Starting phenix.real_space_refine on Thu Jul 31 04:33:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kyc_23075/07_2025/7kyc_23075.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kyc_23075/07_2025/7kyc_23075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kyc_23075/07_2025/7kyc_23075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kyc_23075/07_2025/7kyc_23075.map" model { file = "/net/cci-nas-00/data/ceres_data/7kyc_23075/07_2025/7kyc_23075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kyc_23075/07_2025/7kyc_23075.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 61 5.16 5 Be 1 3.05 5 C 8188 2.51 5 N 2080 2.21 5 O 2360 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 151 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12697 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9409 Classifications: {'peptide': 1178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 1138} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3004 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {' MG': 1, 'BEF': 1, 'POV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.89, per 1000 atoms: 0.62 Number of scatterers: 12697 At special positions: 0 Unit cell: (134.638, 121.422, 132.986, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 61 16.00 P 3 15.00 Mg 1 11.99 F 3 9.00 O 2360 8.00 N 2080 7.00 C 8188 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-4 " NAG C 2 " - " MAN C 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B1001 " - " ASN B 298 " " NAG B1002 " - " ASN B 113 " " NAG C 1 " - " ASN B 240 " " NAG D 1 " - " ASN B 256 " " NAG E 1 " - " ASN B 332 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.8 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 49.2% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.547A pdb=" N VAL A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 274 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 536 removed outlier: 3.907A pdb=" N GLY A 536 " --> pdb=" O MET A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 577 removed outlier: 3.578A pdb=" N ARG A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 577 " --> pdb=" O VAL A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 removed outlier: 4.074A pdb=" N SER A 584 " --> pdb=" O ARG A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 609 removed outlier: 3.584A pdb=" N ILE A 607 " --> pdb=" O TRP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 613 Processing helix chain 'A' and resid 615 through 634 removed outlier: 4.693A pdb=" N ILE A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 694 through 705 removed outlier: 3.589A pdb=" N ALA A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 734 Processing helix chain 'A' and resid 740 through 744 removed outlier: 3.518A pdb=" N GLU A 743 " --> pdb=" O TYR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 757 removed outlier: 3.714A pdb=" N VAL A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 777 Processing helix chain 'A' and resid 798 through 812 removed outlier: 3.530A pdb=" N GLY A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 880 removed outlier: 3.568A pdb=" N ARG A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 906 Processing helix chain 'A' and resid 919 through 936 Processing helix chain 'A' and resid 939 through 953 removed outlier: 4.160A pdb=" N GLU A 943 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 992 through 1003 Processing helix chain 'A' and resid 1018 through 1026 removed outlier: 3.984A pdb=" N GLU A1024 " --> pdb=" O ASP A1020 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A1026 " --> pdb=" O VAL A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1044 Processing helix chain 'A' and resid 1050 through 1060 removed outlier: 3.739A pdb=" N LYS A1059 " --> pdb=" O PHE A1055 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP A1060 " --> pdb=" O GLU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1083 removed outlier: 3.666A pdb=" N LEU A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1096 removed outlier: 3.562A pdb=" N ASN A1096 " --> pdb=" O LEU A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1120 Processing helix chain 'A' and resid 1132 through 1140 removed outlier: 4.169A pdb=" N ALA A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1158 Processing helix chain 'A' and resid 1167 through 1207 removed outlier: 4.276A pdb=" N ARG A1171 " --> pdb=" O ARG A1167 " (cutoff:3.500A) Proline residue: A1189 - end of helix removed outlier: 3.701A pdb=" N PHE A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A1202 " --> pdb=" O PHE A1198 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A1203 " --> pdb=" O ALA A1199 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A1207 " --> pdb=" O PHE A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1228 removed outlier: 5.096A pdb=" N ASN A1226 " --> pdb=" O MET A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1241 removed outlier: 4.479A pdb=" N VAL A1234 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1252 Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'A' and resid 1256 through 1262 removed outlier: 3.742A pdb=" N ILE A1260 " --> pdb=" O TYR A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1293 removed outlier: 3.710A pdb=" N PHE A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) Proline residue: A1288 - end of helix Processing helix chain 'A' and resid 1307 through 1330 Processing helix chain 'A' and resid 1336 through 1358 Processing helix chain 'A' and resid 1367 through 1374 Processing helix chain 'A' and resid 1375 through 1404 removed outlier: 3.748A pdb=" N TRP A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1406 through 1417 Processing helix chain 'B' and resid 37 through 44 Processing helix chain 'B' and resid 71 through 99 Proline residue: B 77 - end of helix removed outlier: 3.704A pdb=" N LYS B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.817A pdb=" N GLU B 290 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.557A pdb=" N ASN B 354 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 400 Processing helix chain 'B' and resid 409 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 393 through 397 removed outlier: 11.395A pdb=" N LYS A 276 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N HIS A 410 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS A 278 " --> pdb=" O ARG A 408 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE A 406 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A 521 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU A 421 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N MET A 523 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE A 419 " --> pdb=" O MET A 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 448 removed outlier: 3.820A pdb=" N TYR A 432 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 648 through 649 removed outlier: 6.620A pdb=" N THR A1125 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE A1145 " --> pdb=" O THR A1125 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA A1127 " --> pdb=" O ILE A1145 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE A1147 " --> pdb=" O ALA A1127 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY A1129 " --> pdb=" O ILE A1147 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N MET A1124 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A1100 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR A1068 " --> pdb=" O ALA A1099 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU A1101 " --> pdb=" O TYR A1068 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A1070 " --> pdb=" O LEU A1101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 687 through 689 removed outlier: 4.953A pdb=" N VAL A 676 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA A 962 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N CYS A 682 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY A 960 " --> pdb=" O CYS A 682 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE A 684 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N LEU A 958 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER A 850 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE A 839 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 852 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 813 through 816 removed outlier: 3.673A pdb=" N ILE A 824 " --> pdb=" O VAL A 816 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1334 through 1335 Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.092A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 120 removed outlier: 5.806A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 227 through 228 removed outlier: 6.109A pdb=" N ILE B 227 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 630 hydrogen bonds defined for protein. 1785 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: 5.07 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2056 1.30 - 1.43: 3495 1.43 - 1.56: 7312 1.56 - 1.68: 25 1.68 - 1.81: 91 Bond restraints: 12979 Sorted by residual: bond pdb=" C31 POV A1603 " pdb=" O31 POV A1603 " ideal model delta sigma weight residual 1.327 1.429 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C31 POV A1604 " pdb=" O31 POV A1604 " ideal model delta sigma weight residual 1.327 1.427 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C31 POV A1605 " pdb=" O31 POV A1605 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C21 POV A1603 " pdb=" O21 POV A1603 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C21 POV A1604 " pdb=" O21 POV A1604 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 12974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 17354 3.79 - 7.59: 186 7.59 - 11.38: 20 11.38 - 15.17: 7 15.17 - 18.97: 1 Bond angle restraints: 17568 Sorted by residual: angle pdb=" N TYR B 136 " pdb=" CA TYR B 136 " pdb=" C TYR B 136 " ideal model delta sigma weight residual 110.97 121.70 -10.73 1.09e+00 8.42e-01 9.70e+01 angle pdb=" N ARG A1363 " pdb=" CA ARG A1363 " pdb=" C ARG A1363 " ideal model delta sigma weight residual 111.07 120.79 -9.72 1.07e+00 8.73e-01 8.25e+01 angle pdb=" N GLY A1304 " pdb=" CA GLY A1304 " pdb=" C GLY A1304 " ideal model delta sigma weight residual 111.03 121.45 -10.42 1.40e+00 5.10e-01 5.54e+01 angle pdb=" N LYS A 668 " pdb=" CA LYS A 668 " pdb=" C LYS A 668 " ideal model delta sigma weight residual 111.36 118.36 -7.00 1.09e+00 8.42e-01 4.13e+01 angle pdb="C212 POV A1605 " pdb="C213 POV A1605 " pdb="C214 POV A1605 " ideal model delta sigma weight residual 112.90 131.87 -18.97 3.00e+00 1.11e-01 4.00e+01 ... (remaining 17563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.20: 7228 30.20 - 60.40: 586 60.40 - 90.61: 42 90.61 - 120.81: 3 120.81 - 151.01: 2 Dihedral angle restraints: 7861 sinusoidal: 3330 harmonic: 4531 Sorted by residual: dihedral pdb=" C ILE A 234 " pdb=" N ILE A 234 " pdb=" CA ILE A 234 " pdb=" CB ILE A 234 " ideal model delta harmonic sigma weight residual -122.00 -140.40 18.40 0 2.50e+00 1.60e-01 5.42e+01 dihedral pdb=" N ILE A 234 " pdb=" C ILE A 234 " pdb=" CA ILE A 234 " pdb=" CB ILE A 234 " ideal model delta harmonic sigma weight residual 123.40 139.11 -15.71 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" CA TYR A1292 " pdb=" C TYR A1292 " pdb=" N HIS A1293 " pdb=" CA HIS A1293 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 7858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 1924 0.181 - 0.362: 28 0.362 - 0.544: 4 0.544 - 0.725: 0 0.725 - 0.906: 1 Chirality restraints: 1957 Sorted by residual: chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 298 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA ILE A 234 " pdb=" N ILE A 234 " pdb=" C ILE A 234 " pdb=" CB ILE A 234 " both_signs ideal model delta sigma weight residual False 2.43 1.93 0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" CA HIS A1176 " pdb=" N HIS A1176 " pdb=" C HIS A1176 " pdb=" CB HIS A1176 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.08e+00 ... (remaining 1954 not shown) Planarity restraints: 2214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C PHE B 398 " -0.062 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1170 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C ALA A1170 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA A1170 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A1171 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1174 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C LEU A1174 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU A1174 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A1175 " -0.020 2.00e-02 2.50e+03 ... (remaining 2211 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 66 2.44 - 3.05: 8175 3.05 - 3.67: 19231 3.67 - 4.28: 31466 4.28 - 4.90: 51510 Nonbonded interactions: 110448 Sorted by model distance: nonbonded pdb=" OE2 GLU A 183 " pdb=" CG GLU A 184 " model vdw 1.822 3.440 nonbonded pdb=" O MET B 169 " pdb=" O LYS B 170 " model vdw 2.000 3.040 nonbonded pdb=" F2 BEF A1601 " pdb="MG MG A1602 " model vdw 2.080 2.120 nonbonded pdb=" OD2 ASP A 667 " pdb="MG MG A1602 " model vdw 2.099 2.170 nonbonded pdb=" O THR A 669 " pdb="MG MG A1602 " model vdw 2.140 2.170 ... (remaining 110443 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 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.290 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 : 0.014 0.809 12991 Z= 0.892 Angle : 1.110 23.131 17599 Z= 0.619 Chirality : 0.067 0.906 1957 Planarity : 0.006 0.057 2209 Dihedral : 19.676 151.010 4945 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.03 % Favored : 95.71 % Rotamer: Outliers : 12.05 % Allowed : 19.49 % Favored : 68.45 % Cbeta Deviations : 0.21 % 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: -1.91 (0.19), residues: 1540 helix: -1.28 (0.17), residues: 691 sheet: 0.13 (0.34), residues: 205 loop : -1.58 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A1379 HIS 0.007 0.002 HIS A1176 PHE 0.024 0.003 PHE A1285 TYR 0.026 0.003 TYR A1326 ARG 0.011 0.001 ARG A 388 Details of bonding type rmsd link_NAG-ASN : bond 0.04010 ( 5) link_NAG-ASN : angle 9.15787 ( 15) link_ALPHA1-4 : bond 0.00528 ( 1) link_ALPHA1-4 : angle 5.72128 ( 3) link_BETA1-4 : bond 0.01164 ( 3) link_BETA1-4 : angle 3.10474 ( 9) hydrogen bonds : bond 0.14988 ( 630) hydrogen bonds : angle 6.72033 ( 1785) SS BOND : bond 0.01039 ( 2) SS BOND : angle 1.25560 ( 4) covalent geometry : bond 0.01226 (12979) covalent geometry : angle 1.07276 (17568) Misc. bond : bond 0.80882 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 168 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7398 (ptmm) REVERT: A 239 ASN cc_start: 0.4259 (OUTLIER) cc_final: 0.3458 (t0) REVERT: A 439 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7736 (p0) REVERT: A 445 LYS cc_start: 0.8400 (mmtp) cc_final: 0.7987 (mmtt) REVERT: A 498 GLU cc_start: 0.8506 (tp30) cc_final: 0.8274 (tt0) REVERT: A 548 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: A 677 MET cc_start: 0.8943 (mmt) cc_final: 0.8736 (mmp) REVERT: A 683 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8592 (t) REVERT: A 722 ASP cc_start: 0.7784 (m-30) cc_final: 0.7188 (t0) REVERT: A 723 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8139 (ttt-90) REVERT: A 753 ARG cc_start: 0.8458 (ttm170) cc_final: 0.7873 (mtt180) REVERT: A 764 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6766 (tm-30) REVERT: A 848 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8082 (ptt-90) REVERT: A 954 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5801 (tm-30) REVERT: A 965 ASP cc_start: 0.8173 (t0) cc_final: 0.7917 (t0) REVERT: A 1030 SER cc_start: 0.8766 (t) cc_final: 0.8095 (p) REVERT: A 1051 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7237 (mp0) REVERT: A 1171 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7697 (ttt180) REVERT: A 1190 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8539 (tp30) REVERT: A 1436 LYS cc_start: 0.7868 (ttpp) cc_final: 0.7613 (tttm) REVERT: B 262 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8079 (mttt) REVERT: B 267 GLU cc_start: 0.7284 (tp30) cc_final: 0.7075 (mm-30) REVERT: B 271 LYS cc_start: 0.8815 (mttm) cc_final: 0.8614 (mttt) outliers start: 162 outliers final: 77 residues processed: 309 average time/residue: 1.1550 time to fit residues: 391.1392 Evaluate side-chains 233 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 144 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1052 GLU Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1171 ARG Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1214 SER Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1300 SER Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 239 ASN A 273 ASN A 278 HIS A 285 ASN A 287 ASN A 379 ASN A 448 GLN A 454 ASN A 504 ASN A 640 ASN A 888 ASN A 902 GLN A 939 ASN A1139 GLN A1154 GLN A1195 ASN A1293 HIS A1295 ASN B 60 GLN B 67 ASN B 97 ASN B 155 GLN B 186 HIS B 246 GLN B 282 GLN B 341 GLN B 347 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.143935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.104086 restraints weight = 14344.802| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.99 r_work: 0.2728 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12991 Z= 0.190 Angle : 0.655 11.197 17599 Z= 0.343 Chirality : 0.045 0.199 1957 Planarity : 0.004 0.038 2209 Dihedral : 14.605 116.398 2188 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 6.77 % Allowed : 23.59 % Favored : 69.64 % 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: -0.62 (0.20), residues: 1540 helix: -0.02 (0.18), residues: 702 sheet: 0.70 (0.34), residues: 206 loop : -1.16 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1379 HIS 0.003 0.001 HIS A1417 PHE 0.015 0.002 PHE A1403 TYR 0.023 0.002 TYR A 923 ARG 0.007 0.001 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 5) link_NAG-ASN : angle 3.16136 ( 15) link_ALPHA1-4 : bond 0.01530 ( 1) link_ALPHA1-4 : angle 4.45771 ( 3) link_BETA1-4 : bond 0.00201 ( 3) link_BETA1-4 : angle 1.70831 ( 9) hydrogen bonds : bond 0.05900 ( 630) hydrogen bonds : angle 5.43085 ( 1785) SS BOND : bond 0.00558 ( 2) SS BOND : angle 0.79883 ( 4) covalent geometry : bond 0.00432 (12979) covalent geometry : angle 0.64480 (17568) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 160 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.8245 (mtp85) cc_final: 0.8037 (mtp180) REVERT: A 439 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8000 (p0) REVERT: A 445 LYS cc_start: 0.8402 (mmtp) cc_final: 0.7868 (mmtt) REVERT: A 494 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5828 (pp20) REVERT: A 498 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: A 501 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8685 (p) REVERT: A 523 MET cc_start: 0.8923 (mmm) cc_final: 0.8722 (tpp) REVERT: A 548 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8303 (mm-30) REVERT: A 704 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.5961 (tt0) REVERT: A 713 ARG cc_start: 0.7796 (mtt-85) cc_final: 0.7589 (mtt180) REVERT: A 722 ASP cc_start: 0.7861 (m-30) cc_final: 0.7020 (t0) REVERT: A 742 GLU cc_start: 0.8217 (mp0) cc_final: 0.7880 (pm20) REVERT: A 753 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7716 (ttt180) REVERT: A 813 PHE cc_start: 0.8567 (m-80) cc_final: 0.8289 (m-80) REVERT: A 848 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8012 (ptt-90) REVERT: A 954 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5850 (tm-30) REVERT: A 1008 ASN cc_start: 0.8137 (m-40) cc_final: 0.7548 (m-40) REVERT: A 1016 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6938 (pttt) REVERT: A 1030 SER cc_start: 0.8427 (t) cc_final: 0.7970 (p) REVERT: A 1051 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7004 (mp0) REVERT: A 1190 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8951 (tp30) REVERT: A 1218 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: A 1223 MET cc_start: 0.8498 (ptp) cc_final: 0.8230 (ptt) REVERT: A 1436 LYS cc_start: 0.7677 (ttpp) cc_final: 0.7290 (tttm) REVERT: B 267 GLU cc_start: 0.8288 (tp30) cc_final: 0.8082 (mm-30) REVERT: B 271 LYS cc_start: 0.9065 (mttm) cc_final: 0.8677 (mttt) outliers start: 91 outliers final: 44 residues processed: 236 average time/residue: 1.6633 time to fit residues: 426.3832 Evaluate side-chains 199 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 362 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 11 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 412 ASN A 899 HIS A 902 GLN B 131 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.105034 restraints weight = 14436.781| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.01 r_work: 0.2746 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12991 Z= 0.159 Angle : 0.603 9.916 17599 Z= 0.315 Chirality : 0.044 0.329 1957 Planarity : 0.004 0.035 2209 Dihedral : 12.987 109.721 2091 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 6.18 % Allowed : 24.11 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1540 helix: 0.57 (0.19), residues: 705 sheet: 0.76 (0.34), residues: 213 loop : -0.99 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 603 HIS 0.005 0.001 HIS A1417 PHE 0.014 0.002 PHE A1403 TYR 0.022 0.002 TYR A 923 ARG 0.005 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 5) link_NAG-ASN : angle 3.40708 ( 15) link_ALPHA1-4 : bond 0.01628 ( 1) link_ALPHA1-4 : angle 4.31925 ( 3) link_BETA1-4 : bond 0.00145 ( 3) link_BETA1-4 : angle 1.76504 ( 9) hydrogen bonds : bond 0.05384 ( 630) hydrogen bonds : angle 5.11978 ( 1785) SS BOND : bond 0.00441 ( 2) SS BOND : angle 0.66025 ( 4) covalent geometry : bond 0.00358 (12979) covalent geometry : angle 0.59158 (17568) Misc. bond : bond 0.00126 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 154 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: A 439 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8017 (p0) REVERT: A 445 LYS cc_start: 0.8444 (mmtp) cc_final: 0.7925 (mmtt) REVERT: A 494 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5889 (pp20) REVERT: A 498 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: A 704 GLN cc_start: 0.6324 (OUTLIER) cc_final: 0.5895 (tt0) REVERT: A 711 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6593 (tt0) REVERT: A 713 ARG cc_start: 0.7794 (mtt-85) cc_final: 0.7578 (mtt180) REVERT: A 722 ASP cc_start: 0.7893 (m-30) cc_final: 0.6989 (t0) REVERT: A 740 TYR cc_start: 0.8232 (m-80) cc_final: 0.7803 (m-80) REVERT: A 742 GLU cc_start: 0.8195 (mp0) cc_final: 0.7864 (pm20) REVERT: A 753 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7787 (ttm170) REVERT: A 813 PHE cc_start: 0.8608 (m-80) cc_final: 0.8352 (m-80) REVERT: A 848 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8030 (ptt-90) REVERT: A 909 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7969 (mtt-85) REVERT: A 945 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6882 (mt-10) REVERT: A 1016 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6991 (pttt) REVERT: A 1051 GLU cc_start: 0.7604 (mm-30) cc_final: 0.6953 (mp0) REVERT: A 1190 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8956 (tp30) REVERT: A 1218 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: A 1223 MET cc_start: 0.8415 (ptp) cc_final: 0.8139 (ptt) REVERT: A 1363 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7751 (mtt180) REVERT: A 1436 LYS cc_start: 0.7641 (ttpp) cc_final: 0.7225 (tttm) REVERT: B 56 ASP cc_start: 0.7888 (t0) cc_final: 0.7642 (m-30) REVERT: B 267 GLU cc_start: 0.8319 (tp30) cc_final: 0.8050 (mm-30) REVERT: B 271 LYS cc_start: 0.9029 (mttm) cc_final: 0.8641 (mttt) outliers start: 83 outliers final: 34 residues processed: 225 average time/residue: 1.2989 time to fit residues: 318.8634 Evaluate side-chains 188 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 91 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 902 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.106429 restraints weight = 14393.369| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.92 r_work: 0.2744 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12991 Z= 0.167 Angle : 0.601 9.104 17599 Z= 0.310 Chirality : 0.044 0.382 1957 Planarity : 0.004 0.042 2209 Dihedral : 12.012 104.000 2069 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.88 % Allowed : 24.93 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.18 (0.21), residues: 1540 helix: 0.78 (0.20), residues: 704 sheet: 0.78 (0.34), residues: 213 loop : -0.83 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 603 HIS 0.004 0.001 HIS A1417 PHE 0.014 0.002 PHE A1403 TYR 0.021 0.002 TYR A 923 ARG 0.008 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00788 ( 5) link_NAG-ASN : angle 3.57485 ( 15) link_ALPHA1-4 : bond 0.01548 ( 1) link_ALPHA1-4 : angle 4.34181 ( 3) link_BETA1-4 : bond 0.00132 ( 3) link_BETA1-4 : angle 1.84979 ( 9) hydrogen bonds : bond 0.05331 ( 630) hydrogen bonds : angle 5.01359 ( 1785) SS BOND : bond 0.00452 ( 2) SS BOND : angle 0.71284 ( 4) covalent geometry : bond 0.00381 (12979) covalent geometry : angle 0.58758 (17568) Misc. bond : bond 0.00111 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 156 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ILE cc_start: 0.4013 (OUTLIER) cc_final: 0.3760 (pp) REVERT: A 439 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8091 (p0) REVERT: A 445 LYS cc_start: 0.8409 (mmtp) cc_final: 0.7841 (mmtt) REVERT: A 494 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5877 (pp20) REVERT: A 498 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: A 677 MET cc_start: 0.9094 (mmp) cc_final: 0.8388 (mmt) REVERT: A 704 GLN cc_start: 0.6253 (OUTLIER) cc_final: 0.5822 (tt0) REVERT: A 711 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6615 (tt0) REVERT: A 713 ARG cc_start: 0.7782 (mtt-85) cc_final: 0.7559 (mtt180) REVERT: A 722 ASP cc_start: 0.7844 (m-30) cc_final: 0.6953 (t0) REVERT: A 740 TYR cc_start: 0.8218 (m-80) cc_final: 0.7794 (m-80) REVERT: A 742 GLU cc_start: 0.8184 (mp0) cc_final: 0.7859 (pm20) REVERT: A 750 GLU cc_start: 0.8005 (mp0) cc_final: 0.7399 (mp0) REVERT: A 753 ARG cc_start: 0.8079 (ttm170) cc_final: 0.7803 (ttt180) REVERT: A 764 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: A 813 PHE cc_start: 0.8674 (m-80) cc_final: 0.8442 (m-80) REVERT: A 880 ARG cc_start: 0.7560 (mtt90) cc_final: 0.7304 (ttm-80) REVERT: A 909 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8410 (ttm110) REVERT: A 1016 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7029 (pttt) REVERT: A 1020 ASP cc_start: 0.4030 (OUTLIER) cc_final: 0.3820 (OUTLIER) REVERT: A 1051 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6901 (mp0) REVERT: A 1190 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8773 (tp30) REVERT: A 1218 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: A 1223 MET cc_start: 0.8483 (ptp) cc_final: 0.8209 (ptt) REVERT: A 1363 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7843 (mtt180) REVERT: A 1436 LYS cc_start: 0.7655 (ttpp) cc_final: 0.7226 (tttm) REVERT: B 56 ASP cc_start: 0.7733 (t0) cc_final: 0.7488 (m-30) REVERT: B 138 THR cc_start: 0.7844 (m) cc_final: 0.7583 (m) REVERT: B 267 GLU cc_start: 0.8319 (tp30) cc_final: 0.8055 (mm-30) REVERT: B 271 LYS cc_start: 0.9010 (mttm) cc_final: 0.8624 (mttt) outliers start: 79 outliers final: 37 residues processed: 224 average time/residue: 1.4005 time to fit residues: 342.0596 Evaluate side-chains 200 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 909 ARG Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 114 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 94 optimal weight: 0.0670 chunk 12 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 410 HIS A 902 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.145026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106003 restraints weight = 14448.311| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.89 r_work: 0.2756 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12991 Z= 0.182 Angle : 0.609 8.957 17599 Z= 0.314 Chirality : 0.045 0.354 1957 Planarity : 0.004 0.042 2209 Dihedral : 11.588 95.659 2059 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 6.10 % Allowed : 24.33 % Favored : 69.57 % 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: 0.26 (0.21), residues: 1540 helix: 0.86 (0.20), residues: 703 sheet: 0.81 (0.35), residues: 215 loop : -0.79 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 314 HIS 0.004 0.001 HIS A1417 PHE 0.014 0.002 PHE A1403 TYR 0.020 0.002 TYR A 923 ARG 0.009 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 5) link_NAG-ASN : angle 3.83606 ( 15) link_ALPHA1-4 : bond 0.01522 ( 1) link_ALPHA1-4 : angle 4.45363 ( 3) link_BETA1-4 : bond 0.00196 ( 3) link_BETA1-4 : angle 1.94004 ( 9) hydrogen bonds : bond 0.05445 ( 630) hydrogen bonds : angle 4.97634 ( 1785) SS BOND : bond 0.00508 ( 2) SS BOND : angle 0.77516 ( 4) covalent geometry : bond 0.00423 (12979) covalent geometry : angle 0.59415 (17568) Misc. bond : bond 0.00131 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 155 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8081 (p0) REVERT: A 445 LYS cc_start: 0.8487 (mmtp) cc_final: 0.7945 (mmtt) REVERT: A 498 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: A 704 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5770 (tt0) REVERT: A 711 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6606 (tt0) REVERT: A 740 TYR cc_start: 0.8253 (m-80) cc_final: 0.7842 (m-80) REVERT: A 742 GLU cc_start: 0.8164 (mp0) cc_final: 0.7844 (pm20) REVERT: A 750 GLU cc_start: 0.8008 (mp0) cc_final: 0.7393 (mp0) REVERT: A 764 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: A 880 ARG cc_start: 0.7560 (mtt90) cc_final: 0.6742 (ttm-80) REVERT: A 1016 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7114 (pttt) REVERT: A 1020 ASP cc_start: 0.4035 (OUTLIER) cc_final: 0.3820 (OUTLIER) REVERT: A 1051 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6949 (mp0) REVERT: A 1190 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8862 (mm-30) REVERT: A 1218 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8312 (tm-30) REVERT: A 1223 MET cc_start: 0.8501 (ptp) cc_final: 0.8248 (ptt) REVERT: A 1363 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7944 (mtt180) REVERT: A 1436 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7345 (tttm) REVERT: B 267 GLU cc_start: 0.8358 (tp30) cc_final: 0.8087 (mm-30) REVERT: B 271 LYS cc_start: 0.9054 (mttm) cc_final: 0.8689 (mttt) outliers start: 82 outliers final: 41 residues processed: 225 average time/residue: 1.3955 time to fit residues: 342.4714 Evaluate side-chains 200 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 410 HIS ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106718 restraints weight = 14614.643| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.92 r_work: 0.2755 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12991 Z= 0.155 Angle : 0.587 9.238 17599 Z= 0.302 Chirality : 0.044 0.463 1957 Planarity : 0.004 0.040 2209 Dihedral : 11.253 88.885 2055 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.65 % Allowed : 24.63 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1540 helix: 0.96 (0.20), residues: 708 sheet: 0.72 (0.34), residues: 221 loop : -0.74 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 314 HIS 0.004 0.001 HIS A1417 PHE 0.013 0.001 PHE A1403 TYR 0.020 0.001 TYR A 923 ARG 0.008 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 5) link_NAG-ASN : angle 3.88789 ( 15) link_ALPHA1-4 : bond 0.01679 ( 1) link_ALPHA1-4 : angle 4.30979 ( 3) link_BETA1-4 : bond 0.00134 ( 3) link_BETA1-4 : angle 1.76382 ( 9) hydrogen bonds : bond 0.05133 ( 630) hydrogen bonds : angle 4.88912 ( 1785) SS BOND : bond 0.00435 ( 2) SS BOND : angle 0.69856 ( 4) covalent geometry : bond 0.00351 (12979) covalent geometry : angle 0.57206 (17568) Misc. bond : bond 0.00083 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 156 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ILE cc_start: 0.4062 (OUTLIER) cc_final: 0.3797 (pp) REVERT: A 439 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8064 (p0) REVERT: A 445 LYS cc_start: 0.8435 (mmtp) cc_final: 0.7887 (mmtt) REVERT: A 498 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: A 691 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8322 (mmm160) REVERT: A 704 GLN cc_start: 0.6301 (OUTLIER) cc_final: 0.5884 (tt0) REVERT: A 711 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6638 (tt0) REVERT: A 722 ASP cc_start: 0.7959 (m-30) cc_final: 0.7666 (t70) REVERT: A 740 TYR cc_start: 0.8235 (m-80) cc_final: 0.7826 (m-80) REVERT: A 742 GLU cc_start: 0.8177 (mp0) cc_final: 0.7847 (pm20) REVERT: A 749 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6841 (pttt) REVERT: A 750 GLU cc_start: 0.7965 (mp0) cc_final: 0.7290 (mp0) REVERT: A 764 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6938 (tt0) REVERT: A 1016 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7137 (pttt) REVERT: A 1051 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6852 (mp0) REVERT: A 1072 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8605 (tt) REVERT: A 1190 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8873 (tp30) REVERT: A 1218 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: A 1223 MET cc_start: 0.8444 (ptp) cc_final: 0.8180 (ptt) REVERT: A 1363 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7908 (mtt180) REVERT: A 1436 LYS cc_start: 0.7684 (ttpp) cc_final: 0.7288 (tttm) REVERT: B 267 GLU cc_start: 0.8338 (tp30) cc_final: 0.8068 (mm-30) REVERT: B 271 LYS cc_start: 0.9008 (mttm) cc_final: 0.8629 (mttt) REVERT: B 401 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.6484 (ptt90) outliers start: 76 outliers final: 40 residues processed: 217 average time/residue: 1.2785 time to fit residues: 301.8096 Evaluate side-chains 200 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 75 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 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 396 ASN A 410 HIS A 902 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.147384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.108237 restraints weight = 14411.444| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.92 r_work: 0.2783 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12991 Z= 0.131 Angle : 0.562 8.667 17599 Z= 0.291 Chirality : 0.042 0.371 1957 Planarity : 0.003 0.042 2209 Dihedral : 10.741 89.639 2051 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.84 % Allowed : 25.82 % Favored : 69.35 % 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: 0.47 (0.22), residues: 1540 helix: 1.04 (0.20), residues: 708 sheet: 0.78 (0.34), residues: 221 loop : -0.67 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1352 HIS 0.004 0.001 HIS A1417 PHE 0.012 0.001 PHE A1403 TYR 0.020 0.001 TYR A 923 ARG 0.009 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 5) link_NAG-ASN : angle 3.40753 ( 15) link_ALPHA1-4 : bond 0.01683 ( 1) link_ALPHA1-4 : angle 4.17772 ( 3) link_BETA1-4 : bond 0.00221 ( 3) link_BETA1-4 : angle 1.57376 ( 9) hydrogen bonds : bond 0.04795 ( 630) hydrogen bonds : angle 4.78957 ( 1785) SS BOND : bond 0.00312 ( 2) SS BOND : angle 0.52267 ( 4) covalent geometry : bond 0.00289 (12979) covalent geometry : angle 0.54976 (17568) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 157 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ILE cc_start: 0.4191 (OUTLIER) cc_final: 0.3915 (pp) REVERT: A 439 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8109 (p0) REVERT: A 445 LYS cc_start: 0.8455 (mmtp) cc_final: 0.7899 (mmtt) REVERT: A 498 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: A 677 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8725 (mmt) REVERT: A 691 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8285 (mmm160) REVERT: A 704 GLN cc_start: 0.6293 (OUTLIER) cc_final: 0.5914 (tt0) REVERT: A 711 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6651 (tt0) REVERT: A 722 ASP cc_start: 0.7948 (m-30) cc_final: 0.7563 (t70) REVERT: A 740 TYR cc_start: 0.8240 (m-80) cc_final: 0.7827 (m-80) REVERT: A 742 GLU cc_start: 0.8190 (mp0) cc_final: 0.7855 (pm20) REVERT: A 749 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6884 (ttpt) REVERT: A 750 GLU cc_start: 0.7974 (mp0) cc_final: 0.7444 (mp0) REVERT: A 761 GLU cc_start: 0.7849 (tp30) cc_final: 0.7315 (mm-30) REVERT: A 880 ARG cc_start: 0.7449 (mtt90) cc_final: 0.6799 (ttm-80) REVERT: A 1016 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7151 (pttt) REVERT: A 1051 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6866 (mp0) REVERT: A 1072 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8598 (tt) REVERT: A 1190 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8807 (mm-30) REVERT: A 1218 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: A 1223 MET cc_start: 0.8369 (ptp) cc_final: 0.8090 (ptt) REVERT: A 1363 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7877 (mpp80) REVERT: A 1436 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7263 (tttm) REVERT: B 267 GLU cc_start: 0.8337 (tp30) cc_final: 0.8097 (mm-30) REVERT: B 271 LYS cc_start: 0.8988 (mttm) cc_final: 0.8613 (mtmt) REVERT: B 401 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.6456 (ptt90) outliers start: 65 outliers final: 34 residues processed: 208 average time/residue: 2.1709 time to fit residues: 495.0668 Evaluate side-chains 192 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 749 LYS Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN A 410 HIS A 902 GLN A1266 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.106175 restraints weight = 14548.771| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.91 r_work: 0.2739 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12991 Z= 0.181 Angle : 0.602 10.007 17599 Z= 0.310 Chirality : 0.044 0.343 1957 Planarity : 0.004 0.043 2209 Dihedral : 10.606 89.416 2041 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.24 % Allowed : 26.41 % Favored : 69.35 % 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: 0.47 (0.22), residues: 1540 helix: 1.04 (0.20), residues: 704 sheet: 0.78 (0.34), residues: 221 loop : -0.66 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 314 HIS 0.003 0.001 HIS A1417 PHE 0.014 0.002 PHE A1285 TYR 0.020 0.002 TYR A 923 ARG 0.009 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 5) link_NAG-ASN : angle 3.56242 ( 15) link_ALPHA1-4 : bond 0.01558 ( 1) link_ALPHA1-4 : angle 4.49930 ( 3) link_BETA1-4 : bond 0.00137 ( 3) link_BETA1-4 : angle 1.88592 ( 9) hydrogen bonds : bond 0.05336 ( 630) hydrogen bonds : angle 4.86858 ( 1785) SS BOND : bond 0.00476 ( 2) SS BOND : angle 0.78615 ( 4) covalent geometry : bond 0.00423 (12979) covalent geometry : angle 0.58906 (17568) Misc. bond : bond 0.00131 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 148 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ILE cc_start: 0.4183 (OUTLIER) cc_final: 0.3913 (pp) REVERT: A 445 LYS cc_start: 0.8471 (mmtp) cc_final: 0.7902 (mmtt) REVERT: A 464 ARG cc_start: 0.6540 (mtt180) cc_final: 0.6315 (mtt180) REVERT: A 498 GLU cc_start: 0.8590 (tp30) cc_final: 0.8288 (tt0) REVERT: A 704 GLN cc_start: 0.6298 (OUTLIER) cc_final: 0.5899 (tt0) REVERT: A 711 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6621 (tt0) REVERT: A 742 GLU cc_start: 0.8223 (mp0) cc_final: 0.7894 (pm20) REVERT: A 750 GLU cc_start: 0.8027 (mp0) cc_final: 0.7578 (mp0) REVERT: A 761 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: A 764 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: A 880 ARG cc_start: 0.7466 (mtt90) cc_final: 0.6846 (ttm170) REVERT: A 1016 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7193 (pttt) REVERT: A 1051 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6898 (mp0) REVERT: A 1072 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8624 (tt) REVERT: A 1133 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.7125 (p0) REVERT: A 1190 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8838 (mm-30) REVERT: A 1218 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: A 1223 MET cc_start: 0.8398 (ptp) cc_final: 0.8149 (ptt) REVERT: A 1266 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8957 (p0) REVERT: A 1305 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8778 (mp) REVERT: A 1363 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8038 (mpp80) REVERT: A 1436 LYS cc_start: 0.7679 (ttpp) cc_final: 0.7277 (tttm) REVERT: B 56 ASP cc_start: 0.7855 (m-30) cc_final: 0.7372 (m-30) REVERT: B 150 ASP cc_start: 0.8451 (t0) cc_final: 0.8150 (t0) REVERT: B 267 GLU cc_start: 0.8342 (tp30) cc_final: 0.8066 (mm-30) REVERT: B 271 LYS cc_start: 0.9018 (mttm) cc_final: 0.8640 (mttt) REVERT: B 401 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.6498 (ptt90) outliers start: 57 outliers final: 32 residues processed: 192 average time/residue: 1.2953 time to fit residues: 270.7843 Evaluate side-chains 189 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 764 GLN Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1266 ASN Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 107 optimal weight: 0.9980 chunk 86 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 902 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.108745 restraints weight = 14434.546| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.91 r_work: 0.2791 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12991 Z= 0.128 Angle : 0.555 9.425 17599 Z= 0.287 Chirality : 0.042 0.329 1957 Planarity : 0.003 0.041 2209 Dihedral : 10.213 89.973 2039 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.65 % Allowed : 27.16 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.22), residues: 1540 helix: 1.12 (0.20), residues: 711 sheet: 0.81 (0.34), residues: 221 loop : -0.64 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1352 HIS 0.004 0.001 HIS A1417 PHE 0.014 0.001 PHE A 842 TYR 0.019 0.001 TYR A 923 ARG 0.009 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 5) link_NAG-ASN : angle 3.12351 ( 15) link_ALPHA1-4 : bond 0.01860 ( 1) link_ALPHA1-4 : angle 4.26683 ( 3) link_BETA1-4 : bond 0.00257 ( 3) link_BETA1-4 : angle 1.50370 ( 9) hydrogen bonds : bond 0.04670 ( 630) hydrogen bonds : angle 4.73057 ( 1785) SS BOND : bond 0.00266 ( 2) SS BOND : angle 0.49250 ( 4) covalent geometry : bond 0.00282 (12979) covalent geometry : angle 0.54385 (17568) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8469 (mt) cc_final: 0.8202 (mm) REVERT: A 234 ILE cc_start: 0.4190 (OUTLIER) cc_final: 0.3917 (pp) REVERT: A 445 LYS cc_start: 0.8486 (mmtp) cc_final: 0.7845 (mmtt) REVERT: A 498 GLU cc_start: 0.8602 (tp30) cc_final: 0.8296 (tt0) REVERT: A 593 SER cc_start: 0.5941 (OUTLIER) cc_final: 0.5728 (m) REVERT: A 704 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5882 (tt0) REVERT: A 711 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6588 (tt0) REVERT: A 740 TYR cc_start: 0.8233 (m-80) cc_final: 0.7903 (m-80) REVERT: A 742 GLU cc_start: 0.8192 (mp0) cc_final: 0.7851 (pm20) REVERT: A 750 GLU cc_start: 0.8010 (mp0) cc_final: 0.7577 (mp0) REVERT: A 761 GLU cc_start: 0.7891 (tp30) cc_final: 0.7362 (mm-30) REVERT: A 880 ARG cc_start: 0.7471 (mtt90) cc_final: 0.6989 (ttm170) REVERT: A 916 ARG cc_start: 0.5662 (ttp80) cc_final: 0.5427 (mmm160) REVERT: A 1016 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7168 (pttt) REVERT: A 1051 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6839 (mp0) REVERT: A 1072 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8607 (tt) REVERT: A 1190 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8787 (mm-30) REVERT: A 1218 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: A 1223 MET cc_start: 0.8307 (ptp) cc_final: 0.8051 (ptt) REVERT: A 1363 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7931 (mpp80) REVERT: A 1436 LYS cc_start: 0.7676 (ttpp) cc_final: 0.7266 (tttm) REVERT: B 54 LYS cc_start: 0.8565 (ptmm) cc_final: 0.7974 (ptmt) REVERT: B 56 ASP cc_start: 0.7881 (m-30) cc_final: 0.7313 (m-30) REVERT: B 150 ASP cc_start: 0.8450 (t0) cc_final: 0.8146 (t0) REVERT: B 267 GLU cc_start: 0.8335 (tp30) cc_final: 0.8091 (mm-30) REVERT: B 271 LYS cc_start: 0.8986 (mttm) cc_final: 0.8612 (mtmt) REVERT: B 401 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.6486 (ptt90) outliers start: 49 outliers final: 29 residues processed: 193 average time/residue: 1.3538 time to fit residues: 283.5859 Evaluate side-chains 185 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1190 GLU Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 128 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 410 HIS A 902 GLN A1266 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.147392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107935 restraints weight = 14413.305| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.88 r_work: 0.2822 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12991 Z= 0.133 Angle : 0.567 9.571 17599 Z= 0.290 Chirality : 0.042 0.314 1957 Planarity : 0.004 0.041 2209 Dihedral : 9.933 89.951 2037 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.12 % Allowed : 27.46 % Favored : 69.42 % 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: 0.62 (0.22), residues: 1540 helix: 1.17 (0.20), residues: 708 sheet: 0.86 (0.34), residues: 221 loop : -0.60 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1352 HIS 0.004 0.001 HIS A1417 PHE 0.013 0.001 PHE A 842 TYR 0.018 0.001 TYR A 923 ARG 0.009 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 5) link_NAG-ASN : angle 3.13007 ( 15) link_ALPHA1-4 : bond 0.01860 ( 1) link_ALPHA1-4 : angle 4.65079 ( 3) link_BETA1-4 : bond 0.00178 ( 3) link_BETA1-4 : angle 1.57545 ( 9) hydrogen bonds : bond 0.04733 ( 630) hydrogen bonds : angle 4.71592 ( 1785) SS BOND : bond 0.00293 ( 2) SS BOND : angle 0.56107 ( 4) covalent geometry : bond 0.00295 (12979) covalent geometry : angle 0.55506 (17568) Misc. bond : bond 0.00061 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8459 (mt) cc_final: 0.8219 (mm) REVERT: A 234 ILE cc_start: 0.4240 (OUTLIER) cc_final: 0.3961 (pp) REVERT: A 281 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7195 (mm-30) REVERT: A 445 LYS cc_start: 0.8511 (mmtp) cc_final: 0.7892 (mmtt) REVERT: A 498 GLU cc_start: 0.8603 (tp30) cc_final: 0.8315 (tt0) REVERT: A 677 MET cc_start: 0.9178 (mmt) cc_final: 0.8829 (mmt) REVERT: A 704 GLN cc_start: 0.6254 (OUTLIER) cc_final: 0.5891 (tt0) REVERT: A 711 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6586 (tt0) REVERT: A 740 TYR cc_start: 0.8284 (m-80) cc_final: 0.7958 (m-80) REVERT: A 742 GLU cc_start: 0.8186 (mp0) cc_final: 0.7855 (pm20) REVERT: A 750 GLU cc_start: 0.8023 (mp0) cc_final: 0.7602 (mp0) REVERT: A 761 GLU cc_start: 0.7940 (tp30) cc_final: 0.7428 (mm-30) REVERT: A 880 ARG cc_start: 0.7489 (mtt90) cc_final: 0.7041 (ttm170) REVERT: A 916 ARG cc_start: 0.5761 (ttp80) cc_final: 0.5542 (mmm160) REVERT: A 1051 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6902 (mp0) REVERT: A 1055 PHE cc_start: 0.8139 (t80) cc_final: 0.7782 (t80) REVERT: A 1072 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8651 (tt) REVERT: A 1218 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: A 1223 MET cc_start: 0.8328 (ptp) cc_final: 0.8075 (ptt) REVERT: A 1363 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8013 (mpp80) REVERT: A 1436 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7336 (tttm) REVERT: B 56 ASP cc_start: 0.7848 (m-30) cc_final: 0.7357 (m-30) REVERT: B 150 ASP cc_start: 0.8453 (t0) cc_final: 0.8151 (t0) REVERT: B 267 GLU cc_start: 0.8330 (tp30) cc_final: 0.8098 (mm-30) REVERT: B 271 LYS cc_start: 0.8992 (mttm) cc_final: 0.8626 (mtmt) REVERT: B 401 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.6486 (ptt90) outliers start: 42 outliers final: 29 residues processed: 183 average time/residue: 1.2922 time to fit residues: 257.5178 Evaluate side-chains 180 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 704 GLN Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 920 TRP Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 1052 GLU Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1133 ASN Chi-restraints excluded: chain A residue 1218 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1360 ILE Chi-restraints excluded: chain A residue 1363 ARG Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 49 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 1 optimal weight: 0.0040 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 902 GLN A1266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.146250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.106450 restraints weight = 14535.257| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.93 r_work: 0.2789 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12991 Z= 0.155 Angle : 0.582 9.502 17599 Z= 0.299 Chirality : 0.043 0.304 1957 Planarity : 0.004 0.042 2209 Dihedral : 9.641 89.610 2032 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.12 % Allowed : 27.68 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.58 (0.22), residues: 1540 helix: 1.13 (0.20), residues: 707 sheet: 0.83 (0.34), residues: 221 loop : -0.61 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 314 HIS 0.003 0.001 HIS A1417 PHE 0.014 0.001 PHE A 842 TYR 0.018 0.001 TYR A 923 ARG 0.009 0.000 ARG A 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 5) link_NAG-ASN : angle 3.24151 ( 15) link_ALPHA1-4 : bond 0.01674 ( 1) link_ALPHA1-4 : angle 5.45666 ( 3) link_BETA1-4 : bond 0.00105 ( 3) link_BETA1-4 : angle 1.72107 ( 9) hydrogen bonds : bond 0.05031 ( 630) hydrogen bonds : angle 4.77090 ( 1785) SS BOND : bond 0.00404 ( 2) SS BOND : angle 0.67656 ( 4) covalent geometry : bond 0.00355 (12979) covalent geometry : angle 0.56874 (17568) Misc. bond : bond 0.00096 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11998.95 seconds wall clock time: 214 minutes 11.06 seconds (12851.06 seconds total)