Starting phenix.real_space_refine on Fri Jul 3 03:51:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pem_13353/07_2026/7pem_13353.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pem_13353/07_2026/7pem_13353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pem_13353/07_2026/7pem_13353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pem_13353/07_2026/7pem_13353.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pem_13353/07_2026/7pem_13353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pem_13353/07_2026/7pem_13353.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7pem_13353/07_2026/7pem_13353.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pem_13353/07_2026/7pem_13353.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 7504 2.51 5 N 1865 2.21 5 O 2195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11620 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8522 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 30, 'TRANS': 1035} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2841 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} 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 chiralities: 2 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 chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 151 Unusual residues: {' MG': 1, '2Y5': 1, 'ATP': 1, 'Q3G': 1} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 2.48, per 1000 atoms: 0.21 Number of scatterers: 11620 At special positions: 0 Unit cell: (88.6832, 105.182, 178.398, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 7 15.00 Mg 1 11.99 O 2195 8.00 N 1865 7.00 C 7504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.04 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 Atom "HETATM11403 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA E 3 " - " BMA E 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG D 1 " - " ASN C 216 " " NAG E 1 " - " ASN C 199 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 501.7 milliseconds 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2680 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 10 sheets defined 43.4% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 226 through 238 removed outlier: 3.821A pdb=" N GLN A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 278 removed outlier: 3.962A pdb=" N GLU A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 438 through 473 removed outlier: 3.592A pdb=" N ARG A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 502 removed outlier: 3.615A pdb=" N PHE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 506 removed outlier: 3.904A pdb=" N VAL A 506 " --> pdb=" O SER A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 509 through 526 removed outlier: 4.212A pdb=" N GLU A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 525 " --> pdb=" O GLN A 521 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 removed outlier: 6.545A pdb=" N ASP A 530 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 552 removed outlier: 3.786A pdb=" N LEU A 551 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 548 through 552' Processing helix chain 'A' and resid 604 through 614 removed outlier: 3.908A pdb=" N LEU A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 630 Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 727 through 731 removed outlier: 3.887A pdb=" N LEU A 731 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 768 through 778 removed outlier: 4.606A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 781 No H-bonds generated for 'chain 'A' and resid 779 through 781' Processing helix chain 'A' and resid 789 through 795 removed outlier: 3.899A pdb=" N ALA A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 795 " --> pdb=" O ASP A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 Processing helix chain 'A' and resid 838 through 845 removed outlier: 3.659A pdb=" N ASN A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 845 " --> pdb=" O THR A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 882 Processing helix chain 'A' and resid 898 through 906 Processing helix chain 'A' and resid 911 through 919 removed outlier: 3.689A pdb=" N LEU A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 919 " --> pdb=" O LEU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 944 removed outlier: 4.076A pdb=" N ALA A 935 " --> pdb=" O PRO A 931 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 957 No H-bonds generated for 'chain 'A' and resid 955 through 957' Processing helix chain 'A' and resid 958 through 963 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.548A pdb=" N SER A 982 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 999 removed outlier: 3.570A pdb=" N LEU A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 998 " --> pdb=" O LYS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1019 removed outlier: 3.769A pdb=" N SER A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.680A pdb=" N TYR A1023 " --> pdb=" O ASN A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'A' and resid 1030 through 1033 removed outlier: 3.744A pdb=" N ASN A1033 " --> pdb=" O VAL A1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1030 through 1033' Processing helix chain 'A' and resid 1042 through 1048 Processing helix chain 'A' and resid 1048 through 1053 removed outlier: 3.751A pdb=" N PHE A1053 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1063 removed outlier: 3.854A pdb=" N PHE A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1074 removed outlier: 3.505A pdb=" N LEU A1073 " --> pdb=" O SER A1069 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1069 through 1074' Processing helix chain 'A' and resid 1076 through 1079 Processing helix chain 'A' and resid 1080 through 1085 Processing helix chain 'A' and resid 1090 through 1116 removed outlier: 3.626A pdb=" N GLY A1096 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP A1097 " --> pdb=" O ILE A1093 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A1100 " --> pdb=" O GLY A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1154 removed outlier: 4.252A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1183 removed outlier: 3.801A pdb=" N LEU A1169 " --> pdb=" O ILE A1165 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A1170 " --> pdb=" O PRO A1166 " (cutoff:3.500A) Proline residue: A1177 - end of helix removed outlier: 3.533A pdb=" N SER A1181 " --> pdb=" O PRO A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1187 removed outlier: 3.533A pdb=" N ASN A1187 " --> pdb=" O PRO A1184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1184 through 1187' Processing helix chain 'A' and resid 1194 through 1200 removed outlier: 3.622A pdb=" N HIS A1198 " --> pdb=" O GLY A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1217 removed outlier: 3.898A pdb=" N LEU A1209 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) Proline residue: A1213 - end of helix Processing helix chain 'A' and resid 1217 through 1230 removed outlier: 3.693A pdb=" N LEU A1222 " --> pdb=" O VAL A1218 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A1225 " --> pdb=" O PHE A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1245 removed outlier: 3.679A pdb=" N VAL A1237 " --> pdb=" O GLU A1233 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A1238 " --> pdb=" O THR A1234 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 67 removed outlier: 3.838A pdb=" N LEU C 46 " --> pdb=" O PRO C 42 " (cutoff:3.500A) Proline residue: C 47 - end of helix Proline residue: C 58 - end of helix removed outlier: 3.698A pdb=" N ALA C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.507A pdb=" N ALA C 84 " --> pdb=" O CYS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 150 through 155 removed outlier: 4.732A pdb=" N GLN C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 244 through 248 removed outlier: 3.740A pdb=" N MET C 248 " --> pdb=" O PRO C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 274 removed outlier: 3.506A pdb=" N ARG C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.995A pdb=" N LEU C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.588A pdb=" N ILE C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AA2, first strand: chain 'A' and resid 294 through 298 removed outlier: 4.587A pdb=" N GLU A 285 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 309 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE A 307 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE A 414 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 349 removed outlier: 3.966A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.630A pdb=" N VAL A 967 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 948 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU A 555 " --> pdb=" O LYS A 830 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N TRP A 832 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 557 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU A 834 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER A 559 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE A 831 " --> pdb=" O VAL A 924 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N CYS A 926 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 833 " --> pdb=" O CYS A 926 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU A 893 " --> pdb=" O ALA A 923 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ILE A 925 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 895 " --> pdb=" O ILE A 925 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N CYS A 927 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 897 " --> pdb=" O CYS A 927 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASN A 857 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 896 " --> pdb=" O ASN A 857 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 580 through 583 removed outlier: 6.917A pdb=" N LYS A 812 " --> pdb=" O ARG A 567 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE A 569 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLU A 810 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU A 571 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA A 808 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N LYS A 573 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 11.840A pdb=" N ALA A 806 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N CYS A 575 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 11.853A pdb=" N ILE A 804 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 11.530A pdb=" N ILE A 577 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 14.661A pdb=" N ILE A 802 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER A 706 " --> pdb=" O CYS A 696 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 637 through 640 Processing sheet with id=AA7, first strand: chain 'A' and resid 667 through 673 removed outlier: 6.705A pdb=" N THR A 678 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG A 672 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.636A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 91 removed outlier: 5.869A pdb=" N ASN C 301 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL C 205 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.287A pdb=" N ILE C 186 " --> pdb=" O VAL C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 428 hydrogen bonds defined for protein. 1200 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: 2.12 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1924 1.32 - 1.46: 4556 1.46 - 1.60: 5317 1.60 - 1.74: 5 1.74 - 1.88: 81 Bond restraints: 11883 Sorted by residual: bond pdb=" O5' ATP A1403 " pdb=" PA ATP A1403 " ideal model delta sigma weight residual 1.579 1.882 -0.303 1.10e-02 8.26e+03 7.61e+02 bond pdb=" O3A ATP A1403 " pdb=" PB ATP A1403 " ideal model delta sigma weight residual 1.592 1.829 -0.237 1.10e-02 8.26e+03 4.66e+02 bond pdb=" C5' ATP A1403 " pdb=" O5' ATP A1403 " ideal model delta sigma weight residual 1.443 1.341 0.102 1.00e-02 1.00e+04 1.04e+02 bond pdb=" O3B ATP A1403 " pdb=" PG ATP A1403 " ideal model delta sigma weight residual 1.600 1.758 -0.158 2.80e-02 1.28e+03 3.18e+01 bond pdb=" C2 ATP A1403 " pdb=" N1 ATP A1403 " ideal model delta sigma weight residual 1.334 1.378 -0.044 1.00e-02 1.00e+04 1.91e+01 ... (remaining 11878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 16055 5.41 - 10.83: 39 10.83 - 16.24: 7 16.24 - 21.66: 3 21.66 - 27.07: 3 Bond angle restraints: 16107 Sorted by residual: angle pdb=" PA ATP A1403 " pdb=" O3A ATP A1403 " pdb=" PB ATP A1403 " ideal model delta sigma weight residual 136.83 109.76 27.07 1.00e+00 1.00e+00 7.33e+02 angle pdb=" PB ATP A1403 " pdb=" O3B ATP A1403 " pdb=" PG ATP A1403 " ideal model delta sigma weight residual 139.87 113.20 26.67 1.00e+00 1.00e+00 7.11e+02 angle pdb=" C5' ATP A1403 " pdb=" O5' ATP A1403 " pdb=" PA ATP A1403 " ideal model delta sigma weight residual 121.27 105.44 15.83 1.00e+00 1.00e+00 2.51e+02 angle pdb=" O2B ATP A1403 " pdb=" PB ATP A1403 " pdb=" O3A ATP A1403 " ideal model delta sigma weight residual 106.94 88.87 18.07 1.88e+00 2.83e-01 9.24e+01 angle pdb=" O3B ATP A1403 " pdb=" PG ATP A1403 " pdb=" O3G ATP A1403 " ideal model delta sigma weight residual 104.48 94.90 9.58 1.14e+00 7.76e-01 7.12e+01 ... (remaining 16102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.57: 6384 23.57 - 47.14: 572 47.14 - 70.71: 81 70.71 - 94.28: 19 94.28 - 117.85: 5 Dihedral angle restraints: 7061 sinusoidal: 2905 harmonic: 4156 Sorted by residual: dihedral pdb=" CB CYS C 176 " pdb=" SG CYS C 176 " pdb=" SG CYS C 190 " pdb=" CB CYS C 190 " ideal model delta sinusoidal sigma weight residual 93.00 35.20 57.80 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" C8 2Y5 A1401 " pdb=" C7 2Y5 A1401 " pdb=" O13 2Y5 A1401 " pdb=" P1 2Y5 A1401 " ideal model delta sinusoidal sigma weight residual 156.14 -86.01 -117.85 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" O1 2Y5 A1401 " pdb=" C1 2Y5 A1401 " pdb=" C2 2Y5 A1401 " pdb=" O2 2Y5 A1401 " ideal model delta sinusoidal sigma weight residual -69.54 40.35 -109.89 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 7058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.988: 1837 0.988 - 1.975: 0 1.975 - 2.963: 0 2.963 - 3.950: 1 3.950 - 4.938: 1 Chirality restraints: 1839 Sorted by residual: chirality pdb=" C1 2Y5 A1401 " pdb=" C2 2Y5 A1401 " pdb=" C6 2Y5 A1401 " pdb=" O1 2Y5 A1401 " both_signs ideal model delta sigma weight residual False -2.53 2.40 -4.94 2.00e-01 2.50e+01 6.10e+02 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN C 288 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 1.07 -3.47 2.00e-01 2.50e+01 3.01e+02 chirality pdb=" C4' ATP A1403 " pdb=" C3' ATP A1403 " pdb=" C5' ATP A1403 " pdb=" O4' ATP A1403 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1836 not shown) Planarity restraints: 2002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 216 " 0.173 2.00e-02 2.50e+03 1.84e-01 4.23e+02 pdb=" CG ASN C 216 " -0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN C 216 " -0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN C 216 " -0.277 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 288 " -0.145 2.00e-02 2.50e+03 1.59e-01 3.16e+02 pdb=" CG ASN C 288 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN C 288 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN C 288 " 0.252 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A1056 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO A1057 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A1057 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1057 " 0.025 5.00e-02 4.00e+02 ... (remaining 1999 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 139 2.64 - 3.20: 10107 3.20 - 3.77: 16973 3.77 - 4.33: 24609 4.33 - 4.90: 40283 Nonbonded interactions: 92111 Sorted by model distance: nonbonded pdb="MG MG A1402 " pdb=" O HOH A1501 " model vdw 2.071 2.170 nonbonded pdb=" O THR A 562 " pdb="MG MG A1402 " model vdw 2.125 2.170 nonbonded pdb=" OD2 ASP C 173 " pdb=" OG SER C 175 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR A 782 " pdb=" OD1 ASP A 784 " model vdw 2.263 3.040 nonbonded pdb=" O PRO A1177 " pdb=" OG SER A1181 " model vdw 2.284 3.040 ... (remaining 92106 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 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.600 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.005 0.303 11893 Z= 0.390 Angle : 0.931 30.959 16135 Z= 0.506 Chirality : 0.147 4.938 1839 Planarity : 0.003 0.046 1999 Dihedral : 17.292 117.850 4375 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.06 % Allowed : 21.29 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.19), residues: 1409 helix: -2.34 (0.19), residues: 554 sheet: -1.22 (0.35), residues: 215 loop : -3.06 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 710 TYR 0.016 0.001 TYR A1225 PHE 0.015 0.001 PHE A 213 TRP 0.005 0.001 TRP A1028 HIS 0.004 0.000 HIS A 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.39 (11883) covalent geometry : angle 0.85197 / 0.49 (16107) SS BOND : bond 0.00379 / 0.27 ( 2) SS BOND : angle 1.02609 / 0.71 ( 4) hydrogen bonds : bond 0.21873 / 13.65 ( 428) hydrogen bonds : angle 7.18994 / 5.23 ( 1200) link_BETA1-3 : bond 0.00614 / 0.41 ( 1) link_BETA1-3 : angle 1.61743 / 0.99 ( 3) link_BETA1-4 : bond 0.00532 / 0.33 ( 4) link_BETA1-4 : angle 1.29498 / 0.95 ( 12) link_NAG-ASN : bond 0.03080 / 1.90 ( 3) link_NAG-ASN : angle 15.87989 / 6.60 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 143 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 203 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7239 (mp) REVERT: A 349 GLN cc_start: 0.7632 (pt0) cc_final: 0.7267 (pt0) REVERT: A 838 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7368 (mtp180) REVERT: A 977 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6231 (mtp) REVERT: A 1178 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7594 (mt) REVERT: A 1193 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.5474 (t80) REVERT: C 121 GLN cc_start: 0.7924 (mt0) cc_final: 0.7589 (mt0) REVERT: C 250 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7978 (tttm) REVERT: C 251 TYR cc_start: 0.8790 (m-10) cc_final: 0.8571 (m-80) REVERT: C 361 MET cc_start: 0.4589 (OUTLIER) cc_final: 0.3770 (ppp) REVERT: C 366 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7311 (t80) outliers start: 76 outliers final: 48 residues processed: 209 average time/residue: 0.0941 time to fit residues: 29.8276 Evaluate side-chains 182 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 127 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1090 SER Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0060 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 238 GLN A 641 GLN A 745 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.152240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110458 restraints weight = 15422.006| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.30 r_work: 0.3119 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11893 Z= 0.127 Angle : 0.560 11.545 16135 Z= 0.278 Chirality : 0.043 0.205 1839 Planarity : 0.003 0.045 1999 Dihedral : 10.059 104.996 1755 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.23 % Allowed : 22.17 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.21), residues: 1409 helix: -1.10 (0.21), residues: 555 sheet: -0.84 (0.34), residues: 221 loop : -2.75 (0.21), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 786 TYR 0.017 0.001 TYR C 77 PHE 0.013 0.001 PHE A 626 TRP 0.012 0.001 TRP A1157 HIS 0.004 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (11883) covalent geometry : angle 0.55518 / 0.28 (16107) SS BOND : bond 0.00735 / 0.52 ( 2) SS BOND : angle 1.72822 / 1.18 ( 4) hydrogen bonds : bond 0.04503 / 2.75 ( 428) hydrogen bonds : angle 4.63415 / 3.32 ( 1200) link_BETA1-3 : bond 0.00560 / 0.37 ( 1) link_BETA1-3 : angle 1.62955 / 0.96 ( 3) link_BETA1-4 : bond 0.00703 / 0.48 ( 4) link_BETA1-4 : angle 1.45680 / 0.98 ( 12) link_NAG-ASN : bond 0.00987 / 0.50 ( 3) link_NAG-ASN : angle 2.20754 / 1.28 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 130 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6374 (t0) cc_final: 0.5651 (t0) REVERT: A 203 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7241 (mp) REVERT: A 349 GLN cc_start: 0.7833 (pt0) cc_final: 0.7472 (pt0) REVERT: A 549 GLU cc_start: 0.7847 (pm20) cc_final: 0.7555 (pm20) REVERT: A 838 ARG cc_start: 0.8323 (mtp180) cc_final: 0.7659 (mtt-85) REVERT: A 932 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7582 (tt) REVERT: A 977 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.7028 (mtm) REVERT: A 1193 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6454 (t80) REVERT: C 55 ILE cc_start: 0.8342 (mm) cc_final: 0.7782 (tt) REVERT: C 121 GLN cc_start: 0.7963 (mt0) cc_final: 0.7689 (mt0) REVERT: C 250 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8062 (ttmm) REVERT: C 251 TYR cc_start: 0.9047 (m-10) cc_final: 0.8807 (m-80) REVERT: C 361 MET cc_start: 0.4859 (ptt) cc_final: 0.3829 (ppp) REVERT: C 366 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.7777 (t80) outliers start: 53 outliers final: 35 residues processed: 172 average time/residue: 0.0893 time to fit residues: 23.3039 Evaluate side-chains 160 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 84 optimal weight: 0.4980 chunk 123 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 521 GLN A 745 HIS ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107506 restraints weight = 15505.882| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.32 r_work: 0.3070 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11893 Z= 0.126 Angle : 0.535 11.625 16135 Z= 0.264 Chirality : 0.043 0.232 1839 Planarity : 0.003 0.045 1999 Dihedral : 9.103 99.766 1702 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.63 % Allowed : 20.97 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.22), residues: 1409 helix: -0.53 (0.22), residues: 564 sheet: -0.40 (0.34), residues: 221 loop : -2.49 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 744 TYR 0.021 0.001 TYR C 77 PHE 0.014 0.001 PHE A 511 TRP 0.008 0.001 TRP A 499 HIS 0.007 0.001 HIS A 745 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11883) covalent geometry : angle 0.53189 / 0.26 (16107) SS BOND : bond 0.00675 / 0.48 ( 2) SS BOND : angle 1.61026 / 1.04 ( 4) hydrogen bonds : bond 0.03893 / 2.40 ( 428) hydrogen bonds : angle 4.20243 / 2.99 ( 1200) link_BETA1-3 : bond 0.00495 / 0.33 ( 1) link_BETA1-3 : angle 1.84006 / 1.09 ( 3) link_BETA1-4 : bond 0.00705 / 0.47 ( 4) link_BETA1-4 : angle 1.46960 / 0.99 ( 12) link_NAG-ASN : bond 0.00551 / 0.28 ( 3) link_NAG-ASN : angle 1.57810 / 1.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 126 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6490 (t0) cc_final: 0.5711 (t0) REVERT: A 349 GLN cc_start: 0.7876 (pt0) cc_final: 0.7504 (pt0) REVERT: A 374 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7579 (mm-40) REVERT: A 549 GLU cc_start: 0.8114 (pm20) cc_final: 0.7625 (pm20) REVERT: A 838 ARG cc_start: 0.8301 (mtp180) cc_final: 0.7703 (mtt-85) REVERT: A 932 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7700 (tt) REVERT: A 977 MET cc_start: 0.7522 (mtm) cc_final: 0.7304 (mtm) REVERT: A 1178 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7319 (mp) REVERT: A 1193 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.6869 (t80) REVERT: C 55 ILE cc_start: 0.8369 (mm) cc_final: 0.7827 (tt) REVERT: C 121 GLN cc_start: 0.8044 (mt0) cc_final: 0.7732 (mt0) REVERT: C 180 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7973 (ttt-90) REVERT: C 250 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8115 (ttmm) REVERT: C 251 TYR cc_start: 0.9144 (m-10) cc_final: 0.8905 (m-80) REVERT: C 361 MET cc_start: 0.4921 (ptt) cc_final: 0.3881 (ppp) REVERT: C 366 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7837 (t80) outliers start: 58 outliers final: 42 residues processed: 174 average time/residue: 0.0906 time to fit residues: 24.3043 Evaluate side-chains 165 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 105 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 GLN A 613 ASN ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.149252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106657 restraints weight = 15513.220| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.29 r_work: 0.3062 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11893 Z= 0.124 Angle : 0.523 11.705 16135 Z= 0.259 Chirality : 0.043 0.217 1839 Planarity : 0.003 0.045 1999 Dihedral : 8.818 91.442 1699 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.55 % Allowed : 21.05 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.22), residues: 1409 helix: -0.22 (0.23), residues: 559 sheet: -0.31 (0.34), residues: 227 loop : -2.33 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 786 TYR 0.021 0.001 TYR C 77 PHE 0.012 0.001 PHE A 511 TRP 0.007 0.001 TRP A 499 HIS 0.005 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (11883) covalent geometry : angle 0.51958 / 0.26 (16107) SS BOND : bond 0.00673 / 0.48 ( 2) SS BOND : angle 1.63585 / 1.07 ( 4) hydrogen bonds : bond 0.03638 / 2.23 ( 428) hydrogen bonds : angle 4.08262 / 2.92 ( 1200) link_BETA1-3 : bond 0.00598 / 0.40 ( 1) link_BETA1-3 : angle 1.87343 / 1.12 ( 3) link_BETA1-4 : bond 0.00718 / 0.48 ( 4) link_BETA1-4 : angle 1.39652 / 0.96 ( 12) link_NAG-ASN : bond 0.00358 / 0.20 ( 3) link_NAG-ASN : angle 1.42018 / 0.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 124 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 GLN cc_start: 0.7868 (pt0) cc_final: 0.7497 (pt0) REVERT: A 664 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7693 (p0) REVERT: A 932 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7703 (tt) REVERT: A 977 MET cc_start: 0.7559 (mtm) cc_final: 0.7345 (mtm) REVERT: A 1193 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7076 (t80) REVERT: C 55 ILE cc_start: 0.8368 (mm) cc_final: 0.7834 (tt) REVERT: C 121 GLN cc_start: 0.8048 (mt0) cc_final: 0.7704 (mt0) REVERT: C 250 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8088 (ttmm) REVERT: C 361 MET cc_start: 0.4949 (ptt) cc_final: 0.3899 (ppp) REVERT: C 366 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7808 (t80) outliers start: 57 outliers final: 39 residues processed: 171 average time/residue: 0.0955 time to fit residues: 24.4440 Evaluate side-chains 164 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 30 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 86 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108439 restraints weight = 15510.051| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.31 r_work: 0.3075 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11893 Z= 0.098 Angle : 0.508 11.646 16135 Z= 0.251 Chirality : 0.042 0.219 1839 Planarity : 0.003 0.044 1999 Dihedral : 8.463 85.661 1695 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.63 % Allowed : 21.13 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.22), residues: 1409 helix: 0.03 (0.23), residues: 557 sheet: -0.19 (0.34), residues: 234 loop : -2.17 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 786 TYR 0.020 0.001 TYR C 77 PHE 0.011 0.001 PHE A 669 TRP 0.007 0.001 TRP A1134 HIS 0.003 0.000 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11883) covalent geometry : angle 0.50565 / 0.25 (16107) SS BOND : bond 0.00575 / 0.41 ( 2) SS BOND : angle 1.34454 / 0.90 ( 4) hydrogen bonds : bond 0.03266 / 2.02 ( 428) hydrogen bonds : angle 3.94194 / 2.81 ( 1200) link_BETA1-3 : bond 0.00597 / 0.40 ( 1) link_BETA1-3 : angle 1.88185 / 1.16 ( 3) link_BETA1-4 : bond 0.00692 / 0.46 ( 4) link_BETA1-4 : angle 1.32323 / 0.90 ( 12) link_NAG-ASN : bond 0.00357 / 0.20 ( 3) link_NAG-ASN : angle 1.27421 / 0.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 128 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 203 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7356 (mp) REVERT: A 349 GLN cc_start: 0.7847 (pt0) cc_final: 0.7484 (pt0) REVERT: A 374 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7648 (mm-40) REVERT: A 664 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7713 (p0) REVERT: A 800 ASN cc_start: 0.7971 (p0) cc_final: 0.7753 (t0) REVERT: A 932 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7688 (tt) REVERT: A 1178 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7326 (mp) REVERT: A 1193 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.6844 (t80) REVERT: A 1228 ARG cc_start: 0.8174 (tpt90) cc_final: 0.6920 (ttt90) REVERT: C 55 ILE cc_start: 0.8340 (mm) cc_final: 0.7871 (tt) REVERT: C 71 GLN cc_start: 0.8891 (mp10) cc_final: 0.8620 (mt0) REVERT: C 121 GLN cc_start: 0.8053 (mt0) cc_final: 0.7758 (mt0) REVERT: C 250 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8109 (ttmm) REVERT: C 361 MET cc_start: 0.5025 (ptt) cc_final: 0.3910 (ppp) REVERT: C 366 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7774 (t80) outliers start: 58 outliers final: 40 residues processed: 176 average time/residue: 0.0948 time to fit residues: 25.4429 Evaluate side-chains 166 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 43 optimal weight: 9.9990 chunk 113 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104702 restraints weight = 15612.359| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.32 r_work: 0.3031 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11893 Z= 0.155 Angle : 0.551 11.680 16135 Z= 0.275 Chirality : 0.044 0.190 1839 Planarity : 0.003 0.045 1999 Dihedral : 8.368 83.798 1690 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.86 % Allowed : 21.29 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.22), residues: 1409 helix: 0.04 (0.23), residues: 559 sheet: -0.08 (0.35), residues: 219 loop : -2.20 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 182 TYR 0.023 0.001 TYR C 77 PHE 0.014 0.001 PHE A1067 TRP 0.009 0.001 TRP A 499 HIS 0.007 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 (11883) covalent geometry : angle 0.54776 / 0.27 (16107) SS BOND : bond 0.00748 / 0.53 ( 2) SS BOND : angle 1.84239 / 1.15 ( 4) hydrogen bonds : bond 0.03865 / 2.38 ( 428) hydrogen bonds : angle 4.03774 / 2.89 ( 1200) link_BETA1-3 : bond 0.00529 / 0.35 ( 1) link_BETA1-3 : angle 1.95148 / 1.15 ( 3) link_BETA1-4 : bond 0.00728 / 0.49 ( 4) link_BETA1-4 : angle 1.40420 / 0.99 ( 12) link_NAG-ASN : bond 0.00307 / 0.20 ( 3) link_NAG-ASN : angle 1.41029 / 1.02 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 124 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 349 GLN cc_start: 0.7846 (pt0) cc_final: 0.7488 (pt0) REVERT: A 664 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7650 (p0) REVERT: A 838 ARG cc_start: 0.8201 (mtp180) cc_final: 0.7709 (mtt-85) REVERT: A 932 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7706 (tt) REVERT: A 1178 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7353 (mp) REVERT: A 1193 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7377 (t80) REVERT: A 1224 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7765 (tttp) REVERT: C 55 ILE cc_start: 0.8375 (mm) cc_final: 0.7889 (tt) REVERT: C 121 GLN cc_start: 0.8015 (mt0) cc_final: 0.7674 (mt0) REVERT: C 250 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8145 (ttmm) REVERT: C 273 MET cc_start: 0.9452 (mmm) cc_final: 0.9184 (mmm) REVERT: C 361 MET cc_start: 0.5040 (ptt) cc_final: 0.3984 (ppp) REVERT: C 366 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7828 (t80) outliers start: 61 outliers final: 43 residues processed: 172 average time/residue: 0.0835 time to fit residues: 22.0611 Evaluate side-chains 169 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1224 LYS Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 137 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 90 optimal weight: 0.0040 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105457 restraints weight = 15528.968| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.32 r_work: 0.3046 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11893 Z= 0.127 Angle : 0.531 11.651 16135 Z= 0.265 Chirality : 0.043 0.190 1839 Planarity : 0.003 0.046 1999 Dihedral : 8.178 84.165 1689 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.70 % Allowed : 21.69 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.22), residues: 1409 helix: 0.13 (0.23), residues: 559 sheet: -0.00 (0.35), residues: 219 loop : -2.12 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.023 0.001 TYR C 77 PHE 0.012 0.001 PHE A1094 TRP 0.007 0.001 TRP A 499 HIS 0.005 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (11883) covalent geometry : angle 0.52773 / 0.26 (16107) SS BOND : bond 0.00641 / 0.46 ( 2) SS BOND : angle 1.58393 / 1.01 ( 4) hydrogen bonds : bond 0.03578 / 2.21 ( 428) hydrogen bonds : angle 3.99135 / 2.85 ( 1200) link_BETA1-3 : bond 0.00500 / 0.33 ( 1) link_BETA1-3 : angle 1.97245 / 1.19 ( 3) link_BETA1-4 : bond 0.00699 / 0.47 ( 4) link_BETA1-4 : angle 1.34090 / 0.93 ( 12) link_NAG-ASN : bond 0.00273 / 0.17 ( 3) link_NAG-ASN : angle 1.32530 / 0.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 122 time to evaluate : 0.487 Fit side-chains REVERT: A 203 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7360 (mp) REVERT: A 349 GLN cc_start: 0.7802 (pt0) cc_final: 0.7451 (pt0) REVERT: A 374 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7662 (mm-40) REVERT: A 664 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7584 (p0) REVERT: A 838 ARG cc_start: 0.8228 (mtp180) cc_final: 0.7710 (mtt-85) REVERT: A 932 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7729 (tt) REVERT: A 943 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8091 (ttm170) REVERT: A 1178 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7375 (mp) REVERT: A 1193 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7262 (t80) REVERT: A 1228 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.6945 (ttt90) REVERT: C 55 ILE cc_start: 0.8358 (mm) cc_final: 0.7872 (tt) REVERT: C 71 GLN cc_start: 0.8889 (mp10) cc_final: 0.8611 (mt0) REVERT: C 121 GLN cc_start: 0.8015 (mt0) cc_final: 0.7675 (mt0) REVERT: C 250 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8150 (ttmm) REVERT: C 361 MET cc_start: 0.5033 (ptt) cc_final: 0.3989 (ppp) REVERT: C 366 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7800 (t80) outliers start: 59 outliers final: 43 residues processed: 170 average time/residue: 0.0949 time to fit residues: 24.3379 Evaluate side-chains 169 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 117 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 35 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.149346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106859 restraints weight = 15484.992| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.33 r_work: 0.3061 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11893 Z= 0.100 Angle : 0.509 11.589 16135 Z= 0.253 Chirality : 0.042 0.189 1839 Planarity : 0.003 0.045 1999 Dihedral : 7.903 85.432 1689 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.15 % Allowed : 22.25 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.23), residues: 1409 helix: 0.30 (0.23), residues: 557 sheet: 0.05 (0.36), residues: 219 loop : -2.02 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 710 TYR 0.022 0.001 TYR C 77 PHE 0.012 0.001 PHE A 669 TRP 0.007 0.001 TRP A1132 HIS 0.004 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (11883) covalent geometry : angle 0.50672 / 0.25 (16107) SS BOND : bond 0.00379 / 0.27 ( 2) SS BOND : angle 1.15259 / 0.71 ( 4) hydrogen bonds : bond 0.03230 / 2.01 ( 428) hydrogen bonds : angle 3.90429 / 2.79 ( 1200) link_BETA1-3 : bond 0.00473 / 0.32 ( 1) link_BETA1-3 : angle 1.92159 / 1.19 ( 3) link_BETA1-4 : bond 0.00725 / 0.48 ( 4) link_BETA1-4 : angle 1.31992 / 0.90 ( 12) link_NAG-ASN : bond 0.00261 / 0.15 ( 3) link_NAG-ASN : angle 1.30043 / 0.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 0.488 Fit side-chains REVERT: A 203 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7356 (mp) REVERT: A 349 GLN cc_start: 0.7777 (pt0) cc_final: 0.7432 (pt0) REVERT: A 414 PHE cc_start: 0.8304 (m-10) cc_final: 0.8057 (m-10) REVERT: A 664 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7636 (p0) REVERT: A 838 ARG cc_start: 0.8247 (mtp180) cc_final: 0.7748 (mtt-85) REVERT: A 932 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7695 (tt) REVERT: A 943 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8068 (ttm170) REVERT: A 1178 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7326 (mp) REVERT: A 1193 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7130 (t80) REVERT: A 1228 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.6917 (ttt90) REVERT: C 55 ILE cc_start: 0.8359 (mm) cc_final: 0.7881 (tt) REVERT: C 71 GLN cc_start: 0.8875 (mp10) cc_final: 0.8608 (mt0) REVERT: C 121 GLN cc_start: 0.8014 (mt0) cc_final: 0.7726 (mt0) REVERT: C 250 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8159 (ttmm) REVERT: C 258 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: C 361 MET cc_start: 0.5090 (ptt) cc_final: 0.4081 (ppp) REVERT: C 366 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7703 (t80) outliers start: 52 outliers final: 38 residues processed: 166 average time/residue: 0.1004 time to fit residues: 25.1446 Evaluate side-chains 168 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 120 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 131 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.149844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107788 restraints weight = 15442.914| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.20 r_work: 0.3050 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11893 Z= 0.102 Angle : 0.507 11.089 16135 Z= 0.252 Chirality : 0.042 0.194 1839 Planarity : 0.003 0.045 1999 Dihedral : 7.616 84.082 1683 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.15 % Allowed : 22.41 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.23), residues: 1409 helix: 0.38 (0.23), residues: 556 sheet: 0.12 (0.36), residues: 218 loop : -2.00 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 710 TYR 0.022 0.001 TYR C 77 PHE 0.012 0.001 PHE A 669 TRP 0.007 0.001 TRP A1134 HIS 0.004 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (11883) covalent geometry : angle 0.50418 / 0.25 (16107) SS BOND : bond 0.00580 / 0.41 ( 2) SS BOND : angle 1.28499 / 0.83 ( 4) hydrogen bonds : bond 0.03223 / 2.01 ( 428) hydrogen bonds : angle 3.86889 / 2.76 ( 1200) link_BETA1-3 : bond 0.00504 / 0.34 ( 1) link_BETA1-3 : angle 1.90406 / 1.17 ( 3) link_BETA1-4 : bond 0.00733 / 0.49 ( 4) link_BETA1-4 : angle 1.35922 / 0.92 ( 12) link_NAG-ASN : bond 0.00218 / 0.14 ( 3) link_NAG-ASN : angle 1.53515 / 0.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 121 time to evaluate : 0.451 Fit side-chains REVERT: A 188 ASN cc_start: 0.6325 (t0) cc_final: 0.5607 (t0) REVERT: A 203 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7398 (mp) REVERT: A 349 GLN cc_start: 0.7780 (pt0) cc_final: 0.7442 (pt0) REVERT: A 374 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7615 (mm-40) REVERT: A 414 PHE cc_start: 0.8283 (m-10) cc_final: 0.8067 (m-10) REVERT: A 419 PHE cc_start: 0.8805 (m-80) cc_final: 0.8452 (m-10) REVERT: A 664 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7661 (p0) REVERT: A 838 ARG cc_start: 0.8240 (mtp180) cc_final: 0.7740 (mtt-85) REVERT: A 932 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7694 (tt) REVERT: A 943 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8086 (ttm170) REVERT: A 1178 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7338 (mp) REVERT: A 1193 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7099 (t80) REVERT: A 1228 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.6929 (ttt90) REVERT: C 55 ILE cc_start: 0.8343 (mm) cc_final: 0.7868 (tt) REVERT: C 71 GLN cc_start: 0.8896 (mp10) cc_final: 0.8625 (mt0) REVERT: C 121 GLN cc_start: 0.8002 (mt0) cc_final: 0.7719 (mt0) REVERT: C 250 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8174 (ttmm) REVERT: C 258 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: C 361 MET cc_start: 0.5037 (ptt) cc_final: 0.4062 (ppp) REVERT: C 366 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7681 (t80) outliers start: 52 outliers final: 37 residues processed: 164 average time/residue: 0.0992 time to fit residues: 24.4858 Evaluate side-chains 168 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 0.0270 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108777 restraints weight = 15545.102| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.29 r_work: 0.3072 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11893 Z= 0.090 Angle : 0.492 8.752 16135 Z= 0.246 Chirality : 0.042 0.198 1839 Planarity : 0.003 0.045 1999 Dihedral : 7.411 84.761 1682 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.75 % Allowed : 22.81 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.23), residues: 1409 helix: 0.51 (0.24), residues: 556 sheet: 0.18 (0.36), residues: 218 loop : -1.95 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 786 TYR 0.022 0.001 TYR C 77 PHE 0.013 0.001 PHE A 669 TRP 0.008 0.001 TRP A1132 HIS 0.003 0.000 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (11883) covalent geometry : angle 0.48850 / 0.24 (16107) SS BOND : bond 0.00432 / 0.31 ( 2) SS BOND : angle 1.03532 / 0.68 ( 4) hydrogen bonds : bond 0.02967 / 1.86 ( 428) hydrogen bonds : angle 3.81654 / 2.73 ( 1200) link_BETA1-3 : bond 0.00532 / 0.35 ( 1) link_BETA1-3 : angle 1.87151 / 1.17 ( 3) link_BETA1-4 : bond 0.00789 / 0.52 ( 4) link_BETA1-4 : angle 1.38990 / 0.91 ( 12) link_NAG-ASN : bond 0.00151 / 0.11 ( 3) link_NAG-ASN : angle 1.79890 / 0.84 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.364 Fit side-chains REVERT: A 203 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7413 (mp) REVERT: A 349 GLN cc_start: 0.7760 (pt0) cc_final: 0.7421 (pt0) REVERT: A 374 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7583 (mm-40) REVERT: A 419 PHE cc_start: 0.8777 (m-80) cc_final: 0.8423 (m-10) REVERT: A 664 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7644 (p0) REVERT: A 800 ASN cc_start: 0.6995 (t0) cc_final: 0.5688 (p0) REVERT: A 838 ARG cc_start: 0.8237 (mtp180) cc_final: 0.7758 (mtt-85) REVERT: A 932 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7676 (tt) REVERT: A 943 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8069 (ttm170) REVERT: A 1178 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7366 (mp) REVERT: A 1193 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.6888 (t80) REVERT: A 1228 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.6912 (ttt90) REVERT: C 55 ILE cc_start: 0.8283 (mm) cc_final: 0.7808 (tt) REVERT: C 71 GLN cc_start: 0.8891 (mp10) cc_final: 0.8653 (mt0) REVERT: C 121 GLN cc_start: 0.8007 (mt0) cc_final: 0.7625 (mt0) REVERT: C 250 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8154 (ttmm) REVERT: C 258 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: C 361 MET cc_start: 0.5003 (ptt) cc_final: 0.4091 (ppp) REVERT: C 366 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7686 (t80) outliers start: 47 outliers final: 35 residues processed: 165 average time/residue: 0.1028 time to fit residues: 25.4310 Evaluate side-chains 166 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 664 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 943 ARG Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 130 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 25 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102583 restraints weight = 15679.625| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.09 r_work: 0.2998 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11893 Z= 0.211 Angle : 0.588 8.454 16135 Z= 0.296 Chirality : 0.045 0.219 1839 Planarity : 0.003 0.047 1999 Dihedral : 7.831 86.127 1682 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.15 % Allowed : 22.57 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.22), residues: 1409 helix: 0.08 (0.23), residues: 565 sheet: 0.07 (0.36), residues: 219 loop : -2.08 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 182 TYR 0.028 0.002 TYR C 77 PHE 0.016 0.002 PHE C 269 TRP 0.009 0.001 TRP A 412 HIS 0.009 0.001 HIS A1198 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.21 (11883) covalent geometry : angle 0.58403 / 0.29 (16107) SS BOND : bond 0.00789 / 0.56 ( 2) SS BOND : angle 1.88300 / 1.12 ( 4) hydrogen bonds : bond 0.04152 / 2.56 ( 428) hydrogen bonds : angle 4.05061 / 2.89 ( 1200) link_BETA1-3 : bond 0.00541 / 0.36 ( 1) link_BETA1-3 : angle 2.03014 / 1.18 ( 3) link_BETA1-4 : bond 0.00814 / 0.54 ( 4) link_BETA1-4 : angle 1.58953 / 1.09 ( 12) link_NAG-ASN : bond 0.00326 / 0.22 ( 3) link_NAG-ASN : angle 1.87132 / 1.11 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.37 seconds wall clock time: 58 minutes 8.96 seconds (3488.96 seconds total)