mtpm) cc_final: 0.7740 (mtpp) REVERT: A 823 LEU cc_start: 0.8493 (mp) cc_final: 0.8073 (mm) REVERT: A 832 GLN cc_start: 0.8632 (tp40) cc_final: 0.8362 (tm-30) REVERT: A 845 ILE cc_start: 0.8643 (mt) cc_final: 0.8402 (mm) REVERT: A 958 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8284 (ttpp) REVERT: A 971 ASP cc_start: 0.8405 (m-30) cc_final: 0.8059 (m-30) REVERT: A 987 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8722 (m) REVERT: A 991 GLU cc_start: 0.7751 (tt0) cc_final: 0.7544 (tt0) REVERT: A 993 ASP cc_start: 0.8042 (p0) cc_final: 0.7832 (p0) REVERT: A 999 PHE cc_start: 0.7612 (m-80) cc_final: 0.6939 (m-80) REVERT: A 1044 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 1061 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8215 (p) REVERT: A 1067 PHE cc_start: 0.8021 (t80) cc_final: 0.7483 (t80) REVERT: A 1073 MET cc_start: 0.8607 (mmm) cc_final: 0.8198 (mmm) REVERT: A 1094 VAL cc_start: 0.8596 (m) cc_final: 0.8313 (p) REVERT: A 1098 ILE cc_start: 0.9030 (tt) cc_final: 0.8704 (tt) REVERT: A 1122 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7605 (tp30) REVERT: A 1127 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8280 (p) REVERT: A 1134 PHE cc_start: 0.8392 (m-80) cc_final: 0.7865 (m-10) REVERT: A 1190 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7594 (ttm-80) REVERT: B 79 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8412 (t) REVERT: B 93 SER cc_start: 0.8250 (m) cc_final: 0.7846 (p) REVERT: B 107 LEU cc_start: 0.8318 (tt) cc_final: 0.8112 (tp) REVERT: B 124 GLU cc_start: 0.7083 (tp30) cc_final: 0.6745 (tm-30) REVERT: B 140 GLN cc_start: 0.8184 (mm110) cc_final: 0.7924 (mp10) REVERT: B 149 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7391 (tm-30) REVERT: B 154 MET cc_start: 0.8288 (tpp) cc_final: 0.7704 (ttm) REVERT: B 160 MET cc_start: 0.7480 (mmt) cc_final: 0.7023 (mmm) REVERT: B 166 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7580 (t) REVERT: B 206 SER cc_start: 0.8428 (t) cc_final: 0.8139 (t) REVERT: B 231 GLU cc_start: 0.7751 (tt0) cc_final: 0.7510 (mt-10) REVERT: B 233 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7322 (tm-30) REVERT: B 319 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8025 (mt) REVERT: B 346 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7697 (mt-10) REVERT: B 375 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8337 (ttpp) REVERT: B 401 MET cc_start: 0.7798 (mmp) cc_final: 0.7592 (mtp) REVERT: B 534 ASP cc_start: 0.7838 (t70) cc_final: 0.7590 (t0) REVERT: B 565 MET cc_start: 0.5037 (ppp) cc_final: 0.4567 (ppp) REVERT: B 579 MET cc_start: 0.7784 (tpt) cc_final: 0.7530 (tpt) REVERT: B 595 TRP cc_start: 0.8656 (m100) cc_final: 0.8307 (m100) REVERT: B 600 HIS cc_start: 0.8366 (m90) cc_final: 0.8146 (m-70) REVERT: B 624 GLN cc_start: 0.7506 (pt0) cc_final: 0.7250 (pt0) REVERT: B 823 LEU cc_start: 0.8420 (mp) cc_final: 0.8123 (mm) REVERT: B 831 ASN cc_start: 0.8385 (t0) cc_final: 0.8111 (m-40) REVERT: B 832 GLN cc_start: 0.8602 (tp40) cc_final: 0.8229 (tm-30) REVERT: B 847 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7564 (mm-30) REVERT: B 897 LYS cc_start: 0.8696 (mmtp) cc_final: 0.8456 (mttp) REVERT: B 940 ARG cc_start: 0.8928 (tpp80) cc_final: 0.8652 (ttm-80) REVERT: B 970 ILE cc_start: 0.9053 (mm) cc_final: 0.8709 (tt) REVERT: B 971 ASP cc_start: 0.8412 (m-30) cc_final: 0.7986 (m-30) REVERT: B 972 PHE cc_start: 0.8240 (t80) cc_final: 0.7966 (t80) REVERT: B 986 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8050 (mt-10) REVERT: B 987 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8734 (m) REVERT: B 994 GLU cc_start: 0.8180 (mp0) cc_final: 0.7845 (mp0) REVERT: B 1044 GLU cc_start: 0.8366 (mp0) cc_final: 0.8023 (mp0) REVERT: B 1061 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 1067 PHE cc_start: 0.7990 (t80) cc_final: 0.7531 (t80) REVERT: B 1094 VAL cc_start: 0.8573 (m) cc_final: 0.8353 (p) REVERT: B 1098 ILE cc_start: 0.9078 (tt) cc_final: 0.8687 (tt) REVERT: B 1104 MET cc_start: 0.7676 (tpp) cc_final: 0.7333 (tpp) REVERT: B 1117 VAL cc_start: 0.8906 (t) cc_final: 0.8579 (t) REVERT: B 1122 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 1127 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8175 (m) REVERT: B 1128 ASP cc_start: 0.7434 (t0) cc_final: 0.7183 (t0) REVERT: B 1134 PHE cc_start: 0.8446 (m-80) cc_final: 0.8108 (m-80) REVERT: B 1141 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8374 (p) REVERT: B 1172 HIS cc_start: 0.7845 (t-90) cc_final: 0.7546 (t-170) REVERT: B 1183 GLU cc_start: 0.7672 (pm20) cc_final: 0.7256 (mp0) REVERT: B 1214 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7362 (mm) outliers start: 100 outliers final: 54 residues processed: 590 average time/residue: 0.2907 time to fit residues: 249.9394 Evaluate side-chains 577 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 508 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 316 ASP 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 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 606 GLU Chi-restraints excluded: chain A residue 610 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 814 THR Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 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 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 404 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 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 958 LYS Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1037 THR Chi-restraints excluded: chain B residue 1045 MET 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 1082 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 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 185 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B 908 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16254 Z= 0.218 Angle : 0.587 9.241 22062 Z= 0.308 Chirality : 0.042 0.171 2660 Planarity : 0.004 0.036 2752 Dihedral : 5.664 58.367 2248 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.95 % Allowed : 21.63 % Favored : 73.42 % 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: 1.28 (0.19), residues: 2050 helix: 1.71 (0.14), residues: 1442 sheet: 0.75 (0.58), residues: 96 loop : -1.67 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 643 HIS 0.005 0.001 HIS A 908 PHE 0.028 0.002 PHE B 248 TYR 0.011 0.001 TYR A1125 ARG 0.006 0.001 ARG A 161 *********************** 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 617 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 534 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 SER cc_start: 0.8269 (m) cc_final: 0.7887 (p) REVERT: A 112 ILE cc_start: 0.8465 (mt) cc_final: 0.8086 (mm) REVERT: A 124 GLU cc_start: 0.7252 (tp30) cc_final: 0.6889 (tp30) REVERT: A 140 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8058 (mp10) REVERT: A 149 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 154 MET cc_start: 0.8225 (tpp) cc_final: 0.7789 (ttm) REVERT: A 155 ASP cc_start: 0.7979 (t70) cc_final: 0.7652 (t70) REVERT: A 180 LEU cc_start: 0.8401 (tt) cc_final: 0.8172 (tp) REVERT: A 183 VAL cc_start: 0.7886 (t) cc_final: 0.7672 (p) REVERT: A 184 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7971 (tp) REVERT: A 186 MET cc_start: 0.7515 (mtp) cc_final: 0.7188 (mtp) REVERT: A 187 ASN cc_start: 0.7753 (m-40) cc_final: 0.7386 (m-40) REVERT: A 206 SER cc_start: 0.8551 (t) cc_final: 0.7903 (t) REVERT: A 233 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7502 (tm-30) REVERT: A 265 VAL cc_start: 0.8502 (t) cc_final: 0.8302 (p) REVERT: A 289 PHE cc_start: 0.8297 (t80) cc_final: 0.8022 (t80) REVERT: A 319 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8120 (mt) REVERT: A 337 GLU cc_start: 0.7948 (mp0) cc_final: 0.7512 (mp0) REVERT: A 346 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7550 (mt-10) REVERT: A 355 MET cc_start: 0.8412 (ttp) cc_final: 0.8071 (ttp) REVERT: A 383 MET cc_start: 0.7136 (mmp) cc_final: 0.6473 (mmm) REVERT: A 387 TYR cc_start: 0.7943 (m-10) cc_final: 0.7741 (m-10) REVERT: A 427 TRP cc_start: 0.8813 (t-100) cc_final: 0.7932 (t-100) REVERT: A 474 ILE cc_start: 0.6716 (tp) cc_final: 0.6395 (tt) REVERT: A 599 GLU cc_start: 0.8201 (tp30) cc_final: 0.7802 (mp0) REVERT: A 606 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: A 622 LYS cc_start: 0.8808 (tppt) cc_final: 0.8342 (tppt) REVERT: A 632 LYS cc_start: 0.8317 (mtpm) cc_final: 0.8021 (mtpp) REVERT: A 832 GLN cc_start: 0.8678 (tp40) cc_final: 0.8425 (tt0) REVERT: A 958 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8211 (ttpp) REVERT: A 971 ASP cc_start: 0.8462 (m-30) cc_final: 0.8102 (m-30) REVERT: A 987 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8676 (m) REVERT: A 999 PHE cc_start: 0.7631 (m-80) cc_final: 0.6940 (m-80) REVERT: A 1044 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8170 (mt-10) REVERT: A 1060 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7404 (mm-30) REVERT: A 1061 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8242 (p) REVERT: A 1067 PHE cc_start: 0.8100 (t80) cc_final: 0.7593 (t80) REVERT: A 1073 MET cc_start: 0.8617 (mmm) cc_final: 0.8178 (mmm) REVERT: A 1094 VAL cc_start: 0.8610 (m) cc_final: 0.8383 (p) REVERT: A 1098 ILE cc_start: 0.9041 (tt) cc_final: 0.8773 (tt) REVERT: A 1107 MET cc_start: 0.8066 (ttm) cc_final: 0.7768 (ttm) REVERT: A 1115 GLU cc_start: 0.8128 (tt0) cc_final: 0.7876 (tp30) REVERT: A 1134 PHE cc_start: 0.8462 (m-80) cc_final: 0.8207 (m-80) REVERT: A 1202 ARG cc_start: 0.7220 (ttt-90) cc_final: 0.6956 (ttt-90) REVERT: B 79 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8376 (p) REVERT: B 93 SER cc_start: 0.8321 (m) cc_final: 0.7925 (p) REVERT: B 113 LEU cc_start: 0.8512 (tp) cc_final: 0.8302 (tt) REVERT: B 124 GLU cc_start: 0.7148 (tp30) cc_final: 0.6804 (tm-30) REVERT: B 140 GLN cc_start: 0.8146 (mm110) cc_final: 0.7865 (mp10) REVERT: B 149 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7413 (tm-30) REVERT: B 154 MET cc_start: 0.8239 (tpp) cc_final: 0.7761 (ttm) REVERT: B 155 ASP cc_start: 0.8094 (p0) cc_final: 0.7729 (p0) REVERT: B 160 MET cc_start: 0.7525 (mmt) cc_final: 0.7147 (mmm) REVERT: B 184 LEU cc_start: 0.7944 (tt) cc_final: 0.7657 (tp) REVERT: B 186 MET cc_start: 0.7501 (mtp) cc_final: 0.7297 (mmt) REVERT: B 187 ASN cc_start: 0.7966 (m-40) cc_final: 0.7740 (m-40) REVERT: B 206 SER cc_start: 0.8626 (t) cc_final: 0.8360 (t) REVERT: B 233 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7407 (tm-30) REVERT: B 319 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8193 (mt) REVERT: B 375 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8372 (ttpt) REVERT: B 387 TYR cc_start: 0.8054 (m-10) cc_final: 0.7687 (m-10) REVERT: B 485 ASP cc_start: 0.7751 (m-30) cc_final: 0.7529 (m-30) REVERT: B 534 ASP cc_start: 0.7829 (t70) cc_final: 0.7597 (t0) REVERT: B 565 MET cc_start: 0.4977 (ppp) cc_final: 0.4507 (ppp) REVERT: B 579 MET cc_start: 0.7897 (tpt) cc_final: 0.7647 (tpt) REVERT: B 595 TRP cc_start: 0.8718 (m100) cc_final: 0.8358 (m100) REVERT: B 600 HIS cc_start: 0.8312 (m90) cc_final: 0.8079 (m-70) REVERT: B 606 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: B 646 ARG cc_start: 0.6437 (ptp-170) cc_final: 0.6147 (ptp-170) REVERT: B 818 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7651 (tp) REVERT: B 823 LEU cc_start: 0.8490 (mp) cc_final: 0.8151 (mm) REVERT: B 832 GLN cc_start: 0.8629 (tp40) cc_final: 0.8216 (tt0) REVERT: B 847 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 855 ASP cc_start: 0.8199 (t70) cc_final: 0.7990 (t70) REVERT: B 940 ARG cc_start: 0.8922 (tpp80) cc_final: 0.8632 (ttm-80) REVERT: B 958 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8489 (ttpp) REVERT: B 971 ASP cc_start: 0.8402 (m-30) cc_final: 0.8081 (m-30) REVERT: B 986 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 987 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8783 (m) REVERT: B 994 GLU cc_start: 0.8211 (mp0) cc_final: 0.7884 (mp0) REVERT: B 1051 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8408 (mtpp) REVERT: B 1061 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8132 (p) REVERT: B 1067 PHE cc_start: 0.8041 (t80) cc_final: 0.7704 (t80) REVERT: B 1072 ASP cc_start: 0.7859 (m-30) cc_final: 0.7468 (m-30) REVERT: B 1098 ILE cc_start: 0.9082 (tt) cc_final: 0.8681 (tt) REVERT: B 1104 MET cc_start: 0.7623 (tpp) cc_final: 0.7265 (tpp) REVERT: B 1117 VAL cc_start: 0.8913 (t) cc_final: 0.8540 (t) REVERT: B 1122 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7691 (mm-30) REVERT: B 1127 VAL cc_start: 0.8494 (t) cc_final: 0.8261 (m) REVERT: B 1134 PHE cc_start: 0.8481 (m-80) cc_final: 0.8051 (m-10) REVERT: B 1141 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8463 (p) REVERT: B 1172 HIS cc_start: 0.7699 (t-90) cc_final: 0.7493 (t-170) REVERT: B 1214 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7269 (mm) REVERT: B 1221 MET cc_start: 0.7633 (mmm) cc_final: 0.6569 (mmm) outliers start: 83 outliers final: 49 residues processed: 575 average time/residue: 0.2837 time to fit residues: 236.6572 Evaluate side-chains 583 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 519 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 104 VAL 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 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 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 606 GLU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 194 ASN 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 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 837 TYR Chi-restraints excluded: chain B residue 915 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 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 1161 ILE Chi-restraints excluded: chain B residue 1212 ILE 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 165 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 2 optimal weight: 0.0970 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 0.0870 chunk 169 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 600 HIS A 886 GLN A 917 GLN A 943 ASN A1137 ASN B 917 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16254 Z= 0.169 Angle : 0.556 7.905 22062 Z= 0.293 Chirality : 0.041 0.157 2660 Planarity : 0.004 0.033 2752 Dihedral : 5.415 58.780 2244 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.96 % Allowed : 22.35 % Favored : 71.69 % 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: 1.63 (0.19), residues: 2050 helix: 1.96 (0.14), residues: 1448 sheet: 0.98 (0.58), residues: 96 loop : -1.56 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 643 HIS 0.004 0.001 HIS A 908 PHE 0.019 0.001 PHE A 972 TYR 0.011 0.001 TYR A1125 ARG 0.007 0.000 ARG B 161 *********************** 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 632 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 532 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8446 (mt) cc_final: 0.8096 (mm) REVERT: A 124 GLU cc_start: 0.7258 (tp30) cc_final: 0.6891 (tm-30) REVERT: A 129 ASP cc_start: 0.6365 (OUTLIER) cc_final: 0.6108 (p0) REVERT: A 137 VAL cc_start: 0.8101 (p) cc_final: 0.7855 (m) REVERT: A 140 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7978 (mp10) REVERT: A 149 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7307 (tm-30) REVERT: A 154 MET cc_start: 0.8230 (tpp) cc_final: 0.7795 (ttm) REVERT: A 155 ASP cc_start: 0.8016 (t70) cc_final: 0.7667 (t70) REVERT: A 160 MET cc_start: 0.8204 (mmt) cc_final: 0.7843 (mmm) REVERT: A 180 LEU cc_start: 0.8382 (tt) cc_final: 0.8144 (mt) REVERT: A 184 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7940 (tp) REVERT: A 206 SER cc_start: 0.8314 (t) cc_final: 0.7930 (t) REVERT: A 217 LEU cc_start: 0.8506 (mt) cc_final: 0.8300 (mm) REVERT: A 233 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7525 (tm-30) REVERT: A 265 VAL cc_start: 0.8580 (t) cc_final: 0.8352 (p) REVERT: A 289 PHE cc_start: 0.8306 (t80) cc_final: 0.8000 (t80) REVERT: A 319 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8042 (mt) REVERT: A 337 GLU cc_start: 0.7940 (mp0) cc_final: 0.7501 (mp0) REVERT: A 346 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7566 (mt-10) REVERT: A 355 MET cc_start: 0.8407 (ttp) cc_final: 0.8050 (ttp) REVERT: A 377 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 383 MET cc_start: 0.7130 (mmp) cc_final: 0.5875 (mmm) REVERT: A 387 TYR cc_start: 0.8017 (m-10) cc_final: 0.7566 (m-10) REVERT: A 398 ILE cc_start: 0.8568 (mt) cc_final: 0.8237 (mm) REVERT: A 410 LEU cc_start: 0.7914 (mp) cc_final: 0.7694 (mt) REVERT: A 427 TRP cc_start: 0.8831 (t-100) cc_final: 0.7926 (t-100) REVERT: A 474 ILE cc_start: 0.6543 (tp) cc_final: 0.6163 (tt) REVERT: A 552 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7655 (tt) REVERT: A 588 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7845 (ttpt) REVERT: A 599 GLU cc_start: 0.8198 (tp30) cc_final: 0.7735 (mp0) REVERT: A 622 LYS cc_start: 0.8724 (tppt) cc_final: 0.8330 (tppt) REVERT: A 632 LYS cc_start: 0.8353 (mtpm) cc_final: 0.8101 (mtpp) REVERT: A 958 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8196 (ttpp) REVERT: A 971 ASP cc_start: 0.8491 (m-30) cc_final: 0.8158 (m-30) REVERT: A 983 ASP cc_start: 0.8295 (p0) cc_final: 0.7946 (p0) REVERT: A 986 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7642 (mt-10) REVERT: A 987 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8781 (m) REVERT: A 994 GLU cc_start: 0.8249 (mp0) cc_final: 0.8027 (mp0) REVERT: A 999 PHE cc_start: 0.7540 (m-80) cc_final: 0.6868 (m-80) REVERT: A 1044 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8157 (mt-10) REVERT: A 1060 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7310 (mm-30) REVERT: A 1061 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8272 (p) REVERT: A 1067 PHE cc_start: 0.8057 (t80) cc_final: 0.7710 (t80) REVERT: A 1073 MET cc_start: 0.8613 (mmm) cc_final: 0.8199 (mmm) REVERT: A 1098 ILE cc_start: 0.9037 (tt) cc_final: 0.8819 (tt) REVERT: A 1115 GLU cc_start: 0.8140 (tt0) cc_final: 0.7899 (tp30) REVERT: A 1122 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7735 (mm-30) REVERT: A 1134 PHE cc_start: 0.8440 (m-80) cc_final: 0.8048 (m-80) REVERT: A 1190 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7438 (mtt-85) REVERT: A 1202 ARG cc_start: 0.7102 (ttt-90) cc_final: 0.6876 (ttt-90) REVERT: B 79 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8334 (p) REVERT: B 93 SER cc_start: 0.8271 (m) cc_final: 0.7874 (p) REVERT: B 124 GLU cc_start: 0.7016 (tp30) cc_final: 0.6682 (tm-30) REVERT: B 149 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7399 (tm-30) REVERT: B 154 MET cc_start: 0.8225 (tpp) cc_final: 0.7764 (ttm) REVERT: B 155 ASP cc_start: 0.8113 (p0) cc_final: 0.7770 (p0) REVERT: B 160 MET cc_start: 0.7552 (mmt) cc_final: 0.7155 (mmm) REVERT: B 184 LEU cc_start: 0.7979 (tt) cc_final: 0.7725 (tp) REVERT: B 197 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7519 (tt0) REVERT: B 231 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: B 233 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7440 (tm-30) REVERT: B 319 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8110 (mt) REVERT: B 387 TYR cc_start: 0.8026 (m-10) cc_final: 0.7585 (m-10) REVERT: B 485 ASP cc_start: 0.7864 (m-30) cc_final: 0.7649 (m-30) REVERT: B 579 MET cc_start: 0.7921 (tpt) cc_final: 0.7671 (tpt) REVERT: B 588 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7944 (ttpm) REVERT: B 595 TRP cc_start: 0.8736 (m100) cc_final: 0.8305 (m100) REVERT: B 600 HIS cc_start: 0.8265 (m90) cc_final: 0.8050 (m-70) REVERT: B 646 ARG cc_start: 0.6484 (ptp-170) cc_final: 0.6178 (ptp-170) REVERT: B 832 GLN cc_start: 0.8571 (tp40) cc_final: 0.8257 (tt0) REVERT: B 847 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7578 (mm-30) REVERT: B 940 ARG cc_start: 0.8898 (tpp80) cc_final: 0.8625 (ttm-80) REVERT: B 971 ASP cc_start: 0.8325 (m-30) cc_final: 0.8040 (m-30) REVERT: B 972 PHE cc_start: 0.8293 (t80) cc_final: 0.8002 (t80) REVERT: B 983 ASP cc_start: 0.8349 (p0) cc_final: 0.8097 (p0) REVERT: B 986 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8093 (mt-10) REVERT: B 987 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8741 (m) REVERT: B 994 GLU cc_start: 0.8206 (mp0) cc_final: 0.7925 (mp0) REVERT: B 999 PHE cc_start: 0.7694 (m-80) cc_final: 0.7032 (m-80) REVERT: B 1044 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 1051 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8376 (mtpp) REVERT: B 1061 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8153 (p) REVERT: B 1067 PHE cc_start: 0.8063 (t80) cc_final: 0.7625 (t80) REVERT: B 1072 ASP cc_start: 0.7809 (m-30) cc_final: 0.7500 (m-30) REVERT: B 1098 ILE cc_start: 0.9084 (tt) cc_final: 0.8683 (tt) REVERT: B 1117 VAL cc_start: 0.8912 (t) cc_final: 0.8693 (t) REVERT: B 1122 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 1134 PHE cc_start: 0.8497 (m-80) cc_final: 0.8020 (m-80) REVERT: B 1214 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7273 (mm) REVERT: B 1221 MET cc_start: 0.7625 (mmm) cc_final: 0.6549 (mmm) outliers start: 100 outliers final: 53 residues processed: 583 average time/residue: 0.2868 time to fit residues: 243.9076 Evaluate side-chains 581 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 512 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 377 LEU Chi-restraints excluded: chain A residue 418 THR 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 588 LYS 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 915 GLU 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 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 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 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 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 821 LEU Chi-restraints excluded: chain B residue 837 TYR 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 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 1094 VAL Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1161 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 66 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 943 ASN B 614 HIS B 917 GLN B 943 ASN B 955 ASN B1154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16254 Z= 0.227 Angle : 0.597 8.261 22062 Z= 0.311 Chirality : 0.042 0.151 2660 Planarity : 0.004 0.034 2752 Dihedral : 5.412 59.626 2244 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.60 % Allowed : 23.30 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 2050 helix: 1.95 (0.14), residues: 1444 sheet: 1.02 (0.59), residues: 96 loop : -1.61 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 643 HIS 0.005 0.001 HIS A 908 PHE 0.017 0.001 PHE B 248 TYR 0.010 0.001 TYR B1125 ARG 0.008 0.001 ARG B 605 *********************** 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 618 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 524 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8431 (mt) cc_final: 0.8076 (mm) REVERT: A 124 GLU cc_start: 0.7265 (tp30) cc_final: 0.6924 (tm-30) REVERT: A 129 ASP cc_start: 0.6459 (OUTLIER) cc_final: 0.6176 (p0) REVERT: A 137 VAL cc_start: 0.8196 (p) cc_final: 0.7969 (m) REVERT: A 140 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7940 (mp10) REVERT: A 149 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 154 MET cc_start: 0.8261 (tpp) cc_final: 0.7831 (ttm) REVERT: A 155 ASP cc_start: 0.8104 (t70) cc_final: 0.7726 (t70) REVERT: A 160 MET cc_start: 0.8318 (mmt) cc_final: 0.7940 (mmm) REVERT: A 184 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7945 (tp) REVERT: A 186 MET cc_start: 0.7548 (mtp) cc_final: 0.7293 (mtt) REVERT: A 191 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: A 199 MET cc_start: 0.8270 (mmm) cc_final: 0.7302 (tpp) REVERT: A 217 LEU cc_start: 0.8563 (mt) cc_final: 0.8299 (mm) REVERT: A 233 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 265 VAL cc_start: 0.8668 (t) cc_final: 0.8439 (p) REVERT: A 289 PHE cc_start: 0.8317 (t80) cc_final: 0.8071 (t80) REVERT: A 319 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8033 (mt) REVERT: A 337 GLU cc_start: 0.7942 (mp0) cc_final: 0.7506 (mp0) REVERT: A 346 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7590 (mt-10) REVERT: A 355 MET cc_start: 0.8414 (ttp) cc_final: 0.8070 (ttp) REVERT: A 372 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8557 (p) REVERT: A 377 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8453 (mp) REVERT: A 383 MET cc_start: 0.7286 (mmp) cc_final: 0.5923 (mmm) REVERT: A 387 TYR cc_start: 0.8196 (m-10) cc_final: 0.7574 (m-10) REVERT: A 398 ILE cc_start: 0.8610 (mt) cc_final: 0.8345 (mt) REVERT: A 484 SER cc_start: 0.8686 (p) cc_final: 0.8345 (t) REVERT: A 524 ASP cc_start: 0.7958 (m-30) cc_final: 0.7756 (m-30) REVERT: A 580 GLU cc_start: 0.7793 (tp30) cc_final: 0.7521 (tp30) REVERT: A 588 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7934 (ttpt) REVERT: A 599 GLU cc_start: 0.8206 (tp30) cc_final: 0.7785 (mp0) REVERT: A 622 LYS cc_start: 0.8704 (tppt) cc_final: 0.8396 (tppt) REVERT: A 630 ASP cc_start: 0.7408 (p0) cc_final: 0.7151 (p0) REVERT: A 632 LYS cc_start: 0.8536 (mtpm) cc_final: 0.8309 (mtpp) REVERT: A 958 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8314 (ttpp) REVERT: A 971 ASP cc_start: 0.8454 (m-30) cc_final: 0.8130 (m-30) REVERT: A 986 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7875 (mt-10) REVERT: A 987 VAL cc_start: 0.9076 (OUTLIER) cc_final: 0.8824 (m) REVERT: A 994 GLU cc_start: 0.8251 (mp0) cc_final: 0.7928 (mp0) REVERT: A 999 PHE cc_start: 0.7541 (m-80) cc_final: 0.6910 (m-80) REVERT: A 1044 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8252 (mt-10) REVERT: A 1060 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 1061 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8306 (p) REVERT: A 1067 PHE cc_start: 0.8121 (t80) cc_final: 0.7770 (t80) REVERT: A 1087 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 1098 ILE cc_start: 0.9013 (tt) cc_final: 0.8774 (tt) REVERT: A 1104 MET cc_start: 0.7760 (tpp) cc_final: 0.7514 (mmm) REVERT: A 1115 GLU cc_start: 0.8114 (tt0) cc_final: 0.7873 (tp30) REVERT: A 1122 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7724 (mm-30) REVERT: A 1134 PHE cc_start: 0.8484 (m-80) cc_final: 0.8070 (m-80) REVERT: A 1190 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7445 (mtt-85) REVERT: A 1202 ARG cc_start: 0.7088 (ttt-90) cc_final: 0.6880 (ttt-90) REVERT: B 79 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8398 (p) REVERT: B 93 SER cc_start: 0.8333 (m) cc_final: 0.7923 (p) REVERT: B 124 GLU cc_start: 0.7302 (tp30) cc_final: 0.6891 (tm-30) REVERT: B 133 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7470 (mtm) REVERT: B 149 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 154 MET cc_start: 0.8246 (tpp) cc_final: 0.7782 (ttm) REVERT: B 155 ASP cc_start: 0.8157 (p0) cc_final: 0.7757 (p0) REVERT: B 160 MET cc_start: 0.7811 (mmt) cc_final: 0.7451 (mmm) REVERT: B 179 VAL cc_start: 0.8324 (t) cc_final: 0.8081 (t) REVERT: B 231 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: B 233 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7556 (tm-30) REVERT: B 319 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8081 (mt) REVERT: B 383 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.5601 (mmt) REVERT: B 387 TYR cc_start: 0.8176 (m-10) cc_final: 0.7589 (m-10) REVERT: B 451 ILE cc_start: 0.8484 (tt) cc_final: 0.8153 (tt) REVERT: B 484 SER cc_start: 0.8699 (p) cc_final: 0.8461 (t) REVERT: B 485 ASP cc_start: 0.7948 (m-30) cc_final: 0.7693 (m-30) REVERT: B 577 ASP cc_start: 0.7667 (m-30) cc_final: 0.7374 (m-30) REVERT: B 588 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7955 (ttpm) REVERT: B 590 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8201 (mt-10) REVERT: B 595 TRP cc_start: 0.8799 (m100) cc_final: 0.8330 (m100) REVERT: B 626 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8070 (mt) REVERT: B 646 ARG cc_start: 0.6763 (ptp-170) cc_final: 0.6438 (ptp-170) REVERT: B 832 GLN cc_start: 0.8572 (tp40) cc_final: 0.8336 (tt0) REVERT: B 847 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7526 (mm-30) REVERT: B 940 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8660 (ttm-80) REVERT: B 967 MET cc_start: 0.8533 (mmp) cc_final: 0.8210 (mmp) REVERT: B 971 ASP cc_start: 0.8234 (m-30) cc_final: 0.7965 (m-30) REVERT: B 976 ARG cc_start: 0.7948 (mtt90) cc_final: 0.7619 (ttm-80) REVERT: B 983 ASP cc_start: 0.8358 (p0) cc_final: 0.8146 (p0) REVERT: B 986 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8002 (mt-10) REVERT: B 987 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8794 (m) REVERT: B 1051 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8460 (mtpp) REVERT: B 1061 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8147 (p) REVERT: B 1067 PHE cc_start: 0.8103 (t80) cc_final: 0.7715 (t80) REVERT: B 1098 ILE cc_start: 0.9063 (tt) cc_final: 0.8662 (tp) REVERT: B 1104 MET cc_start: 0.7686 (tpp) cc_final: 0.7477 (tpp) REVERT: B 1117 VAL cc_start: 0.8892 (t) cc_final: 0.8596 (t) REVERT: B 1122 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 1134 PHE cc_start: 0.8544 (m-80) cc_final: 0.8097 (m-10) REVERT: B 1214 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7200 (mm) REVERT: B 1221 MET cc_start: 0.7737 (mmm) cc_final: 0.6694 (mmm) outliers start: 94 outliers final: 62 residues processed: 561 average time/residue: 0.2928 time to fit residues: 240.8521 Evaluate side-chains 598 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 516 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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 194 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 418 THR 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 621 GLU Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 855 ASP 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 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 1061 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1114 GLN Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 383 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 884 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain B residue 1038 VAL Chi-restraints excluded: chain B residue 1050 LYS Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1077 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1142 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 198 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 121 optimal weight: 0.2980 chunk 91 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 ASN B 614 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5908 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= 0.193 Angle : 0.593 9.500 22062 Z= 0.305 Chirality : 0.041 0.153 2660 Planarity : 0.004 0.031 2752 Dihedral : 5.392 59.862 2244 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.72 % Allowed : 23.54 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.19), residues: 2050 helix: 2.06 (0.14), residues: 1442 sheet: 0.92 (0.58), residues: 96 loop : -1.57 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 643 HIS 0.005 0.001 HIS A 908 PHE 0.023 0.001 PHE B 972 TYR 0.010 0.001 TYR A1125 ARG 0.007 0.000 ARG B 605 *********************** 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 598 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 502 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8402 (mt) cc_final: 0.8046 (mm) REVERT: A 124 GLU cc_start: 0.7315 (tp30) cc_final: 0.6923 (tm-30) REVERT: A 129 ASP cc_start: 0.6424 (OUTLIER) cc_final: 0.6152 (p0) REVERT: A 133 MET cc_start: 0.8015 (ttm) cc_final: 0.7272 (mtm) REVERT: A 137 VAL cc_start: 0.8127 (p) cc_final: 0.7838 (m) REVERT: A 140 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7951 (mp10) REVERT: A 149 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7515 (tp30) REVERT: A 154 MET cc_start: 0.8258 (tpp) cc_final: 0.7949 (tpp) REVERT: A 155 ASP cc_start: 0.8113 (t70) cc_final: 0.7721 (t70) REVERT: A 160 MET cc_start: 0.8328 (mmt) cc_final: 0.7952 (mmm) REVERT: A 184 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7893 (tp) REVERT: A 186 MET cc_start: 0.7531 (mtp) cc_final: 0.7276 (mtt) REVERT: A 191 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: A 217 LEU cc_start: 0.8584 (mt) cc_final: 0.8307 (mm) REVERT: A 233 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 249 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8046 (ttp) REVERT: A 266 LEU cc_start: 0.8104 (tp) cc_final: 0.7780 (tp) REVERT: A 289 PHE cc_start: 0.8326 (t80) cc_final: 0.8043 (t80) REVERT: A 319 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7895 (mp) REVERT: A 337 GLU cc_start: 0.7947 (mp0) cc_final: 0.7500 (mp0) REVERT: A 346 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7583 (mt-10) REVERT: A 355 MET cc_start: 0.8408 (ttp) cc_final: 0.8059 (ttp) REVERT: A 372 VAL cc_start: 0.8795 (p) cc_final: 0.8548 (p) REVERT: A 377 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8449 (mp) REVERT: A 383 MET cc_start: 0.7268 (mmp) cc_final: 0.5998 (mmm) REVERT: A 387 TYR cc_start: 0.8184 (m-10) cc_final: 0.7409 (m-10) REVERT: A 398 ILE cc_start: 0.8619 (mt) cc_final: 0.8338 (mt) REVERT: A 427 TRP cc_start: 0.8817 (t-100) cc_final: 0.8526 (t-100) REVERT: A 484 SER cc_start: 0.8678 (p) cc_final: 0.8405 (t) REVERT: A 552 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7797 (tt) REVERT: A 580 GLU cc_start: 0.7771 (tp30) cc_final: 0.7504 (tp30) REVERT: A 588 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7917 (tttt) REVERT: A 622 LYS cc_start: 0.8658 (tppt) cc_final: 0.8360 (tppt) REVERT: A 630 ASP cc_start: 0.7480 (p0) cc_final: 0.7169 (p0) REVERT: A 632 LYS cc_start: 0.8568 (mtpm) cc_final: 0.8326 (mtpp) REVERT: A 646 ARG cc_start: 0.6815 (ptp90) cc_final: 0.6409 (ptp90) REVERT: A 943 ASN cc_start: 0.8327 (m-40) cc_final: 0.7982 (p0) REVERT: A 986 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 987 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8818 (m) REVERT: A 999 PHE cc_start: 0.7488 (m-80) cc_final: 0.6821 (m-80) REVERT: A 1060 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 1061 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8305 (p) REVERT: A 1067 PHE cc_start: 0.8204 (t80) cc_final: 0.7841 (t80) REVERT: A 1098 ILE cc_start: 0.9000 (tt) cc_final: 0.8765 (tt) REVERT: A 1104 MET cc_start: 0.7747 (tpp) cc_final: 0.7405 (mmm) REVERT: A 1115 GLU cc_start: 0.8084 (tt0) cc_final: 0.7851 (tp30) REVERT: A 1134 PHE cc_start: 0.8515 (m-80) cc_final: 0.8104 (m-80) REVERT: A 1170 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8261 (t) REVERT: A 1190 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7433 (mtt-85) REVERT: B 79 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8388 (p) REVERT: B 93 SER cc_start: 0.8284 (m) cc_final: 0.7865 (p) REVERT: B 124 GLU cc_start: 0.7250 (tp30) cc_final: 0.6855 (tm-30) REVERT: B 154 MET cc_start: 0.8225 (tpp) cc_final: 0.7769 (ttm) REVERT: B 155 ASP cc_start: 0.8140 (p0) cc_final: 0.7748 (p0) REVERT: B 160 MET cc_start: 0.7863 (mmt) cc_final: 0.7482 (mmm) REVERT: B 197 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: B 231 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: B 233 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7542 (tm-30) REVERT: B 253 PHE cc_start: 0.8044 (m-10) cc_final: 0.7722 (m-80) REVERT: B 300 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 319 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8015 (mt) REVERT: B 383 MET cc_start: 0.6583 (mmt) cc_final: 0.5586 (mmt) REVERT: B 386 PHE cc_start: 0.8268 (t80) cc_final: 0.8031 (t80) REVERT: B 387 TYR cc_start: 0.8180 (m-10) cc_final: 0.7566 (m-10) REVERT: B 484 SER cc_start: 0.8688 (p) cc_final: 0.8456 (t) REVERT: B 485 ASP cc_start: 0.7981 (m-30) cc_final: 0.7736 (m-30) REVERT: B 577 ASP cc_start: 0.7694 (m-30) cc_final: 0.7371 (m-30) REVERT: B 588 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7905 (ttpm) REVERT: B 595 TRP cc_start: 0.8791 (m100) cc_final: 0.8336 (m100) REVERT: B 600 HIS cc_start: 0.8198 (m90) cc_final: 0.7937 (m-70) REVERT: B 626 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8131 (mt) REVERT: B 646 ARG cc_start: 0.6787 (ptp-170) cc_final: 0.6464 (ptp-170) REVERT: B 832 GLN cc_start: 0.8571 (tp40) cc_final: 0.8348 (tt0) REVERT: B 847 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7875 (mm-30) REVERT: B 876 LEU cc_start: 0.8731 (mt) cc_final: 0.8528 (mp) REVERT: B 940 ARG cc_start: 0.8900 (tpp80) cc_final: 0.8666 (ttm-80) REVERT: B 967 MET cc_start: 0.8483 (mmp) cc_final: 0.8170 (mmp) REVERT: B 971 ASP cc_start: 0.8196 (m-30) cc_final: 0.7899 (m-30) REVERT: B 976 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7604 (ttm170) REVERT: B 983 ASP cc_start: 0.8355 (p0) cc_final: 0.8104 (p0) REVERT: B 986 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7984 (mt-10) REVERT: B 987 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8790 (m) REVERT: B 994 GLU cc_start: 0.8173 (mp0) cc_final: 0.7905 (mp0) REVERT: B 1044 GLU cc_start: 0.8388 (mp0) cc_final: 0.8145 (mp0) REVERT: B 1051 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8424 (mtpp) REVERT: B 1060 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7488 (mm-30) REVERT: B 1061 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8215 (p) REVERT: B 1067 PHE cc_start: 0.8114 (t80) cc_final: 0.7694 (t80) REVERT: B 1072 ASP cc_start: 0.7813 (m-30) cc_final: 0.7391 (m-30) REVERT: B 1098 ILE cc_start: 0.9070 (tt) cc_final: 0.8663 (tp) REVERT: B 1104 MET cc_start: 0.7673 (tpp) cc_final: 0.7470 (tpp) REVERT: B 1117 VAL cc_start: 0.8876 (t) cc_final: 0.8578 (t) REVERT: B 1122 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 1172 HIS cc_start: 0.7711 (t-170) cc_final: 0.7276 (t-170) REVERT: B 1214 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7187 (mm) REVERT: B 1221 MET cc_start: 0.7731 (mmm) cc_final: 0.6814 (mmm) outliers start: 96 outliers final: 60 residues processed: 541 average time/residue: 0.2801 time to fit residues: 221.1968 Evaluate side-chains 579 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 499 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 249 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 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 624 GLN Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 822 ILE 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 1127 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain 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 186 MET Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 197 GLU 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 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 817 LEU Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 884 LEU 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 1033 GLU 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 1094 VAL Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1142 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 98 optimal weight: 0.0670 chunk 18 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16254 Z= 0.200 Angle : 0.591 9.296 22062 Z= 0.306 Chirality : 0.041 0.169 2660 Planarity : 0.004 0.066 2752 Dihedral : 5.347 59.405 2244 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.18 % Allowed : 24.08 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.19), residues: 2050 helix: 2.07 (0.14), residues: 1438 sheet: 0.90 (0.59), residues: 96 loop : -1.50 (0.27), residues: 516 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 0.016 0.001 PHE B 248 TYR 0.013 0.001 TYR B 280 ARG 0.012 0.000 ARG A1092 *********************** 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 587 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 500 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8408 (mt) cc_final: 0.8048 (mm) REVERT: A 124 GLU cc_start: 0.7282 (tp30) cc_final: 0.6890 (tm-30) REVERT: A 129 ASP cc_start: 0.6437 (OUTLIER) cc_final: 0.6169 (p0) REVERT: A 133 MET cc_start: 0.8023 (ttm) cc_final: 0.7263 (mtm) REVERT: A 137 VAL cc_start: 0.8130 (p) cc_final: 0.7860 (m) REVERT: A 149 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7514 (tp30) REVERT: A 154 MET cc_start: 0.8259 (tpp) cc_final: 0.7889 (ttm) REVERT: A 155 ASP cc_start: 0.8119 (t70) cc_final: 0.7719 (t70) REVERT: A 160 MET cc_start: 0.8356 (mmt) cc_final: 0.7945 (mmm) REVERT: A 184 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7894 (tp) REVERT: A 186 MET cc_start: 0.7524 (mtp) cc_final: 0.7295 (mtt) REVERT: A 217 LEU cc_start: 0.8623 (mt) cc_final: 0.8345 (mm) REVERT: A 233 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 249 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8085 (ttp) REVERT: A 266 LEU cc_start: 0.8181 (tp) cc_final: 0.7845 (tp) REVERT: A 289 PHE cc_start: 0.8333 (t80) cc_final: 0.8054 (t80) REVERT: A 319 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7715 (mt) REVERT: A 337 GLU cc_start: 0.7911 (mp0) cc_final: 0.7512 (mp0) REVERT: A 346 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7506 (mt-10) REVERT: A 355 MET cc_start: 0.8410 (ttp) cc_final: 0.8065 (ttp) REVERT: A 366 MET cc_start: 0.8612 (mmm) cc_final: 0.8358 (mmt) REVERT: A 372 VAL cc_start: 0.8805 (p) cc_final: 0.8569 (p) REVERT: A 377 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8440 (mp) REVERT: A 383 MET cc_start: 0.7320 (mmp) cc_final: 0.5988 (mmm) REVERT: A 387 TYR cc_start: 0.8223 (m-10) cc_final: 0.7310 (m-10) REVERT: A 398 ILE cc_start: 0.8652 (mt) cc_final: 0.8303 (mp) REVERT: A 484 SER cc_start: 0.8700 (p) cc_final: 0.8388 (t) REVERT: A 580 GLU cc_start: 0.7843 (tp30) cc_final: 0.7589 (tp30) REVERT: A 588 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7959 (tttm) REVERT: A 622 LYS cc_start: 0.8603 (tppt) cc_final: 0.8304 (tppt) REVERT: A 630 ASP cc_start: 0.7562 (p0) cc_final: 0.7237 (p0) REVERT: A 632 LYS cc_start: 0.8546 (mtpm) cc_final: 0.8297 (mtpp) REVERT: A 646 ARG cc_start: 0.6835 (ptp90) cc_final: 0.6608 (ptp90) REVERT: A 943 ASN cc_start: 0.8432 (m-40) cc_final: 0.8076 (p0) REVERT: A 986 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7813 (mt-10) REVERT: A 987 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8826 (m) REVERT: A 999 PHE cc_start: 0.7493 (m-80) cc_final: 0.6868 (m-80) REVERT: A 1060 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 1061 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8289 (p) REVERT: A 1067 PHE cc_start: 0.8253 (t80) cc_final: 0.7809 (t80) REVERT: A 1098 ILE cc_start: 0.9022 (tt) cc_final: 0.8777 (tt) REVERT: A 1104 MET cc_start: 0.7751 (tpp) cc_final: 0.7380 (mmm) REVERT: A 1115 GLU cc_start: 0.8128 (tt0) cc_final: 0.7892 (tp30) REVERT: A 1134 PHE cc_start: 0.8553 (m-80) cc_final: 0.8124 (m-80) REVERT: A 1170 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8264 (t) REVERT: A 1190 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7496 (mtt-85) REVERT: A 1202 ARG cc_start: 0.7050 (ttt-90) cc_final: 0.6328 (ptt-90) REVERT: B 79 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8400 (p) REVERT: B 93 SER cc_start: 0.8270 (m) cc_final: 0.7840 (p) REVERT: B 124 GLU cc_start: 0.7264 (tp30) cc_final: 0.6874 (tm-30) REVERT: B 154 MET cc_start: 0.8247 (tpp) cc_final: 0.7795 (ttm) REVERT: B 155 ASP cc_start: 0.8120 (p0) cc_final: 0.7693 (p0) REVERT: B 231 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: B 233 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 319 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8011 (mt) REVERT: B 386 PHE cc_start: 0.8293 (t80) cc_final: 0.8016 (t80) REVERT: B 387 TYR cc_start: 0.8219 (m-10) cc_final: 0.7579 (m-10) REVERT: B 484 SER cc_start: 0.8683 (p) cc_final: 0.8453 (t) REVERT: B 485 ASP cc_start: 0.7999 (m-30) cc_final: 0.7767 (m-30) REVERT: B 499 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7755 (ttm-80) REVERT: B 580 GLU cc_start: 0.7864 (tp30) cc_final: 0.7347 (tp30) REVERT: B 588 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7932 (ttpm) REVERT: B 595 TRP cc_start: 0.8798 (m100) cc_final: 0.8338 (m100) REVERT: B 626 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8128 (mt) REVERT: B 630 ASP cc_start: 0.7752 (p0) cc_final: 0.7220 (p0) REVERT: B 646 ARG cc_start: 0.6886 (ptp-170) cc_final: 0.6596 (ptp-170) REVERT: B 832 GLN cc_start: 0.8565 (tp40) cc_final: 0.8360 (tt0) REVERT: B 847 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7813 (mm-30) REVERT: B 876 LEU cc_start: 0.8748 (mt) cc_final: 0.8520 (mp) REVERT: B 940 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8558 (ttm-80) REVERT: B 943 ASN cc_start: 0.8321 (m-40) cc_final: 0.7905 (p0) REVERT: B 967 MET cc_start: 0.8495 (mmp) cc_final: 0.8112 (mmp) REVERT: B 971 ASP cc_start: 0.8142 (m-30) cc_final: 0.7853 (m-30) REVERT: B 976 ARG cc_start: 0.7949 (mtt90) cc_final: 0.7639 (ttm170) REVERT: B 983 ASP cc_start: 0.8327 (p0) cc_final: 0.8095 (p0) REVERT: B 986 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 994 GLU cc_start: 0.8233 (mp0) cc_final: 0.7877 (mp0) REVERT: B 999 PHE cc_start: 0.7700 (m-80) cc_final: 0.7118 (m-80) REVERT: B 1051 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8438 (mtpp) REVERT: B 1060 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 1061 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8153 (p) REVERT: B 1067 PHE cc_start: 0.8025 (t80) cc_final: 0.7682 (t80) REVERT: B 1072 ASP cc_start: 0.7830 (m-30) cc_final: 0.7454 (m-30) REVERT: B 1098 ILE cc_start: 0.9063 (tt) cc_final: 0.8631 (tp) REVERT: B 1117 VAL cc_start: 0.8876 (t) cc_final: 0.8579 (t) REVERT: B 1122 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 1172 HIS cc_start: 0.7670 (t-170) cc_final: 0.7252 (t-170) REVERT: B 1214 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7167 (mm) REVERT: B 1221 MET cc_start: 0.7789 (mmm) cc_final: 0.6851 (mmm) outliers start: 87 outliers final: 51 residues processed: 534 average time/residue: 0.2859 time to fit residues: 221.8508 Evaluate side-chains 561 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 494 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 105 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 405 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 626 ILE Chi-restraints excluded: chain A residue 647 LYS 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 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain 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 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 377 LEU Chi-restraints excluded: chain B residue 448 ASN 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 884 LEU Chi-restraints excluded: chain B residue 963 LEU 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 1077 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1142 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 180 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 174 optimal weight: 0.7980 chunk 184 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 HIS B 917 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16254 Z= 0.212 Angle : 0.610 9.672 22062 Z= 0.312 Chirality : 0.041 0.164 2660 Planarity : 0.004 0.050 2752 Dihedral : 5.221 59.688 2240 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.95 % Allowed : 24.37 % Favored : 70.68 % 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: 1.75 (0.19), residues: 2050 helix: 2.06 (0.14), residues: 1438 sheet: 0.89 (0.59), residues: 96 loop : -1.47 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.005 0.001 HIS A 908 PHE 0.021 0.001 PHE B 253 TYR 0.016 0.001 TYR B1178 ARG 0.004 0.000 ARG B 161 *********************** 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 582 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 499 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8425 (mt) cc_final: 0.8062 (mm) REVERT: A 124 GLU cc_start: 0.7305 (tp30) cc_final: 0.6940 (tm-30) REVERT: A 129 ASP cc_start: 0.6441 (OUTLIER) cc_final: 0.6168 (p0) REVERT: A 133 MET cc_start: 0.8024 (ttm) cc_final: 0.7301 (mtm) REVERT: A 137 VAL cc_start: 0.8171 (p) cc_final: 0.7910 (m) REVERT: A 149 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7509 (tp30) REVERT: A 154 MET cc_start: 0.8264 (tpp) cc_final: 0.7899 (ttm) REVERT: A 155 ASP cc_start: 0.8111 (t70) cc_final: 0.7693 (t70) REVERT: A 160 MET cc_start: 0.8382 (mmt) cc_final: 0.8006 (mmm) REVERT: A 184 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7825 (tp) REVERT: A 186 MET cc_start: 0.7559 (mtp) cc_final: 0.7323 (mtt) REVERT: A 217 LEU cc_start: 0.8637 (mt) cc_final: 0.8350 (mm) REVERT: A 233 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7587 (tt0) REVERT: A 249 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8088 (ttp) REVERT: A 266 LEU cc_start: 0.8204 (tp) cc_final: 0.7897 (tp) REVERT: A 289 PHE cc_start: 0.8336 (t80) cc_final: 0.8061 (t80) REVERT: A 319 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7797 (mt) REVERT: A 337 GLU cc_start: 0.7900 (mp0) cc_final: 0.7502 (mp0) REVERT: A 355 MET cc_start: 0.8417 (ttp) cc_final: 0.8070 (ttp) REVERT: A 366 MET cc_start: 0.8607 (mmm) cc_final: 0.8361 (mmt) REVERT: A 372 VAL cc_start: 0.8805 (p) cc_final: 0.8570 (p) REVERT: A 377 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8437 (mp) REVERT: A 387 TYR cc_start: 0.8258 (m-10) cc_final: 0.7462 (m-80) REVERT: A 398 ILE cc_start: 0.8683 (mt) cc_final: 0.8319 (mp) REVERT: A 531 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7507 (tp30) REVERT: A 580 GLU cc_start: 0.7894 (tp30) cc_final: 0.7680 (tp30) REVERT: A 622 LYS cc_start: 0.8531 (tppt) cc_final: 0.8277 (tppt) REVERT: A 630 ASP cc_start: 0.7615 (p0) cc_final: 0.7304 (p0) REVERT: A 632 LYS cc_start: 0.8583 (mtpm) cc_final: 0.8313 (mtpp) REVERT: A 646 ARG cc_start: 0.6966 (ptp90) cc_final: 0.6612 (ptp90) REVERT: A 943 ASN cc_start: 0.8412 (m-40) cc_final: 0.8076 (p0) REVERT: A 957 LEU cc_start: 0.8605 (tp) cc_final: 0.8222 (mp) REVERT: A 986 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7929 (mt-10) REVERT: A 987 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8838 (m) REVERT: A 994 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 999 PHE cc_start: 0.7486 (m-80) cc_final: 0.6977 (m-80) REVERT: A 1067 PHE cc_start: 0.8271 (t80) cc_final: 0.7867 (t80) REVERT: A 1073 MET cc_start: 0.8663 (mmm) cc_final: 0.8353 (mmm) REVERT: A 1104 MET cc_start: 0.7736 (tpp) cc_final: 0.7385 (mmm) REVERT: A 1115 GLU cc_start: 0.8083 (tt0) cc_final: 0.7860 (tp30) REVERT: A 1134 PHE cc_start: 0.8544 (m-80) cc_final: 0.8149 (m-80) REVERT: A 1170 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8233 (t) REVERT: B 79 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8407 (p) REVERT: B 93 SER cc_start: 0.8366 (m) cc_final: 0.7922 (p) REVERT: B 124 GLU cc_start: 0.7289 (tp30) cc_final: 0.6877 (tm-30) REVERT: B 154 MET cc_start: 0.8251 (tpp) cc_final: 0.7800 (ttm) REVERT: B 155 ASP cc_start: 0.8120 (p0) cc_final: 0.7698 (p0) REVERT: B 160 MET cc_start: 0.8188 (mmt) cc_final: 0.7814 (mmm) REVERT: B 231 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: B 233 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7538 (tm-30) REVERT: B 265 VAL cc_start: 0.8644 (p) cc_final: 0.8398 (p) REVERT: B 266 LEU cc_start: 0.8254 (tp) cc_final: 0.7939 (tp) REVERT: B 319 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7968 (mt) REVERT: B 386 PHE cc_start: 0.8296 (t80) cc_final: 0.8038 (t80) REVERT: B 387 TYR cc_start: 0.8246 (m-10) cc_final: 0.7540 (m-10) REVERT: B 484 SER cc_start: 0.8680 (p) cc_final: 0.8449 (t) REVERT: B 485 ASP cc_start: 0.8007 (m-30) cc_final: 0.7789 (m-30) REVERT: B 499 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7751 (ttm-80) REVERT: B 580 GLU cc_start: 0.7893 (tp30) cc_final: 0.7367 (tp30) REVERT: B 588 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7937 (ttpm) REVERT: B 595 TRP cc_start: 0.8805 (m100) cc_final: 0.8347 (m100) REVERT: B 626 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8145 (mt) REVERT: B 630 ASP cc_start: 0.7773 (p0) cc_final: 0.7228 (p0) REVERT: B 646 ARG cc_start: 0.7026 (ptp-170) cc_final: 0.6731 (ptp-170) REVERT: B 847 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7906 (mm-30) REVERT: B 876 LEU cc_start: 0.8756 (mt) cc_final: 0.8532 (mp) REVERT: B 940 ARG cc_start: 0.8920 (tpp80) cc_final: 0.8567 (ttm-80) REVERT: B 943 ASN cc_start: 0.8325 (m-40) cc_final: 0.7930 (p0) REVERT: B 967 MET cc_start: 0.8433 (mmp) cc_final: 0.8051 (mmp) REVERT: B 971 ASP cc_start: 0.8115 (m-30) cc_final: 0.7804 (m-30) REVERT: B 976 ARG cc_start: 0.7952 (mtt90) cc_final: 0.7615 (ttm170) REVERT: B 983 ASP cc_start: 0.8321 (p0) cc_final: 0.8070 (p0) REVERT: B 986 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7929 (mt-10) REVERT: B 994 GLU cc_start: 0.8202 (mp0) cc_final: 0.7924 (mp0) REVERT: B 1047 VAL cc_start: 0.8714 (p) cc_final: 0.8510 (t) REVERT: B 1051 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8436 (mtpp) REVERT: B 1060 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 1061 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8216 (p) REVERT: B 1067 PHE cc_start: 0.8045 (t80) cc_final: 0.7698 (t80) REVERT: B 1072 ASP cc_start: 0.7825 (m-30) cc_final: 0.7438 (m-30) REVERT: B 1098 ILE cc_start: 0.9068 (tt) cc_final: 0.8634 (tp) REVERT: B 1122 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 1172 HIS cc_start: 0.7622 (t-170) cc_final: 0.7166 (t-170) REVERT: B 1221 MET cc_start: 0.7827 (mmm) cc_final: 0.6896 (mmm) outliers start: 83 outliers final: 61 residues processed: 533 average time/residue: 0.2930 time to fit residues: 227.6820 Evaluate side-chains 567 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 492 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 105 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 249 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 405 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 626 ILE 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 1066 TYR Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1212 ILE 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 129 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 448 ASN 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 584 LEU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 884 LEU 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 1077 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1142 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 205 optimal weight: 20.0000 chunk 188 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1154 ASN B 237 ASN B 917 GLN ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.6488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16254 Z= 0.215 Angle : 0.614 9.898 22062 Z= 0.315 Chirality : 0.041 0.185 2660 Planarity : 0.004 0.046 2752 Dihedral : 5.213 58.963 2240 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.83 % Allowed : 24.91 % Favored : 70.26 % 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: 1.75 (0.19), residues: 2050 helix: 2.07 (0.14), residues: 1438 sheet: 0.89 (0.64), residues: 76 loop : -1.39 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.005 0.001 HIS A 908 PHE 0.016 0.001 PHE B 253 TYR 0.017 0.001 TYR B 280 ARG 0.007 0.000 ARG A1190 ********************** 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 581 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 500 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8423 (mt) cc_final: 0.8061 (mm) REVERT: A 124 GLU cc_start: 0.7326 (tp30) cc_final: 0.6957 (tm-30) REVERT: A 129 ASP cc_start: 0.6414 (OUTLIER) cc_final: 0.6140 (p0) REVERT: A 133 MET cc_start: 0.8036 (ttm) cc_final: 0.7313 (mtm) REVERT: A 137 VAL cc_start: 0.8173 (p) cc_final: 0.7911 (m) REVERT: A 149 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7511 (tp30) REVERT: A 154 MET cc_start: 0.8265 (tpp) cc_final: 0.7916 (ttm) REVERT: A 155 ASP cc_start: 0.8093 (t70) cc_final: 0.7731 (t70) REVERT: A 160 MET cc_start: 0.8392 (mmt) cc_final: 0.8016 (mmm) REVERT: A 184 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7860 (tp) REVERT: A 186 MET cc_start: 0.7564 (mtp) cc_final: 0.7332 (mtt) REVERT: A 217 LEU cc_start: 0.8661 (mt) cc_final: 0.8362 (mm) REVERT: A 233 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7686 (tt0) REVERT: A 249 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8101 (ttp) REVERT: A 266 LEU cc_start: 0.8262 (tp) cc_final: 0.7963 (tp) REVERT: A 289 PHE cc_start: 0.8341 (t80) cc_final: 0.8107 (t80) REVERT: A 319 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7732 (mt) REVERT: A 337 GLU cc_start: 0.7954 (mp0) cc_final: 0.7541 (mp0) REVERT: A 355 MET cc_start: 0.8415 (ttp) cc_final: 0.8071 (ttp) REVERT: A 366 MET cc_start: 0.8606 (mmm) cc_final: 0.8369 (mmt) REVERT: A 372 VAL cc_start: 0.8817 (p) cc_final: 0.8580 (p) REVERT: A 377 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 387 TYR cc_start: 0.8269 (m-10) cc_final: 0.7505 (m-10) REVERT: A 398 ILE cc_start: 0.8674 (mt) cc_final: 0.8304 (mp) REVERT: A 427 TRP cc_start: 0.8836 (t-100) cc_final: 0.8510 (t-100) REVERT: A 484 SER cc_start: 0.8707 (p) cc_final: 0.8411 (t) REVERT: A 531 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7507 (tp30) REVERT: A 580 GLU cc_start: 0.7936 (tp30) cc_final: 0.7382 (tp30) REVERT: A 629 ASP cc_start: 0.7843 (m-30) cc_final: 0.7572 (m-30) REVERT: A 630 ASP cc_start: 0.7692 (p0) cc_final: 0.7363 (p0) REVERT: A 632 LYS cc_start: 0.8612 (mtpm) cc_final: 0.8408 (mtpp) REVERT: A 861 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7756 (mmtp) REVERT: A 872 GLU cc_start: 0.8154 (tp30) cc_final: 0.7925 (tp30) REVERT: A 943 ASN cc_start: 0.8443 (m-40) cc_final: 0.8103 (p0) REVERT: A 957 LEU cc_start: 0.8607 (tp) cc_final: 0.8197 (mp) REVERT: A 986 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7925 (mt-10) REVERT: A 987 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8834 (m) REVERT: A 994 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 999 PHE cc_start: 0.7485 (m-80) cc_final: 0.7056 (m-80) REVERT: A 1067 PHE cc_start: 0.8277 (t80) cc_final: 0.7908 (t80) REVERT: A 1094 VAL cc_start: 0.8635 (m) cc_final: 0.8432 (p) REVERT: A 1104 MET cc_start: 0.7750 (tpp) cc_final: 0.7415 (mmm) REVERT: A 1115 GLU cc_start: 0.8075 (tt0) cc_final: 0.7848 (tp30) REVERT: A 1134 PHE cc_start: 0.8557 (m-80) cc_final: 0.8162 (m-10) REVERT: A 1170 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8226 (t) REVERT: A 1202 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6366 (ptt-90) REVERT: B 79 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8406 (p) REVERT: B 93 SER cc_start: 0.8341 (m) cc_final: 0.7895 (p) REVERT: B 124 GLU cc_start: 0.7319 (tp30) cc_final: 0.6906 (tm-30) REVERT: B 154 MET cc_start: 0.8254 (tpp) cc_final: 0.7808 (ttm) REVERT: B 155 ASP cc_start: 0.8108 (p0) cc_final: 0.7707 (p0) REVERT: B 160 MET cc_start: 0.8242 (mmt) cc_final: 0.7957 (mmm) REVERT: B 161 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.8107 (mtm-85) REVERT: B 223 SER cc_start: 0.7768 (m) cc_final: 0.7445 (p) REVERT: B 231 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: B 233 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7505 (tm-30) REVERT: B 265 VAL cc_start: 0.8700 (p) cc_final: 0.8459 (p) REVERT: B 319 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7932 (mt) REVERT: B 387 TYR cc_start: 0.8262 (m-10) cc_final: 0.7605 (m-10) REVERT: B 477 LEU cc_start: 0.8613 (tp) cc_final: 0.8349 (tp) REVERT: B 484 SER cc_start: 0.8690 (p) cc_final: 0.8470 (t) REVERT: B 485 ASP cc_start: 0.8030 (m-30) cc_final: 0.7733 (m-30) REVERT: B 499 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7729 (ttm-80) REVERT: B 580 GLU cc_start: 0.7943 (tp30) cc_final: 0.7592 (tp30) REVERT: B 588 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7956 (ttpm) REVERT: B 595 TRP cc_start: 0.8810 (m100) cc_final: 0.8355 (m100) REVERT: B 623 ASP cc_start: 0.8603 (m-30) cc_final: 0.8399 (t0) REVERT: B 626 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8127 (mt) REVERT: B 630 ASP cc_start: 0.7802 (p0) cc_final: 0.7253 (p0) REVERT: B 646 ARG cc_start: 0.7121 (ptp-170) cc_final: 0.6838 (ptp-170) REVERT: B 847 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 940 ARG cc_start: 0.8921 (tpp80) cc_final: 0.8507 (ttm110) REVERT: B 943 ASN cc_start: 0.8339 (m-40) cc_final: 0.7944 (p0) REVERT: B 967 MET cc_start: 0.8425 (mmp) cc_final: 0.8055 (mmp) REVERT: B 971 ASP cc_start: 0.8074 (m-30) cc_final: 0.7753 (m-30) REVERT: B 983 ASP cc_start: 0.8321 (p0) cc_final: 0.8094 (p0) REVERT: B 986 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 994 GLU cc_start: 0.8205 (mp0) cc_final: 0.7923 (mp0) REVERT: B 1044 GLU cc_start: 0.8465 (mp0) cc_final: 0.8115 (mt-10) REVERT: B 1047 VAL cc_start: 0.8686 (p) cc_final: 0.8480 (t) REVERT: B 1051 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8432 (mtpp) REVERT: B 1060 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7586 (mm-30) REVERT: B 1061 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8184 (p) REVERT: B 1079 THR cc_start: 0.8803 (m) cc_final: 0.8511 (m) REVERT: B 1098 ILE cc_start: 0.9064 (tt) cc_final: 0.8638 (tp) REVERT: B 1122 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7674 (mm-30) REVERT: B 1172 HIS cc_start: 0.7629 (t-170) cc_final: 0.7234 (t-170) REVERT: B 1221 MET cc_start: 0.7838 (mmm) cc_final: 0.6914 (mmm) outliers start: 81 outliers final: 61 residues processed: 533 average time/residue: 0.2955 time to fit residues: 229.3319 Evaluate side-chains 573 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 497 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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 105 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 249 MET Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 405 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 626 ILE 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 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 1066 TYR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1202 ARG Chi-restraints excluded: chain A residue 1212 ILE 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 129 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 448 ASN 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 584 LEU Chi-restraints excluded: chain B residue 588 LYS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 862 LYS Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 1033 GLU 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 1094 VAL Chi-restraints excluded: chain B residue 1142 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 0.3980 chunk 174 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 163 optimal weight: 8.9990 chunk 68 optimal weight: 0.3980 chunk 168 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 GLN A1154 ASN B 917 GLN ** B 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117067 restraints weight = 24483.559| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.14 r_work: 0.3393 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16254 Z= 0.200 Angle : 0.616 9.438 22062 Z= 0.315 Chirality : 0.041 0.184 2660 Planarity : 0.004 0.057 2752 Dihedral : 5.200 59.513 2240 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.83 % Allowed : 25.27 % Favored : 69.90 % 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: 1434 sheet: 0.98 (0.65), residues: 76 loop : -1.37 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.004 0.001 HIS A 908 PHE 0.015 0.001 PHE B 248 TYR 0.018 0.001 TYR B 280 ARG 0.009 0.001 ARG A 887 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4649.14 seconds wall clock time: 82 minutes 54.95 seconds (4974.95 seconds total)