Starting phenix.real_space_refine on Wed Jul 30 07:18:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6roh_4972/07_2025/6roh_4972.cif Found real_map, /net/cci-nas-00/data/ceres_data/6roh_4972/07_2025/6roh_4972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6roh_4972/07_2025/6roh_4972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6roh_4972/07_2025/6roh_4972.map" model { file = "/net/cci-nas-00/data/ceres_data/6roh_4972/07_2025/6roh_4972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6roh_4972/07_2025/6roh_4972.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 48 5.16 5 Be 1 3.05 5 C 7580 2.51 5 N 1917 2.21 5 O 2207 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11758 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8895 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 30, 'TRANS': 1081} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2738 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 20, 'TRANS': 316} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'PSF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 7.16, per 1000 atoms: 0.61 Number of scatterers: 11758 At special positions: 0 Unit cell: (74.313, 96.93, 173.397, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 1 15.00 Mg 1 11.99 F 3 9.00 O 2207 8.00 N 1917 7.00 C 7580 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA D 3 " - " BMA D 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 503 " - " ASN C 216 " " NAG D 1 " - " ASN C 199 " Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.6 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2740 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 41.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 212 through 223 removed outlier: 3.845A pdb=" N LYS A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 removed outlier: 3.658A pdb=" N LEU A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 270 removed outlier: 3.587A pdb=" N THR A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.600A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.635A pdb=" N ASN A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 473 removed outlier: 3.758A pdb=" N ARG A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 502 removed outlier: 3.832A pdb=" N PHE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 506 removed outlier: 3.517A 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 510 through 526 removed outlier: 3.508A pdb=" N LEU A 516 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.846A pdb=" N LEU A 547 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 548 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLU A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 550 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 551 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 618 through 631 removed outlier: 4.526A pdb=" N ILE A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 664 removed outlier: 3.510A pdb=" N VAL A 659 " --> pdb=" O GLU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 738 through 751 removed outlier: 3.767A pdb=" N ARG A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 removed outlier: 3.747A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 838 through 849 removed outlier: 3.533A pdb=" N ASN A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 881 removed outlier: 3.759A pdb=" N GLU A 870 " --> pdb=" O ARG A 866 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN A 881 " --> pdb=" O ILE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 899 through 905 removed outlier: 3.546A pdb=" N PHE A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 919 removed outlier: 3.591A pdb=" N VAL A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 943 removed outlier: 3.969A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 958 removed outlier: 3.603A pdb=" N ASP A 958 " --> pdb=" O GLY A 955 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 955 through 958' Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 978 through 983 removed outlier: 3.586A pdb=" N SER A 982 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 991 No H-bonds generated for 'chain 'A' and resid 989 through 991' Processing helix chain 'A' and resid 992 through 999 Processing helix chain 'A' and resid 999 through 1019 removed outlier: 3.667A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.629A pdb=" N TYR A1023 " --> pdb=" O ASN A1019 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A1024 " --> pdb=" O THR A1020 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1019 through 1024' Processing helix chain 'A' and resid 1024 through 1029 Processing helix chain 'A' and resid 1030 through 1032 No H-bonds generated for 'chain 'A' and resid 1030 through 1032' Processing helix chain 'A' and resid 1046 through 1052 removed outlier: 4.175A pdb=" N ASN A1050 " --> pdb=" O MET A1046 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1065 removed outlier: 3.533A pdb=" N PHE A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A1062 " --> pdb=" O PRO A1058 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP A1065 " --> pdb=" O ILE A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1076 removed outlier: 3.640A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A1075 " --> pdb=" O ARG A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1079 No H-bonds generated for 'chain 'A' and resid 1077 through 1079' Processing helix chain 'A' and resid 1080 through 1085 removed outlier: 3.520A pdb=" N GLN A1084 " --> pdb=" O TYR A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1115 removed outlier: 3.629A pdb=" N ASN A1100 " --> pdb=" O GLY A1096 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1115 " --> pdb=" O GLY A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1154 removed outlier: 3.685A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1152 " --> pdb=" O GLY A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1180 Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1181 through 1187 Proline residue: A1184 - end of helix Processing helix chain 'A' and resid 1194 through 1201 Processing helix chain 'A' and resid 1202 through 1209 removed outlier: 3.957A pdb=" N TRP A1206 " --> pdb=" O SER A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1217 Processing helix chain 'A' and resid 1217 through 1230 Processing helix chain 'A' and resid 1253 through 1258 removed outlier: 3.968A pdb=" N GLN A1257 " --> pdb=" O VAL A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1263 removed outlier: 3.604A pdb=" N LYS A1262 " --> pdb=" O ALA A1259 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A1263 " --> pdb=" O ILE A1260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1259 through 1263' Processing helix chain 'A' and resid 1280 through 1284 removed outlier: 4.253A pdb=" N GLY A1284 " --> pdb=" O GLU A1281 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.529A pdb=" N ALA C 67 " --> pdb=" O LEU C 63 " (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: 4.358A pdb=" N GLN C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 266 through 274 removed outlier: 3.749A pdb=" N VAL C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 346 Processing helix chain 'C' and resid 349 through 356 removed outlier: 3.806A pdb=" N LYS C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 354 " --> pdb=" O PHE C 350 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 356 " --> pdb=" O VAL C 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 356' 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 293 through 298 removed outlier: 3.929A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 288 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU A 285 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 315 removed outlier: 3.763A pdb=" N GLU A 314 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 401 removed outlier: 6.676A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 542 removed outlier: 6.636A pdb=" N LEU A 949 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL A 969 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA A 951 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE A 971 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLY A 953 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 948 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU A 555 " --> pdb=" O LYS A 830 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TRP A 832 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 557 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 834 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER A 559 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 831 " --> pdb=" O VAL A 924 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N CYS A 926 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A 833 " --> pdb=" O CYS A 926 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU A 893 " --> pdb=" O ALA A 923 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ILE A 925 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 895 " --> pdb=" O ILE A 925 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N CYS A 927 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 897 " --> pdb=" O CYS A 927 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 580 through 583 removed outlier: 6.613A pdb=" N MET A 570 " --> pdb=" O LYS A 812 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS A 812 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE A 572 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A 810 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU A 803 " --> pdb=" O MET A 761 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET A 761 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 694 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG A 672 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR A 678 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 670 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 640 Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 100 Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.590A pdb=" N GLU C 90 " --> pdb=" O TRP C 111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 296 " --> pdb=" O ILE C 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.590A pdb=" N GLU C 90 " --> pdb=" O TRP C 111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 296 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN C 301 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL C 205 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 137 through 143 removed outlier: 3.507A pdb=" N ILE C 137 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.099A pdb=" N ILE C 186 " --> pdb=" O VAL C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 405 hydrogen bonds defined for protein. 1161 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: 4.45 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3276 1.33 - 1.46: 2850 1.46 - 1.58: 5813 1.58 - 1.71: 2 1.71 - 1.83: 77 Bond restraints: 12018 Sorted by residual: bond pdb=" OD1 BFD A 560 " pdb="BE BFD A 560 " ideal model delta sigma weight residual 1.737 1.527 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" O2 PSF A2101 " pdb=" P PSF A2101 " ideal model delta sigma weight residual 1.637 1.701 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 BMA D 4 " pdb=" C2 BMA D 4 " ideal model delta sigma weight residual 1.519 1.578 -0.059 2.00e-02 2.50e+03 8.63e+00 bond pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.35e-02 5.49e+03 5.59e+00 bond pdb=" CA BFD A 560 " pdb=" C BFD A 560 " ideal model delta sigma weight residual 1.525 1.570 -0.045 2.10e-02 2.27e+03 4.52e+00 ... (remaining 12013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 15686 2.04 - 4.08: 512 4.08 - 6.13: 58 6.13 - 8.17: 18 8.17 - 10.21: 9 Bond angle restraints: 16283 Sorted by residual: angle pdb=" N ILE A1174 " pdb=" CA ILE A1174 " pdb=" C ILE A1174 " ideal model delta sigma weight residual 111.90 107.86 4.04 8.10e-01 1.52e+00 2.48e+01 angle pdb=" C ASP A 784 " pdb=" N ASN A 785 " pdb=" CA ASN A 785 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C CYS C 176 " pdb=" N SER C 177 " pdb=" CA SER C 177 " ideal model delta sigma weight residual 119.78 125.42 -5.64 1.24e+00 6.50e-01 2.07e+01 angle pdb=" CA CYS C 176 " pdb=" CB CYS C 176 " pdb=" SG CYS C 176 " ideal model delta sigma weight residual 114.40 123.44 -9.04 2.30e+00 1.89e-01 1.55e+01 angle pdb=" C PRO A 240 " pdb=" N HIS A 241 " pdb=" CA HIS A 241 " ideal model delta sigma weight residual 123.47 129.36 -5.89 1.53e+00 4.27e-01 1.48e+01 ... (remaining 16278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 6782 22.53 - 45.06: 416 45.06 - 67.59: 50 67.59 - 90.12: 18 90.12 - 112.65: 7 Dihedral angle restraints: 7273 sinusoidal: 3025 harmonic: 4248 Sorted by residual: dihedral pdb=" CA LEU A1114 " pdb=" C LEU A1114 " pdb=" N ILE A1115 " pdb=" CA ILE A1115 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA THR C 320 " pdb=" C THR C 320 " pdb=" N THR C 321 " pdb=" CA THR C 321 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LEU A 490 " pdb=" C LEU A 490 " pdb=" N PHE A 491 " pdb=" CA PHE A 491 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 7270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1427 0.059 - 0.118: 351 0.118 - 0.177: 63 0.177 - 0.236: 13 0.236 - 0.295: 1 Chirality restraints: 1855 Sorted by residual: chirality pdb=" C5 BMA D 4 " pdb=" C4 BMA D 4 " pdb=" C6 BMA D 4 " pdb=" O5 BMA D 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.51 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CG LEU A 480 " pdb=" CB LEU A 480 " pdb=" CD1 LEU A 480 " pdb=" CD2 LEU A 480 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1852 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 111 " 0.026 2.00e-02 2.50e+03 2.60e-02 1.68e+01 pdb=" CG TRP C 111 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP C 111 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 111 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 111 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 111 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 111 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 111 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 111 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 111 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1057 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A1058 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 977 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.37e+00 pdb=" C MET A 977 " -0.047 2.00e-02 2.50e+03 pdb=" O MET A 977 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN A 978 " 0.016 2.00e-02 2.50e+03 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 20 2.35 - 2.99: 5542 2.99 - 3.62: 16798 3.62 - 4.26: 28335 4.26 - 4.90: 46220 Nonbonded interactions: 96915 Sorted by model distance: nonbonded pdb=" F2 BFD A 560 " pdb="MG MG A2102 " model vdw 1.709 2.120 nonbonded pdb="MG MG A2102 " pdb=" O HOH A2201 " model vdw 1.742 2.170 nonbonded pdb="MG MG A2102 " pdb=" O HOH A2202 " model vdw 1.906 2.170 nonbonded pdb=" O THR A 562 " pdb=" O HOH A2201 " model vdw 1.909 3.040 nonbonded pdb=" O THR A 562 " pdb="MG MG A2102 " model vdw 2.042 2.170 ... (remaining 96910 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.110 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.210 12027 Z= 0.282 Angle : 0.901 10.208 16308 Z= 0.504 Chirality : 0.055 0.295 1855 Planarity : 0.006 0.073 2039 Dihedral : 14.973 112.654 4527 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.23 % Allowed : 5.71 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.17), residues: 1440 helix: -4.68 (0.08), residues: 565 sheet: -1.21 (0.33), residues: 234 loop : -2.22 (0.20), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP C 111 HIS 0.010 0.001 HIS A 634 PHE 0.028 0.002 PHE A1094 TYR 0.018 0.002 TYR C 141 ARG 0.006 0.001 ARG A 755 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 3) link_NAG-ASN : angle 4.74640 ( 9) link_BETA1-4 : bond 0.00720 ( 3) link_BETA1-4 : angle 1.79778 ( 9) hydrogen bonds : bond 0.29641 ( 393) hydrogen bonds : angle 9.95180 ( 1161) SS BOND : bond 0.01207 ( 2) SS BOND : angle 1.31670 ( 4) link_BETA1-3 : bond 0.00377 ( 1) link_BETA1-3 : angle 2.63258 ( 3) covalent geometry : bond 0.00626 (12018) covalent geometry : angle 0.89285 (16283) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 223 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 SER cc_start: 0.7218 (p) cc_final: 0.6902 (p) REVERT: A 263 MET cc_start: 0.6907 (mtt) cc_final: 0.6519 (mmp) REVERT: A 291 HIS cc_start: 0.6491 (t70) cc_final: 0.6291 (t70) REVERT: A 335 GLU cc_start: 0.7569 (tt0) cc_final: 0.7328 (tt0) REVERT: A 356 LYS cc_start: 0.7472 (mmtm) cc_final: 0.7268 (mtpt) REVERT: A 400 MET cc_start: 0.7561 (ttt) cc_final: 0.7156 (tpt) REVERT: A 469 MET cc_start: 0.8151 (ttm) cc_final: 0.7885 (mtp) REVERT: A 520 TYR cc_start: 0.6702 (t80) cc_final: 0.6416 (t80) REVERT: A 535 LYS cc_start: 0.8221 (tttm) cc_final: 0.7594 (ttmm) REVERT: A 540 THR cc_start: 0.8626 (t) cc_final: 0.8351 (m) REVERT: A 571 GLU cc_start: 0.7089 (tt0) cc_final: 0.6641 (mt-10) REVERT: A 604 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7562 (mtpp) REVERT: A 724 ASP cc_start: 0.8116 (p0) cc_final: 0.7845 (p0) REVERT: A 838 ARG cc_start: 0.7376 (mtm-85) cc_final: 0.7162 (mtt90) REVERT: A 856 MET cc_start: 0.8409 (ttt) cc_final: 0.8168 (ttm) REVERT: A 871 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7532 (mtp180) REVERT: A 881 ASN cc_start: 0.7158 (t0) cc_final: 0.6082 (p0) REVERT: A 1156 GLN cc_start: 0.8369 (tt0) cc_final: 0.7814 (tt0) REVERT: A 1269 MET cc_start: 0.7130 (mmm) cc_final: 0.6799 (mmp) REVERT: A 1285 GLN cc_start: 0.7973 (pm20) cc_final: 0.7503 (pm20) REVERT: A 1296 GLN cc_start: 0.7576 (tt0) cc_final: 0.7130 (tt0) REVERT: C 114 THR cc_start: 0.8177 (m) cc_final: 0.7802 (m) REVERT: C 124 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7616 (mt-10) REVERT: C 135 LYS cc_start: 0.8146 (mttt) cc_final: 0.7495 (ttpp) REVERT: C 197 MET cc_start: 0.8891 (ttt) cc_final: 0.8654 (ttt) REVERT: C 229 HIS cc_start: 0.7194 (m90) cc_final: 0.6638 (m-70) REVERT: C 250 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8164 (tttt) REVERT: C 295 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7598 (tptt) outliers start: 3 outliers final: 1 residues processed: 225 average time/residue: 1.2527 time to fit residues: 305.6358 Evaluate side-chains 131 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 877 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 130 optimal weight: 0.0980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN A 422 HIS A 580 HIS A 649 GLN A 694 ASN A 736 ASN A 891 ASN A1019 ASN A1038 GLN A1050 ASN C 30 GLN C 37 GLN C 121 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.154442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121078 restraints weight = 13543.216| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.07 r_work: 0.3203 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12027 Z= 0.142 Angle : 0.630 9.688 16308 Z= 0.328 Chirality : 0.045 0.178 1855 Planarity : 0.005 0.047 2039 Dihedral : 9.618 81.718 1741 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.19 % Allowed : 12.51 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.19), residues: 1440 helix: -2.99 (0.15), residues: 585 sheet: -0.94 (0.33), residues: 230 loop : -1.67 (0.22), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 111 HIS 0.006 0.001 HIS A 634 PHE 0.020 0.001 PHE A1094 TYR 0.011 0.001 TYR A1116 ARG 0.005 0.000 ARG C 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 3) link_NAG-ASN : angle 3.32185 ( 9) link_BETA1-4 : bond 0.00253 ( 3) link_BETA1-4 : angle 2.39435 ( 9) hydrogen bonds : bond 0.05155 ( 393) hydrogen bonds : angle 5.27927 ( 1161) SS BOND : bond 0.00767 ( 2) SS BOND : angle 0.91092 ( 4) link_BETA1-3 : bond 0.00702 ( 1) link_BETA1-3 : angle 4.14683 ( 3) covalent geometry : bond 0.00326 (12018) covalent geometry : angle 0.62068 (16283) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7751 (mtt) cc_final: 0.7191 (mmp) REVERT: A 342 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7950 (mt-10) REVERT: A 356 LYS cc_start: 0.7571 (mmtm) cc_final: 0.7206 (mtmt) REVERT: A 364 LYS cc_start: 0.8264 (pttm) cc_final: 0.7788 (ptmm) REVERT: A 385 THR cc_start: 0.8279 (m) cc_final: 0.8026 (t) REVERT: A 401 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.7908 (mt) REVERT: A 469 MET cc_start: 0.8412 (ttm) cc_final: 0.8195 (ttt) REVERT: A 490 LEU cc_start: 0.6237 (pp) cc_final: 0.5873 (mp) REVERT: A 535 LYS cc_start: 0.8472 (tttm) cc_final: 0.7876 (ttmm) REVERT: A 571 GLU cc_start: 0.8235 (tt0) cc_final: 0.7753 (mt-10) REVERT: A 838 ARG cc_start: 0.8017 (mtm-85) cc_final: 0.7362 (mmt-90) REVERT: A 871 ARG cc_start: 0.8251 (mtt180) cc_final: 0.8045 (mtt180) REVERT: A 1155 ASN cc_start: 0.7326 (m-40) cc_final: 0.6976 (m110) REVERT: A 1156 GLN cc_start: 0.8554 (tt0) cc_final: 0.8042 (tt0) REVERT: A 1296 GLN cc_start: 0.7740 (tt0) cc_final: 0.7272 (tt0) REVERT: C 47 PRO cc_start: 0.6913 (Cg_exo) cc_final: 0.6665 (Cg_endo) REVERT: C 135 LYS cc_start: 0.8501 (mttt) cc_final: 0.7823 (ttpp) REVERT: C 229 HIS cc_start: 0.7626 (m90) cc_final: 0.7158 (m-70) REVERT: C 295 LYS cc_start: 0.8525 (ttpt) cc_final: 0.7897 (tptt) outliers start: 28 outliers final: 9 residues processed: 172 average time/residue: 1.2148 time to fit residues: 229.6096 Evaluate side-chains 137 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1069 SER Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 0.0270 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 374 GLN A 736 ASN A1254 GLN C 37 GLN C 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117565 restraints weight = 13665.049| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.10 r_work: 0.3160 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12027 Z= 0.182 Angle : 0.626 8.603 16308 Z= 0.321 Chirality : 0.046 0.179 1855 Planarity : 0.004 0.041 2039 Dihedral : 7.991 66.911 1739 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.28 % Allowed : 15.25 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.20), residues: 1440 helix: -2.03 (0.19), residues: 590 sheet: -0.79 (0.33), residues: 230 loop : -1.37 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 111 HIS 0.008 0.001 HIS A 634 PHE 0.022 0.002 PHE A1094 TYR 0.011 0.001 TYR C 188 ARG 0.002 0.000 ARG A1273 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 3) link_NAG-ASN : angle 3.50649 ( 9) link_BETA1-4 : bond 0.00269 ( 3) link_BETA1-4 : angle 2.43989 ( 9) hydrogen bonds : bond 0.04527 ( 393) hydrogen bonds : angle 4.80381 ( 1161) SS BOND : bond 0.00746 ( 2) SS BOND : angle 1.09626 ( 4) link_BETA1-3 : bond 0.00787 ( 1) link_BETA1-3 : angle 4.33352 ( 3) covalent geometry : bond 0.00431 (12018) covalent geometry : angle 0.61525 (16283) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.5649 (p90) REVERT: A 263 MET cc_start: 0.7836 (mtt) cc_final: 0.7240 (mmp) REVERT: A 385 THR cc_start: 0.8335 (m) cc_final: 0.8067 (t) REVERT: A 391 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6968 (mtp85) REVERT: A 401 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8159 (mt) REVERT: A 469 MET cc_start: 0.8420 (ttm) cc_final: 0.8196 (ttt) REVERT: A 490 LEU cc_start: 0.6243 (pp) cc_final: 0.5904 (mp) REVERT: A 535 LYS cc_start: 0.8506 (tttm) cc_final: 0.7917 (ttmm) REVERT: A 549 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8105 (pp20) REVERT: A 571 GLU cc_start: 0.8270 (tt0) cc_final: 0.7937 (mt-10) REVERT: A 610 LYS cc_start: 0.8048 (mttm) cc_final: 0.7674 (mmtp) REVERT: A 689 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: A 697 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: A 838 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7371 (mmt-90) REVERT: A 871 ARG cc_start: 0.8241 (mtt180) cc_final: 0.8039 (mtt180) REVERT: A 1156 GLN cc_start: 0.8495 (tt0) cc_final: 0.8042 (tt0) REVERT: A 1190 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7884 (mtm180) REVERT: A 1296 GLN cc_start: 0.7842 (tt0) cc_final: 0.7345 (tt0) REVERT: C 47 PRO cc_start: 0.6887 (Cg_exo) cc_final: 0.6654 (Cg_endo) REVERT: C 114 THR cc_start: 0.8166 (m) cc_final: 0.7882 (m) REVERT: C 135 LYS cc_start: 0.8545 (mttt) cc_final: 0.7883 (ttpp) REVERT: C 229 HIS cc_start: 0.7595 (m90) cc_final: 0.7156 (m-70) REVERT: C 295 LYS cc_start: 0.8504 (ttpt) cc_final: 0.7913 (tptt) outliers start: 42 outliers final: 16 residues processed: 166 average time/residue: 1.4889 time to fit residues: 271.0919 Evaluate side-chains 142 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1069 SER Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN C 25 ASN C 37 GLN C 299 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115848 restraints weight = 13528.154| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.07 r_work: 0.3129 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12027 Z= 0.244 Angle : 0.677 10.699 16308 Z= 0.345 Chirality : 0.048 0.190 1855 Planarity : 0.004 0.041 2039 Dihedral : 7.435 64.022 1739 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.44 % Allowed : 16.58 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.21), residues: 1440 helix: -1.67 (0.20), residues: 590 sheet: -0.58 (0.34), residues: 220 loop : -1.21 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 111 HIS 0.011 0.001 HIS A 634 PHE 0.024 0.002 PHE A1094 TYR 0.015 0.002 TYR C 153 ARG 0.010 0.001 ARG A 981 Details of bonding type rmsd link_NAG-ASN : bond 0.00758 ( 3) link_NAG-ASN : angle 4.00458 ( 9) link_BETA1-4 : bond 0.00448 ( 3) link_BETA1-4 : angle 2.20273 ( 9) hydrogen bonds : bond 0.04679 ( 393) hydrogen bonds : angle 4.75550 ( 1161) SS BOND : bond 0.00810 ( 2) SS BOND : angle 1.27438 ( 4) link_BETA1-3 : bond 0.00813 ( 1) link_BETA1-3 : angle 4.20765 ( 3) covalent geometry : bond 0.00584 (12018) covalent geometry : angle 0.66667 (16283) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.5494 (p90) REVERT: A 263 MET cc_start: 0.7771 (mtt) cc_final: 0.7189 (mmp) REVERT: A 351 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7657 (mmm160) REVERT: A 385 THR cc_start: 0.8392 (m) cc_final: 0.8112 (t) REVERT: A 401 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8187 (mt) REVERT: A 469 MET cc_start: 0.8465 (ttm) cc_final: 0.8222 (ttt) REVERT: A 490 LEU cc_start: 0.6215 (pp) cc_final: 0.5920 (mp) REVERT: A 535 LYS cc_start: 0.8546 (tttm) cc_final: 0.7943 (ttmm) REVERT: A 549 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8253 (pp20) REVERT: A 571 GLU cc_start: 0.8323 (tt0) cc_final: 0.7946 (mt-10) REVERT: A 689 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: A 697 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: A 748 ASP cc_start: 0.8277 (m-30) cc_final: 0.7923 (t0) REVERT: A 838 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7466 (mmt-90) REVERT: A 944 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8455 (mptt) REVERT: A 1094 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7847 (t80) REVERT: A 1190 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8084 (mtm180) REVERT: A 1296 GLN cc_start: 0.7967 (tt0) cc_final: 0.7505 (tt0) REVERT: C 47 PRO cc_start: 0.6757 (Cg_exo) cc_final: 0.6521 (Cg_endo) REVERT: C 114 THR cc_start: 0.8175 (m) cc_final: 0.7869 (m) REVERT: C 135 LYS cc_start: 0.8610 (mttt) cc_final: 0.7887 (ttpp) REVERT: C 229 HIS cc_start: 0.7654 (m90) cc_final: 0.7245 (m-70) REVERT: C 295 LYS cc_start: 0.8485 (ttpt) cc_final: 0.7924 (tptt) outliers start: 44 outliers final: 17 residues processed: 158 average time/residue: 1.1735 time to fit residues: 202.9858 Evaluate side-chains 137 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 291 HIS A 649 GLN A 736 ASN A 844 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.153106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118372 restraints weight = 13404.759| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.01 r_work: 0.3188 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12027 Z= 0.130 Angle : 0.567 8.603 16308 Z= 0.289 Chirality : 0.044 0.177 1855 Planarity : 0.003 0.042 2039 Dihedral : 6.934 71.660 1739 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.21 % Allowed : 17.98 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.21), residues: 1440 helix: -1.25 (0.21), residues: 590 sheet: -0.50 (0.34), residues: 220 loop : -1.04 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 111 HIS 0.005 0.001 HIS A 634 PHE 0.022 0.001 PHE A 491 TYR 0.012 0.001 TYR C 141 ARG 0.008 0.000 ARG A 981 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 3) link_NAG-ASN : angle 2.90497 ( 9) link_BETA1-4 : bond 0.00262 ( 3) link_BETA1-4 : angle 1.78309 ( 9) hydrogen bonds : bond 0.03657 ( 393) hydrogen bonds : angle 4.49100 ( 1161) SS BOND : bond 0.00567 ( 2) SS BOND : angle 0.91094 ( 4) link_BETA1-3 : bond 0.00868 ( 1) link_BETA1-3 : angle 3.88517 ( 3) covalent geometry : bond 0.00308 (12018) covalent geometry : angle 0.55959 (16283) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.5390 (p90) REVERT: A 263 MET cc_start: 0.7710 (mtt) cc_final: 0.7422 (mtp) REVERT: A 385 THR cc_start: 0.8387 (m) cc_final: 0.8126 (t) REVERT: A 391 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6749 (mtp85) REVERT: A 401 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8249 (mt) REVERT: A 469 MET cc_start: 0.8455 (ttm) cc_final: 0.8216 (ttt) REVERT: A 535 LYS cc_start: 0.8501 (tttm) cc_final: 0.7958 (ttmm) REVERT: A 571 GLU cc_start: 0.8233 (tt0) cc_final: 0.7906 (mt-10) REVERT: A 610 LYS cc_start: 0.7966 (mttm) cc_final: 0.7657 (mmtp) REVERT: A 689 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: A 697 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: A 748 ASP cc_start: 0.8280 (m-30) cc_final: 0.7954 (t0) REVERT: A 812 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8525 (mptp) REVERT: A 838 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7437 (mmt-90) REVERT: A 871 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7631 (mtt180) REVERT: A 1094 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7319 (t80) REVERT: A 1190 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8103 (mtm180) REVERT: A 1296 GLN cc_start: 0.7970 (tt0) cc_final: 0.7495 (tt0) REVERT: C 47 PRO cc_start: 0.6680 (Cg_exo) cc_final: 0.6448 (Cg_endo) REVERT: C 114 THR cc_start: 0.8195 (m) cc_final: 0.7817 (m) REVERT: C 124 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7864 (mt-10) REVERT: C 135 LYS cc_start: 0.8633 (mttt) cc_final: 0.7880 (ttpp) REVERT: C 213 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7747 (tp30) REVERT: C 229 HIS cc_start: 0.7642 (m90) cc_final: 0.7204 (m-70) REVERT: C 295 LYS cc_start: 0.8532 (ttpt) cc_final: 0.7929 (tptt) outliers start: 41 outliers final: 17 residues processed: 162 average time/residue: 1.2783 time to fit residues: 226.0102 Evaluate side-chains 139 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 48 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 111 optimal weight: 0.0980 chunk 130 optimal weight: 6.9990 chunk 109 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 649 GLN A 736 ASN C 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118788 restraints weight = 13497.971| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.03 r_work: 0.3173 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12027 Z= 0.124 Angle : 0.558 8.621 16308 Z= 0.284 Chirality : 0.043 0.175 1855 Planarity : 0.003 0.041 2039 Dihedral : 6.737 78.103 1739 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.75 % Allowed : 17.59 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.21), residues: 1440 helix: -0.99 (0.21), residues: 590 sheet: -0.41 (0.34), residues: 218 loop : -0.92 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.006 0.001 HIS A 634 PHE 0.022 0.001 PHE A1094 TYR 0.012 0.001 TYR C 141 ARG 0.006 0.000 ARG A 981 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 3) link_NAG-ASN : angle 2.89473 ( 9) link_BETA1-4 : bond 0.00212 ( 3) link_BETA1-4 : angle 1.75834 ( 9) hydrogen bonds : bond 0.03487 ( 393) hydrogen bonds : angle 4.41188 ( 1161) SS BOND : bond 0.00549 ( 2) SS BOND : angle 0.87903 ( 4) link_BETA1-3 : bond 0.00679 ( 1) link_BETA1-3 : angle 3.59520 ( 3) covalent geometry : bond 0.00296 (12018) covalent geometry : angle 0.55012 (16283) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.5305 (p90) REVERT: A 263 MET cc_start: 0.7650 (mtt) cc_final: 0.7358 (mtp) REVERT: A 351 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7685 (mmm160) REVERT: A 385 THR cc_start: 0.8313 (m) cc_final: 0.8038 (t) REVERT: A 391 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6997 (mtp85) REVERT: A 401 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8231 (mt) REVERT: A 469 MET cc_start: 0.8440 (ttm) cc_final: 0.8192 (ttt) REVERT: A 535 LYS cc_start: 0.8579 (tttm) cc_final: 0.7975 (ttmm) REVERT: A 571 GLU cc_start: 0.8281 (tt0) cc_final: 0.7817 (mt-10) REVERT: A 577 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7175 (tp) REVERT: A 610 LYS cc_start: 0.7907 (mttm) cc_final: 0.7571 (mmtp) REVERT: A 697 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: A 838 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7384 (mmt-90) REVERT: A 871 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7447 (mtt180) REVERT: A 944 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8468 (mptt) REVERT: A 1094 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7446 (t80) REVERT: A 1190 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8128 (mtm180) REVERT: A 1296 GLN cc_start: 0.7930 (tt0) cc_final: 0.7445 (tt0) REVERT: C 47 PRO cc_start: 0.6595 (Cg_exo) cc_final: 0.6356 (Cg_endo) REVERT: C 114 THR cc_start: 0.8139 (m) cc_final: 0.7862 (m) REVERT: C 135 LYS cc_start: 0.8515 (mttt) cc_final: 0.7766 (ttpp) REVERT: C 229 HIS cc_start: 0.7605 (m90) cc_final: 0.7168 (m-70) REVERT: C 250 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8649 (tttt) REVERT: C 295 LYS cc_start: 0.8491 (ttpt) cc_final: 0.7873 (tptt) outliers start: 48 outliers final: 21 residues processed: 161 average time/residue: 1.4372 time to fit residues: 253.9970 Evaluate side-chains 151 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 106 optimal weight: 0.1980 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 736 ASN A1258 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118444 restraints weight = 13553.772| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.05 r_work: 0.3167 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12027 Z= 0.150 Angle : 0.577 8.802 16308 Z= 0.293 Chirality : 0.044 0.177 1855 Planarity : 0.003 0.042 2039 Dihedral : 6.712 82.346 1739 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.60 % Allowed : 18.22 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1440 helix: -0.91 (0.21), residues: 592 sheet: -0.38 (0.34), residues: 220 loop : -0.88 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 111 HIS 0.007 0.001 HIS A 634 PHE 0.023 0.002 PHE A 491 TYR 0.012 0.001 TYR C 141 ARG 0.006 0.000 ARG A 981 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 3) link_NAG-ASN : angle 3.08777 ( 9) link_BETA1-4 : bond 0.00221 ( 3) link_BETA1-4 : angle 1.77853 ( 9) hydrogen bonds : bond 0.03676 ( 393) hydrogen bonds : angle 4.42318 ( 1161) SS BOND : bond 0.00620 ( 2) SS BOND : angle 0.98774 ( 4) link_BETA1-3 : bond 0.00619 ( 1) link_BETA1-3 : angle 3.29445 ( 3) covalent geometry : bond 0.00360 (12018) covalent geometry : angle 0.56955 (16283) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.5348 (p90) REVERT: A 263 MET cc_start: 0.7662 (mtt) cc_final: 0.7388 (mtp) REVERT: A 351 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7687 (mmm160) REVERT: A 385 THR cc_start: 0.8340 (m) cc_final: 0.8080 (t) REVERT: A 401 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8256 (mt) REVERT: A 469 MET cc_start: 0.8432 (ttm) cc_final: 0.8183 (ttt) REVERT: A 535 LYS cc_start: 0.8579 (tttm) cc_final: 0.7964 (ttmm) REVERT: A 571 GLU cc_start: 0.8247 (tt0) cc_final: 0.7796 (mt-10) REVERT: A 577 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7249 (tp) REVERT: A 610 LYS cc_start: 0.7953 (mttm) cc_final: 0.7662 (mmtp) REVERT: A 697 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: A 838 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7390 (mmt-90) REVERT: A 855 ASP cc_start: 0.7181 (m-30) cc_final: 0.6725 (m-30) REVERT: A 871 ARG cc_start: 0.7741 (mtt180) cc_final: 0.7448 (mtt180) REVERT: A 1094 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7551 (t80) REVERT: A 1190 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8097 (mtm180) REVERT: A 1296 GLN cc_start: 0.7927 (tt0) cc_final: 0.7451 (tt0) REVERT: A 1304 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6623 (tt) REVERT: C 47 PRO cc_start: 0.6596 (Cg_exo) cc_final: 0.6360 (Cg_endo) REVERT: C 114 THR cc_start: 0.8132 (m) cc_final: 0.7850 (m) REVERT: C 135 LYS cc_start: 0.8527 (mttt) cc_final: 0.7792 (ttpp) REVERT: C 174 THR cc_start: 0.8616 (t) cc_final: 0.8389 (t) REVERT: C 229 HIS cc_start: 0.7623 (m90) cc_final: 0.7221 (m-70) REVERT: C 295 LYS cc_start: 0.8506 (ttpt) cc_final: 0.7888 (tptt) outliers start: 46 outliers final: 26 residues processed: 165 average time/residue: 1.1233 time to fit residues: 203.3517 Evaluate side-chains 154 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1093 ILE Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 114 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 736 ASN C 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.153874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119588 restraints weight = 13554.192| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.01 r_work: 0.3183 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12027 Z= 0.124 Angle : 0.558 8.907 16308 Z= 0.284 Chirality : 0.043 0.174 1855 Planarity : 0.003 0.041 2039 Dihedral : 6.655 86.589 1739 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.28 % Allowed : 18.92 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1440 helix: -0.78 (0.21), residues: 591 sheet: -0.35 (0.34), residues: 218 loop : -0.83 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.006 0.001 HIS A 634 PHE 0.022 0.001 PHE A1094 TYR 0.012 0.001 TYR C 141 ARG 0.005 0.000 ARG A 981 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 3) link_NAG-ASN : angle 2.84906 ( 9) link_BETA1-4 : bond 0.00207 ( 3) link_BETA1-4 : angle 1.66351 ( 9) hydrogen bonds : bond 0.03417 ( 393) hydrogen bonds : angle 4.35686 ( 1161) SS BOND : bond 0.00549 ( 2) SS BOND : angle 0.90940 ( 4) link_BETA1-3 : bond 0.00675 ( 1) link_BETA1-3 : angle 3.12673 ( 3) covalent geometry : bond 0.00294 (12018) covalent geometry : angle 0.55148 (16283) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.5338 (p90) REVERT: A 263 MET cc_start: 0.7742 (mtt) cc_final: 0.7445 (mtp) REVERT: A 385 THR cc_start: 0.8343 (m) cc_final: 0.8067 (t) REVERT: A 391 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6906 (mtp85) REVERT: A 469 MET cc_start: 0.8423 (ttm) cc_final: 0.8171 (ttt) REVERT: A 535 LYS cc_start: 0.8543 (tttm) cc_final: 0.7963 (ttmm) REVERT: A 571 GLU cc_start: 0.8193 (tt0) cc_final: 0.7754 (mt-10) REVERT: A 577 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7244 (tp) REVERT: A 610 LYS cc_start: 0.7973 (mttm) cc_final: 0.7693 (mmtp) REVERT: A 689 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: A 697 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: A 736 ASN cc_start: 0.7307 (OUTLIER) cc_final: 0.7074 (p0) REVERT: A 838 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7378 (mmt-90) REVERT: A 855 ASP cc_start: 0.7041 (m-30) cc_final: 0.6604 (m-30) REVERT: A 871 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7493 (mtt180) REVERT: A 1094 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7405 (t80) REVERT: A 1190 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8140 (mtm180) REVERT: A 1296 GLN cc_start: 0.7932 (tt0) cc_final: 0.7460 (tt0) REVERT: A 1304 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6567 (tt) REVERT: C 47 PRO cc_start: 0.6592 (Cg_exo) cc_final: 0.6365 (Cg_endo) REVERT: C 114 THR cc_start: 0.8137 (m) cc_final: 0.7868 (m) REVERT: C 135 LYS cc_start: 0.8487 (mttt) cc_final: 0.7766 (ttpp) REVERT: C 174 THR cc_start: 0.8592 (t) cc_final: 0.8348 (t) REVERT: C 229 HIS cc_start: 0.7572 (m90) cc_final: 0.7149 (m-70) REVERT: C 250 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8638 (tttt) REVERT: C 295 LYS cc_start: 0.8501 (ttpt) cc_final: 0.7885 (tptt) outliers start: 42 outliers final: 23 residues processed: 166 average time/residue: 1.2400 time to fit residues: 227.1351 Evaluate side-chains 154 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 11 optimal weight: 6.9990 chunk 122 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 736 ASN A 800 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120036 restraints weight = 13589.947| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.02 r_work: 0.3188 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12027 Z= 0.117 Angle : 0.556 8.950 16308 Z= 0.280 Chirality : 0.043 0.223 1855 Planarity : 0.003 0.041 2039 Dihedral : 6.594 89.968 1739 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.74 % Allowed : 19.62 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.22), residues: 1440 helix: -0.67 (0.22), residues: 593 sheet: -0.32 (0.34), residues: 218 loop : -0.81 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 111 HIS 0.005 0.001 HIS A 634 PHE 0.025 0.001 PHE A 491 TYR 0.019 0.001 TYR A 382 ARG 0.005 0.000 ARG A 981 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 3) link_NAG-ASN : angle 2.75710 ( 9) link_BETA1-4 : bond 0.00255 ( 3) link_BETA1-4 : angle 1.61742 ( 9) hydrogen bonds : bond 0.03308 ( 393) hydrogen bonds : angle 4.30652 ( 1161) SS BOND : bond 0.00568 ( 2) SS BOND : angle 0.87069 ( 4) link_BETA1-3 : bond 0.00654 ( 1) link_BETA1-3 : angle 2.99056 ( 3) covalent geometry : bond 0.00277 (12018) covalent geometry : angle 0.54968 (16283) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.5220 (p90) REVERT: A 263 MET cc_start: 0.7735 (mtt) cc_final: 0.7455 (mtp) REVERT: A 385 THR cc_start: 0.8341 (m) cc_final: 0.8060 (t) REVERT: A 391 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7030 (mtp85) REVERT: A 453 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7473 (p) REVERT: A 469 MET cc_start: 0.8414 (ttm) cc_final: 0.8161 (ttt) REVERT: A 535 LYS cc_start: 0.8541 (tttm) cc_final: 0.7956 (ttmm) REVERT: A 571 GLU cc_start: 0.8218 (tt0) cc_final: 0.7764 (mt-10) REVERT: A 610 LYS cc_start: 0.7937 (mttm) cc_final: 0.7656 (mmtp) REVERT: A 689 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: A 697 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: A 736 ASN cc_start: 0.7212 (OUTLIER) cc_final: 0.6953 (p0) REVERT: A 838 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7337 (mmt-90) REVERT: A 855 ASP cc_start: 0.7037 (m-30) cc_final: 0.6613 (m-30) REVERT: A 871 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7467 (mtt180) REVERT: A 1094 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7399 (t80) REVERT: A 1190 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8154 (mtm180) REVERT: A 1296 GLN cc_start: 0.7901 (tt0) cc_final: 0.7427 (tt0) REVERT: A 1304 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6529 (tt) REVERT: C 47 PRO cc_start: 0.6592 (Cg_exo) cc_final: 0.6362 (Cg_endo) REVERT: C 114 THR cc_start: 0.8135 (m) cc_final: 0.7868 (m) REVERT: C 135 LYS cc_start: 0.8522 (mttt) cc_final: 0.7773 (ttpp) REVERT: C 174 THR cc_start: 0.8497 (t) cc_final: 0.8262 (t) REVERT: C 229 HIS cc_start: 0.7563 (m90) cc_final: 0.7136 (m-70) REVERT: C 250 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8613 (tttt) REVERT: C 295 LYS cc_start: 0.8486 (ttpt) cc_final: 0.7869 (tptt) outliers start: 35 outliers final: 25 residues processed: 158 average time/residue: 1.1444 time to fit residues: 198.4170 Evaluate side-chains 155 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 291 HIS A 736 ASN C 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.121252 restraints weight = 13380.564| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.04 r_work: 0.3217 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12027 Z= 0.110 Angle : 0.553 8.931 16308 Z= 0.279 Chirality : 0.043 0.173 1855 Planarity : 0.003 0.041 2039 Dihedral : 6.387 83.973 1739 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.97 % Allowed : 19.78 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.22), residues: 1440 helix: -0.60 (0.22), residues: 591 sheet: -0.29 (0.34), residues: 218 loop : -0.78 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 111 HIS 0.005 0.001 HIS A 634 PHE 0.021 0.001 PHE A1094 TYR 0.022 0.001 TYR A 382 ARG 0.005 0.000 ARG A 981 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 3) link_NAG-ASN : angle 2.63167 ( 9) link_BETA1-4 : bond 0.00230 ( 3) link_BETA1-4 : angle 1.55190 ( 9) hydrogen bonds : bond 0.03196 ( 393) hydrogen bonds : angle 4.26156 ( 1161) SS BOND : bond 0.00560 ( 2) SS BOND : angle 0.82724 ( 4) link_BETA1-3 : bond 0.00672 ( 1) link_BETA1-3 : angle 2.86156 ( 3) covalent geometry : bond 0.00259 (12018) covalent geometry : angle 0.54678 (16283) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.5238 (p90) REVERT: A 263 MET cc_start: 0.7760 (mtt) cc_final: 0.7511 (mtp) REVERT: A 385 THR cc_start: 0.8266 (m) cc_final: 0.8005 (t) REVERT: A 391 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6980 (mtp85) REVERT: A 401 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8151 (mt) REVERT: A 453 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7548 (p) REVERT: A 469 MET cc_start: 0.8420 (ttm) cc_final: 0.8170 (ttt) REVERT: A 535 LYS cc_start: 0.8498 (tttm) cc_final: 0.7903 (ttmm) REVERT: A 571 GLU cc_start: 0.8018 (tt0) cc_final: 0.7608 (mt-10) REVERT: A 577 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7210 (tp) REVERT: A 610 LYS cc_start: 0.8071 (mttm) cc_final: 0.7803 (mmtp) REVERT: A 697 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: A 838 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7328 (mmt-90) REVERT: A 855 ASP cc_start: 0.6885 (m-30) cc_final: 0.6491 (m-30) REVERT: A 889 ASP cc_start: 0.7310 (t0) cc_final: 0.6957 (t0) REVERT: A 1094 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7380 (t80) REVERT: A 1190 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8118 (mtm180) REVERT: A 1296 GLN cc_start: 0.7914 (tt0) cc_final: 0.7448 (tt0) REVERT: A 1304 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6572 (tt) REVERT: C 47 PRO cc_start: 0.6577 (Cg_exo) cc_final: 0.6351 (Cg_endo) REVERT: C 114 THR cc_start: 0.8126 (m) cc_final: 0.7872 (m) REVERT: C 135 LYS cc_start: 0.8502 (mttt) cc_final: 0.7780 (ttpp) REVERT: C 174 THR cc_start: 0.8472 (t) cc_final: 0.8243 (t) REVERT: C 229 HIS cc_start: 0.7563 (m90) cc_final: 0.7123 (m-70) REVERT: C 250 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8567 (tttt) REVERT: C 295 LYS cc_start: 0.8490 (ttpt) cc_final: 0.7867 (tptt) outliers start: 38 outliers final: 22 residues processed: 156 average time/residue: 1.1196 time to fit residues: 191.7425 Evaluate side-chains 157 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1190 ARG Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 111 optimal weight: 0.0040 chunk 23 optimal weight: 0.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 291 HIS A 736 ASN A1000 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.122044 restraints weight = 13319.075| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.09 r_work: 0.3225 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12027 Z= 0.105 Angle : 0.547 9.914 16308 Z= 0.276 Chirality : 0.042 0.173 1855 Planarity : 0.003 0.041 2039 Dihedral : 6.015 71.391 1739 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.66 % Allowed : 20.09 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.22), residues: 1440 helix: -0.48 (0.22), residues: 590 sheet: -0.28 (0.35), residues: 216 loop : -0.76 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.005 0.001 HIS A 634 PHE 0.021 0.001 PHE A1094 TYR 0.021 0.001 TYR A 382 ARG 0.007 0.000 ARG A 943 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 3) link_NAG-ASN : angle 2.49513 ( 9) link_BETA1-4 : bond 0.00294 ( 3) link_BETA1-4 : angle 1.50524 ( 9) hydrogen bonds : bond 0.03083 ( 393) hydrogen bonds : angle 4.19915 ( 1161) SS BOND : bond 0.00583 ( 2) SS BOND : angle 0.83683 ( 4) link_BETA1-3 : bond 0.00709 ( 1) link_BETA1-3 : angle 2.61895 ( 3) covalent geometry : bond 0.00249 (12018) covalent geometry : angle 0.54194 (16283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9474.71 seconds wall clock time: 168 minutes 6.92 seconds (10086.92 seconds total)