Starting phenix.real_space_refine on Wed May 6 11:42:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x2c_66477/05_2026/9x2c_66477.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x2c_66477/05_2026/9x2c_66477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x2c_66477/05_2026/9x2c_66477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x2c_66477/05_2026/9x2c_66477.map" model { file = "/net/cci-nas-00/data/ceres_data/9x2c_66477/05_2026/9x2c_66477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x2c_66477/05_2026/9x2c_66477.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 12101 2.51 5 N 3343 2.21 5 O 3680 1.98 5 H 18890 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38110 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1262, 19061 Classifications: {'peptide': 1262} Link IDs: {'PTRANS': 80, 'TRANS': 1181} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 19049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1261, 19049 Classifications: {'peptide': 1261} Link IDs: {'PTRANS': 80, 'TRANS': 1180} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 6.31, per 1000 atoms: 0.17 Number of scatterers: 38110 At special positions: 0 Unit cell: (210.9, 93.98, 133.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 3680 8.00 N 3343 7.00 C 12101 6.00 H 18890 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4642 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 17 sheets defined 38.6% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 removed outlier: 3.710A pdb=" N SER A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.553A pdb=" N GLY A 54 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.545A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.520A pdb=" N ARG A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.795A pdb=" N THR A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 169 removed outlier: 4.473A pdb=" N LEU A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.859A pdb=" N SER A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 199 removed outlier: 3.609A pdb=" N HIS A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.513A pdb=" N GLN A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.620A pdb=" N PHE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 370 through 384 Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 486 through 501 Processing helix chain 'A' and resid 507 through 518 Processing helix chain 'A' and resid 532 through 546 removed outlier: 3.559A pdb=" N LYS A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 removed outlier: 3.701A pdb=" N ALA A 592 " --> pdb=" O GLN A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 610 removed outlier: 3.502A pdb=" N ILE A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 634 through 656 Proline residue: A 640 - end of helix removed outlier: 3.536A pdb=" N ALA A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 678 Processing helix chain 'A' and resid 681 through 695 Processing helix chain 'A' and resid 696 through 699 Processing helix chain 'A' and resid 717 through 724 Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 748 through 763 removed outlier: 3.522A pdb=" N HIS A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 783 Proline residue: A 782 - end of helix Processing helix chain 'A' and resid 784 through 795 removed outlier: 3.761A pdb=" N GLY A 795 " --> pdb=" O ILE A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 821 through 827 Processing helix chain 'A' and resid 828 through 836 removed outlier: 3.600A pdb=" N ASP A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 851 Processing helix chain 'A' and resid 867 through 880 removed outlier: 3.613A pdb=" N ILE A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 911 Processing helix chain 'A' and resid 916 through 923 Processing helix chain 'A' and resid 925 through 927 No H-bonds generated for 'chain 'A' and resid 925 through 927' Processing helix chain 'A' and resid 928 through 933 removed outlier: 3.786A pdb=" N ASN A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 999 Processing helix chain 'A' and resid 1012 through 1026 removed outlier: 3.764A pdb=" N VAL A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1137 removed outlier: 3.552A pdb=" N ILE A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1164 through 1169 Processing helix chain 'A' and resid 1174 through 1183 Processing helix chain 'A' and resid 1183 through 1190 removed outlier: 3.710A pdb=" N ALA A1190 " --> pdb=" O LEU A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1217 removed outlier: 3.574A pdb=" N THR A1216 " --> pdb=" O PRO A1213 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A1217 " --> pdb=" O SER A1214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1213 through 1217' Processing helix chain 'B' and resid 26 through 36 removed outlier: 3.670A pdb=" N SER B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.572A pdb=" N GLU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 115 Processing helix chain 'B' and resid 135 through 144 removed outlier: 3.882A pdb=" N ASP B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 170 removed outlier: 4.484A pdb=" N LEU B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 215 through 223 removed outlier: 3.538A pdb=" N THR B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 289 through 304 Processing helix chain 'B' and resid 328 through 341 Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 368 through 384 removed outlier: 3.500A pdb=" N ILE B 374 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 486 through 503 removed outlier: 3.644A pdb=" N GLU B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG B 503 " --> pdb=" O GLU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 518 Processing helix chain 'B' and resid 532 through 546 Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 595 through 611 removed outlier: 3.784A pdb=" N LEU B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 634 through 656 Proline residue: B 640 - end of helix Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 681 through 696 Processing helix chain 'B' and resid 697 through 699 No H-bonds generated for 'chain 'B' and resid 697 through 699' Processing helix chain 'B' and resid 715 through 724 removed outlier: 3.664A pdb=" N ALA B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 Processing helix chain 'B' and resid 777 through 782 Proline residue: B 782 - end of helix Processing helix chain 'B' and resid 783 through 795 removed outlier: 3.947A pdb=" N TYR B 787 " --> pdb=" O CYS B 783 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 795 " --> pdb=" O ILE B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 820 No H-bonds generated for 'chain 'B' and resid 818 through 820' Processing helix chain 'B' and resid 821 through 827 Processing helix chain 'B' and resid 828 through 836 removed outlier: 3.657A pdb=" N ASP B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 851 Processing helix chain 'B' and resid 867 through 880 Processing helix chain 'B' and resid 894 through 911 Processing helix chain 'B' and resid 916 through 923 Processing helix chain 'B' and resid 925 through 927 No H-bonds generated for 'chain 'B' and resid 925 through 927' Processing helix chain 'B' and resid 928 through 933 removed outlier: 3.733A pdb=" N ASN B 933 " --> pdb=" O ALA B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 962 Processing helix chain 'B' and resid 996 through 999 Processing helix chain 'B' and resid 1012 through 1026 removed outlier: 3.687A pdb=" N VAL B1016 " --> pdb=" O ALA B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1137 removed outlier: 3.517A pdb=" N GLU B1135 " --> pdb=" O ALA B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1145 Processing helix chain 'B' and resid 1164 through 1169 Processing helix chain 'B' and resid 1174 through 1183 Processing helix chain 'B' and resid 1183 through 1190 removed outlier: 3.708A pdb=" N ALA B1190 " --> pdb=" O LEU B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1213 through 1217 removed outlier: 3.569A pdb=" N THR B1216 " --> pdb=" O PRO B1213 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B1217 " --> pdb=" O SER B1214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1213 through 1217' Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 408 removed outlier: 3.972A pdb=" N TYR A 317 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN A 437 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A 276 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS A 439 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR A 274 " --> pdb=" O HIS A 439 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 441 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 269 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 11 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE A 253 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR A 16 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 251 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N CYS A 18 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 249 " --> pdb=" O CYS A 18 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER A 127 " --> pdb=" O CYS A 205 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY A 207 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR A 129 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N SER A 209 " --> pdb=" O TYR A 129 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLY A 131 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE A 176 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA A 128 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL A 178 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N MET A 130 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 177 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ILE B 176 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA B 128 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL B 178 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N MET B 130 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER B 127 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLY B 207 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR B 129 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N SER B 209 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY B 131 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 249 " --> pdb=" O CYS B 18 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS B 18 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 251 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR B 16 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE B 253 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 11 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA B 269 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE B 441 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 274 " --> pdb=" O HIS B 439 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS B 439 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B 276 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN B 437 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR B 317 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 386 Processing sheet with id=AA4, first strand: chain 'A' and resid 480 through 484 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 806 removed outlier: 3.608A pdb=" N MET A 662 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 733 through 736 removed outlier: 6.352A pdb=" N THR A 744 " --> pdb=" O ALA A 735 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 974 through 975 removed outlier: 6.642A pdb=" N LEU A1080 " --> pdb=" O ALA A1093 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 974 through 975 removed outlier: 6.642A pdb=" N LEU A1080 " --> pdb=" O ALA A1093 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA A1093 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA A1040 " --> pdb=" O ALA A1093 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR A1095 " --> pdb=" O ASP A1038 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP A1038 " --> pdb=" O THR A1095 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N HIS A1097 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU A1036 " --> pdb=" O HIS A1097 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG A1099 " --> pdb=" O ILE A1034 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE A1034 " --> pdb=" O ARG A1099 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR A1101 " --> pdb=" O GLN A1032 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A1034 " --> pdb=" O PHE A1211 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLY A1207 " --> pdb=" O ASP A1038 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA A1040 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA A1205 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A1266 " --> pdb=" O THR A1204 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE A1206 " --> pdb=" O ASP A1264 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASP A1264 " --> pdb=" O ILE A1206 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG A1208 " --> pdb=" O ILE A1262 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE A1262 " --> pdb=" O ARG A1208 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A1210 " --> pdb=" O ILE A1260 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A1260 " --> pdb=" O VAL A1210 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A1250 " --> pdb=" O GLN A1259 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN A1261 " --> pdb=" O MET A1248 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET A1248 " --> pdb=" O GLN A1261 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU A1263 " --> pdb=" O GLY A1246 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY A1246 " --> pdb=" O GLU A1263 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE A1265 " --> pdb=" O LEU A1244 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A1244 " --> pdb=" O PHE A1265 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR A1243 " --> pdb=" O PHE A1233 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N PHE A1233 " --> pdb=" O THR A1243 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A1245 " --> pdb=" O THR A1231 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A1160 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER A1149 " --> pdb=" O THR A1160 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA A1162 " --> pdb=" O MET A1147 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N MET A1147 " --> pdb=" O ALA A1162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1006 through 1007 Processing sheet with id=AB1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AB2, first strand: chain 'B' and resid 385 through 386 Processing sheet with id=AB3, first strand: chain 'B' and resid 480 through 484 Processing sheet with id=AB4, first strand: chain 'B' and resid 805 through 806 removed outlier: 3.525A pdb=" N MET B 662 " --> pdb=" O ILE B 572 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 743 through 744 Processing sheet with id=AB6, first strand: chain 'B' and resid 974 through 975 removed outlier: 6.520A pdb=" N LEU B1080 " --> pdb=" O ALA B1093 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 974 through 975 removed outlier: 6.520A pdb=" N LEU B1080 " --> pdb=" O ALA B1093 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA B1093 " --> pdb=" O ALA B1040 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA B1040 " --> pdb=" O ALA B1093 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR B1095 " --> pdb=" O ASP B1038 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP B1038 " --> pdb=" O THR B1095 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N HIS B1097 " --> pdb=" O LEU B1036 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B1036 " --> pdb=" O HIS B1097 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG B1099 " --> pdb=" O ILE B1034 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B1034 " --> pdb=" O ARG B1099 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR B1101 " --> pdb=" O GLN B1032 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B1034 " --> pdb=" O PHE B1211 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY B1207 " --> pdb=" O ASP B1038 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B1040 " --> pdb=" O ALA B1205 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B1205 " --> pdb=" O ALA B1040 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B1266 " --> pdb=" O THR B1204 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE B1206 " --> pdb=" O ASP B1264 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP B1264 " --> pdb=" O ILE B1206 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG B1208 " --> pdb=" O ILE B1262 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE B1262 " --> pdb=" O ARG B1208 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B1210 " --> pdb=" O ILE B1260 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE B1260 " --> pdb=" O VAL B1210 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B1250 " --> pdb=" O GLN B1259 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN B1261 " --> pdb=" O MET B1248 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET B1248 " --> pdb=" O GLN B1261 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLU B1263 " --> pdb=" O GLY B1246 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY B1246 " --> pdb=" O GLU B1263 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE B1265 " --> pdb=" O LEU B1244 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B1244 " --> pdb=" O PHE B1265 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR B1243 " --> pdb=" O PHE B1233 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE B1233 " --> pdb=" O THR B1243 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR B1245 " --> pdb=" O THR B1231 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR B1160 " --> pdb=" O SER B1149 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER B1149 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA B1162 " --> pdb=" O MET B1147 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N MET B1147 " --> pdb=" O ALA B1162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1006 through 1007 802 hydrogen bonds defined for protein. 2238 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: 9.72 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18858 1.03 - 1.23: 96 1.23 - 1.42: 8145 1.42 - 1.62: 11300 1.62 - 1.82: 160 Bond restraints: 38559 Sorted by residual: bond pdb=" CB LYS B 741 " pdb=" CG LYS B 741 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.92e+00 bond pdb=" CA ALA B 181 " pdb=" CB ALA B 181 " ideal model delta sigma weight residual 1.530 1.506 0.025 1.69e-02 3.50e+03 2.13e+00 bond pdb=" C ALA A 934 " pdb=" N PRO A 935 " ideal model delta sigma weight residual 1.326 1.345 -0.019 1.44e-02 4.82e+03 1.66e+00 bond pdb=" CA ILE A 478 " pdb=" CB ILE A 478 " ideal model delta sigma weight residual 1.546 1.536 0.010 8.80e-03 1.29e+04 1.39e+00 bond pdb=" N ALA B 181 " pdb=" CA ALA B 181 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.35e+00 ... (remaining 38554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.03: 69683 7.03 - 14.07: 4 14.07 - 21.10: 0 21.10 - 28.13: 5 28.13 - 35.16: 7 Bond angle restraints: 69699 Sorted by residual: angle pdb=" C THR A 156 " pdb=" CA THR A 156 " pdb=" HA THR A 156 " ideal model delta sigma weight residual 109.00 73.84 35.16 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N THR A 156 " pdb=" CA THR A 156 " pdb=" HA THR A 156 " ideal model delta sigma weight residual 110.00 75.74 34.26 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CB THR A 156 " pdb=" CA THR A 156 " pdb=" HA THR A 156 " ideal model delta sigma weight residual 109.00 75.60 33.40 3.00e+00 1.11e-01 1.24e+02 angle pdb=" HZ1 LYS A 959 " pdb=" NZ LYS A 959 " pdb=" HZ3 LYS A 959 " ideal model delta sigma weight residual 109.00 79.09 29.91 3.00e+00 1.11e-01 9.94e+01 angle pdb=" HZ1 LYS A 959 " pdb=" NZ LYS A 959 " pdb=" HZ2 LYS A 959 " ideal model delta sigma weight residual 109.00 79.30 29.70 3.00e+00 1.11e-01 9.80e+01 ... (remaining 69694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 16377 17.85 - 35.70: 1326 35.70 - 53.56: 478 53.56 - 71.41: 126 71.41 - 89.26: 35 Dihedral angle restraints: 18342 sinusoidal: 9976 harmonic: 8366 Sorted by residual: dihedral pdb=" C THR A 156 " pdb=" N THR A 156 " pdb=" CA THR A 156 " pdb=" CB THR A 156 " ideal model delta harmonic sigma weight residual -122.00 -131.73 9.73 0 2.50e+00 1.60e-01 1.51e+01 dihedral pdb=" CA ARG B1152 " pdb=" C ARG B1152 " pdb=" N ARG B1153 " pdb=" CA ARG B1153 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ARG A1152 " pdb=" C ARG A1152 " pdb=" N ARG A1153 " pdb=" CA ARG A1153 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 18339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 2979 0.279 - 0.558: 1 0.558 - 0.837: 0 0.837 - 1.116: 0 1.116 - 1.395: 1 Chirality restraints: 2981 Sorted by residual: chirality pdb=" CB THR A 256 " pdb=" CA THR A 256 " pdb=" OG1 THR A 256 " pdb=" CG2 THR A 256 " both_signs ideal model delta sigma weight residual False 2.55 1.16 1.39 2.00e-01 2.50e+01 4.86e+01 chirality pdb=" CA THR A 156 " pdb=" N THR A 156 " pdb=" C THR A 156 " pdb=" CB THR A 156 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA PRO A 938 " pdb=" N PRO A 938 " pdb=" C PRO A 938 " pdb=" CB PRO A 938 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 2978 not shown) Planarity restraints: 5869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 741 " 0.011 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C LYS B 741 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS B 741 " 0.014 2.00e-02 2.50e+03 pdb=" N SER B 742 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 639 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 640 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 640 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 640 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 976 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 977 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 977 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 977 " -0.023 5.00e-02 4.00e+02 ... (remaining 5866 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 848 2.13 - 2.74: 67630 2.74 - 3.36: 105666 3.36 - 3.98: 135610 3.98 - 4.60: 217281 Nonbonded interactions: 527035 Sorted by model distance: nonbonded pdb=" OE1 GLU B 993 " pdb=" H GLU B 993 " model vdw 1.507 2.450 nonbonded pdb=" H ALA B 735 " pdb=" O THR B 744 " model vdw 1.512 2.450 nonbonded pdb=" OE1 GLU A 882 " pdb=" H GLU A 882 " model vdw 1.529 2.450 nonbonded pdb=" O TYR A 218 " pdb=" HG1 THR A 222 " model vdw 1.580 2.450 nonbonded pdb=" OE1 GLU A 682 " pdb=" H GLU A 682 " model vdw 1.635 2.450 ... (remaining 527030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 1276) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.490 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.670 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 34.730 Find NCS groups from input model: 0.460 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:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.003 0.051 19669 Z= 0.153 Angle : 0.603 11.046 26742 Z= 0.341 Chirality : 0.050 1.395 2981 Planarity : 0.005 0.053 3510 Dihedral : 15.195 89.262 7184 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.68 % Allowed : 18.62 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2515 helix: 0.67 (0.19), residues: 832 sheet: -0.41 (0.27), residues: 355 loop : -0.86 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 876 TYR 0.012 0.001 TYR A1237 PHE 0.016 0.001 PHE A 403 TRP 0.008 0.001 TRP B 31 HIS 0.004 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00325 (19669) covalent geometry : angle 0.60321 (26742) hydrogen bonds : bond 0.20880 ( 768) hydrogen bonds : angle 7.77694 ( 2238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 237 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7041 (ttt180) REVERT: A 499 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7420 (tt0) REVERT: A 505 GLU cc_start: 0.7790 (tt0) cc_final: 0.7530 (tp30) REVERT: A 602 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7606 (tt0) REVERT: A 621 GLU cc_start: 0.7819 (tp30) cc_final: 0.7498 (tp30) REVERT: A 667 SER cc_start: 0.8317 (t) cc_final: 0.7939 (p) REVERT: A 822 ASP cc_start: 0.7128 (m-30) cc_final: 0.6495 (t0) REVERT: A 949 LYS cc_start: 0.8355 (tttt) cc_final: 0.8030 (tttp) REVERT: A 966 ASP cc_start: 0.8251 (m-30) cc_final: 0.7531 (p0) REVERT: A 1091 ARG cc_start: 0.8143 (mtm180) cc_final: 0.7901 (mtp180) REVERT: A 1208 ARG cc_start: 0.8240 (tmt170) cc_final: 0.7729 (ttt-90) REVERT: A 1259 GLN cc_start: 0.8041 (mm110) cc_final: 0.7783 (mm-40) REVERT: B 499 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7480 (tt0) REVERT: B 621 GLU cc_start: 0.7745 (tp30) cc_final: 0.7528 (tt0) REVERT: B 662 MET cc_start: 0.8380 (ttp) cc_final: 0.8015 (tpp) REVERT: B 741 LYS cc_start: 0.6577 (pptt) cc_final: 0.5729 (mttp) REVERT: B 985 ARG cc_start: 0.6507 (mpp-170) cc_final: 0.5601 (mpt180) REVERT: B 1031 VAL cc_start: 0.8786 (m) cc_final: 0.8529 (t) REVERT: B 1208 ARG cc_start: 0.8077 (ttt-90) cc_final: 0.7735 (tmm-80) REVERT: B 1209 MET cc_start: 0.8520 (ttt) cc_final: 0.8240 (ttp) REVERT: B 1249 SER cc_start: 0.8294 (m) cc_final: 0.8059 (t) REVERT: B 1259 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7547 (mm-40) REVERT: B 1267 MET cc_start: 0.7672 (mtp) cc_final: 0.7334 (mtt) outliers start: 14 outliers final: 9 residues processed: 247 average time/residue: 1.4541 time to fit residues: 400.8131 Evaluate side-chains 190 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 1141 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.2980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN B 57 ASN B 210 ASN B 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123521 restraints weight = 61493.669| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.82 r_work: 0.2863 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19669 Z= 0.138 Angle : 0.557 11.062 26742 Z= 0.289 Chirality : 0.050 1.362 2981 Planarity : 0.005 0.045 3510 Dihedral : 4.421 49.586 2746 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.56 % Allowed : 17.94 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2515 helix: 0.90 (0.18), residues: 856 sheet: -0.16 (0.27), residues: 359 loop : -0.90 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1099 TYR 0.012 0.001 TYR B1237 PHE 0.014 0.001 PHE A 403 TRP 0.012 0.001 TRP B1177 HIS 0.004 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00327 (19669) covalent geometry : angle 0.55701 (26742) hydrogen bonds : bond 0.05134 ( 768) hydrogen bonds : angle 5.65528 ( 2238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8026 (mt) REVERT: A 382 ARG cc_start: 0.8041 (mtt-85) cc_final: 0.7239 (ttt180) REVERT: A 499 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7423 (tt0) REVERT: A 602 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7674 (tt0) REVERT: A 606 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7091 (pt0) REVERT: A 621 GLU cc_start: 0.8000 (tp30) cc_final: 0.7652 (tp30) REVERT: A 949 LYS cc_start: 0.8447 (tttt) cc_final: 0.8179 (tttp) REVERT: A 1020 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: A 1181 CYS cc_start: 0.7430 (m) cc_final: 0.6483 (p) REVERT: A 1208 ARG cc_start: 0.8259 (tmt170) cc_final: 0.7757 (ttt-90) REVERT: A 1259 GLN cc_start: 0.8131 (mm110) cc_final: 0.7820 (mm-40) REVERT: A 1261 GLN cc_start: 0.7859 (tt0) cc_final: 0.7514 (tp40) REVERT: B 499 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7487 (tt0) REVERT: B 516 ASN cc_start: 0.7509 (m-40) cc_final: 0.7291 (m-40) REVERT: B 662 MET cc_start: 0.8444 (ttp) cc_final: 0.8132 (tpp) REVERT: B 985 ARG cc_start: 0.6665 (mpp-170) cc_final: 0.6005 (mmt-90) REVERT: B 992 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.6930 (mmt) REVERT: B 1031 VAL cc_start: 0.8842 (m) cc_final: 0.8551 (t) REVERT: B 1150 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.6289 (tpt) REVERT: B 1208 ARG cc_start: 0.8159 (ttt-90) cc_final: 0.7802 (ttt90) REVERT: B 1209 MET cc_start: 0.8616 (ttt) cc_final: 0.8387 (ttp) REVERT: B 1229 HIS cc_start: 0.7313 (m90) cc_final: 0.6826 (m170) REVERT: B 1259 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7699 (mm-40) REVERT: B 1267 MET cc_start: 0.7801 (mtp) cc_final: 0.7525 (mtt) outliers start: 32 outliers final: 11 residues processed: 210 average time/residue: 1.5719 time to fit residues: 367.3279 Evaluate side-chains 191 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 992 MET Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1150 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 88 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.168314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122344 restraints weight = 61325.081| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.81 r_work: 0.2850 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19669 Z= 0.125 Angle : 0.525 10.897 26742 Z= 0.267 Chirality : 0.050 1.351 2981 Planarity : 0.005 0.054 3510 Dihedral : 4.088 31.939 2735 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.60 % Allowed : 17.31 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2515 helix: 1.18 (0.18), residues: 859 sheet: -0.07 (0.26), residues: 368 loop : -0.93 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 331 TYR 0.012 0.001 TYR A1237 PHE 0.012 0.001 PHE B1251 TRP 0.012 0.001 TRP B1177 HIS 0.004 0.001 HIS B1001 Details of bonding type rmsd covalent geometry : bond 0.00298 (19669) covalent geometry : angle 0.52470 (26742) hydrogen bonds : bond 0.04314 ( 768) hydrogen bonds : angle 5.08573 ( 2238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7238 (ttt180) REVERT: A 499 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7452 (tt0) REVERT: A 602 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7686 (tt0) REVERT: A 606 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7056 (pt0) REVERT: A 621 GLU cc_start: 0.8031 (tp30) cc_final: 0.7646 (tp30) REVERT: A 817 MET cc_start: 0.7580 (mmm) cc_final: 0.7343 (mmm) REVERT: A 949 LYS cc_start: 0.8354 (tttt) cc_final: 0.8124 (tttp) REVERT: A 1020 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: A 1181 CYS cc_start: 0.7396 (m) cc_final: 0.6472 (p) REVERT: A 1208 ARG cc_start: 0.8241 (tmt170) cc_final: 0.7731 (ttt-90) REVERT: A 1229 HIS cc_start: 0.7264 (m90) cc_final: 0.6992 (m-70) REVERT: A 1259 GLN cc_start: 0.8188 (mm110) cc_final: 0.7823 (mm-40) REVERT: A 1261 GLN cc_start: 0.7968 (tt0) cc_final: 0.7704 (tp40) REVERT: B 154 THR cc_start: 0.7065 (OUTLIER) cc_final: 0.6594 (p) REVERT: B 499 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7450 (tt0) REVERT: B 516 ASN cc_start: 0.7521 (m-40) cc_final: 0.7306 (m-40) REVERT: B 662 MET cc_start: 0.8441 (ttp) cc_final: 0.8106 (tpp) REVERT: B 876 ARG cc_start: 0.7266 (ttp-170) cc_final: 0.6964 (ttp80) REVERT: B 985 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.5994 (mmt-90) REVERT: B 992 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.6879 (mmt) REVERT: B 1031 VAL cc_start: 0.8845 (m) cc_final: 0.8517 (t) REVERT: B 1208 ARG cc_start: 0.8160 (ttt-90) cc_final: 0.7764 (tmm-80) REVERT: B 1209 MET cc_start: 0.8591 (ttt) cc_final: 0.8331 (ttp) REVERT: B 1259 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7771 (mm-40) outliers start: 33 outliers final: 16 residues processed: 214 average time/residue: 1.5700 time to fit residues: 373.0852 Evaluate side-chains 192 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 985 ARG Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 985 ARG Chi-restraints excluded: chain B residue 992 MET Chi-restraints excluded: chain B residue 1141 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 125 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 222 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 237 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.109086 restraints weight = 61724.881| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.80 r_work: 0.2921 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19669 Z= 0.183 Angle : 0.572 10.604 26742 Z= 0.294 Chirality : 0.051 1.319 2981 Planarity : 0.006 0.064 3510 Dihedral : 4.252 32.470 2734 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.33 % Allowed : 16.92 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 2515 helix: 1.18 (0.18), residues: 862 sheet: -0.12 (0.26), residues: 371 loop : -1.05 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1061 TYR 0.014 0.001 TYR A1237 PHE 0.014 0.002 PHE A 403 TRP 0.013 0.001 TRP B1177 HIS 0.006 0.001 HIS B1001 Details of bonding type rmsd covalent geometry : bond 0.00460 (19669) covalent geometry : angle 0.57215 (26742) hydrogen bonds : bond 0.04519 ( 768) hydrogen bonds : angle 4.97597 ( 2238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7168 (ttt180) REVERT: A 499 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7521 (tt0) REVERT: A 602 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7641 (tt0) REVERT: A 606 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7000 (pp20) REVERT: A 621 GLU cc_start: 0.7975 (tp30) cc_final: 0.7745 (tt0) REVERT: A 662 MET cc_start: 0.8507 (ttm) cc_final: 0.8036 (tpp) REVERT: A 949 LYS cc_start: 0.8354 (tttt) cc_final: 0.8105 (tttp) REVERT: A 1004 GLN cc_start: 0.7787 (mt0) cc_final: 0.6928 (mp-120) REVERT: A 1208 ARG cc_start: 0.8312 (tmt170) cc_final: 0.7780 (ttt-90) REVERT: A 1259 GLN cc_start: 0.8263 (mm110) cc_final: 0.7885 (mm-40) REVERT: A 1261 GLN cc_start: 0.8203 (tt0) cc_final: 0.7843 (tp40) REVERT: B 499 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7473 (tt0) REVERT: B 516 ASN cc_start: 0.7546 (m-40) cc_final: 0.7314 (m-40) REVERT: B 662 MET cc_start: 0.8507 (ttp) cc_final: 0.8225 (tpp) REVERT: B 741 LYS cc_start: 0.7228 (pptt) cc_final: 0.6820 (pptt) REVERT: B 873 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6391 (tp30) REVERT: B 876 ARG cc_start: 0.7304 (ttp-170) cc_final: 0.6952 (ttp80) REVERT: B 890 ASP cc_start: 0.8131 (t0) cc_final: 0.7897 (t0) REVERT: B 992 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.6987 (mmt) REVERT: B 1004 GLN cc_start: 0.7867 (mt0) cc_final: 0.7027 (mp-120) REVERT: B 1150 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.6350 (tpt) REVERT: B 1259 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7841 (mm-40) outliers start: 48 outliers final: 19 residues processed: 219 average time/residue: 1.4993 time to fit residues: 365.3162 Evaluate side-chains 200 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 992 MET Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1150 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 243 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN B 814 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.109098 restraints weight = 61939.913| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.79 r_work: 0.2943 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19669 Z= 0.162 Angle : 0.542 10.647 26742 Z= 0.279 Chirality : 0.050 1.320 2981 Planarity : 0.005 0.048 3510 Dihedral : 4.235 33.127 2734 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.99 % Allowed : 16.77 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.16), residues: 2515 helix: 1.24 (0.18), residues: 863 sheet: -0.01 (0.26), residues: 364 loop : -1.12 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1208 TYR 0.013 0.001 TYR B1237 PHE 0.016 0.002 PHE A1129 TRP 0.013 0.001 TRP B1177 HIS 0.006 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00400 (19669) covalent geometry : angle 0.54240 (26742) hydrogen bonds : bond 0.04245 ( 768) hydrogen bonds : angle 4.85857 ( 2238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8813 (pt) cc_final: 0.8093 (mt) REVERT: A 382 ARG cc_start: 0.8099 (mtt-85) cc_final: 0.7316 (ttt180) REVERT: A 499 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7615 (tt0) REVERT: A 571 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8644 (mtpt) REVERT: A 602 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7659 (tt0) REVERT: A 606 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7025 (pp20) REVERT: A 621 GLU cc_start: 0.8013 (tp30) cc_final: 0.7799 (tt0) REVERT: A 662 MET cc_start: 0.8582 (ttm) cc_final: 0.8230 (tpp) REVERT: A 667 SER cc_start: 0.8106 (t) cc_final: 0.7624 (p) REVERT: A 1004 GLN cc_start: 0.7938 (mt0) cc_final: 0.7136 (mp-120) REVERT: A 1020 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: A 1208 ARG cc_start: 0.8361 (tmt170) cc_final: 0.8096 (ttt-90) REVERT: A 1259 GLN cc_start: 0.8400 (mm110) cc_final: 0.8052 (mm-40) REVERT: A 1261 GLN cc_start: 0.8277 (tt0) cc_final: 0.7962 (tp40) REVERT: B 153 ILE cc_start: 0.7431 (mt) cc_final: 0.7085 (mt) REVERT: B 154 THR cc_start: 0.7251 (OUTLIER) cc_final: 0.6750 (p) REVERT: B 499 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7559 (tt0) REVERT: B 516 ASN cc_start: 0.7647 (m-40) cc_final: 0.7425 (m-40) REVERT: B 563 GLU cc_start: 0.7891 (mp0) cc_final: 0.7182 (mm-30) REVERT: B 662 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8349 (tpp) REVERT: B 741 LYS cc_start: 0.7309 (pptt) cc_final: 0.6851 (pptt) REVERT: B 873 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6594 (tp30) REVERT: B 876 ARG cc_start: 0.7383 (ttp-170) cc_final: 0.7115 (ttp80) REVERT: B 992 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.6944 (mmt) REVERT: B 1004 GLN cc_start: 0.7902 (mt0) cc_final: 0.7291 (mm110) REVERT: B 1208 ARG cc_start: 0.8204 (ttt-90) cc_final: 0.7891 (ttt90) REVERT: B 1259 GLN cc_start: 0.8477 (mm-40) cc_final: 0.7962 (mm-40) outliers start: 41 outliers final: 23 residues processed: 219 average time/residue: 1.5480 time to fit residues: 377.6364 Evaluate side-chains 213 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 738 ASN Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 992 MET Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 68 optimal weight: 0.0060 chunk 107 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 251 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN A 579 GLN B 283 GLN B1261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109605 restraints weight = 61799.395| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.79 r_work: 0.2946 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19669 Z= 0.130 Angle : 0.516 10.823 26742 Z= 0.264 Chirality : 0.050 1.337 2981 Planarity : 0.005 0.046 3510 Dihedral : 4.106 33.339 2734 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.80 % Allowed : 16.77 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2515 helix: 1.45 (0.18), residues: 860 sheet: 0.05 (0.26), residues: 364 loop : -1.06 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1099 TYR 0.012 0.001 TYR A1237 PHE 0.013 0.001 PHE A1182 TRP 0.013 0.001 TRP A1177 HIS 0.006 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00325 (19669) covalent geometry : angle 0.51590 (26742) hydrogen bonds : bond 0.03750 ( 768) hydrogen bonds : angle 4.69865 ( 2238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8791 (pt) cc_final: 0.8127 (mt) REVERT: A 281 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.6918 (ttp-170) REVERT: A 382 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7317 (ttt180) REVERT: A 499 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7605 (tt0) REVERT: A 571 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8649 (mtpt) REVERT: A 602 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7742 (tt0) REVERT: A 606 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7093 (pt0) REVERT: A 621 GLU cc_start: 0.7986 (tp30) cc_final: 0.7786 (tt0) REVERT: A 662 MET cc_start: 0.8548 (ttm) cc_final: 0.8157 (tpp) REVERT: A 1004 GLN cc_start: 0.7901 (mt0) cc_final: 0.7142 (mp-120) REVERT: A 1020 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: A 1208 ARG cc_start: 0.8378 (tmt170) cc_final: 0.8083 (ttt-90) REVERT: A 1259 GLN cc_start: 0.8363 (mm110) cc_final: 0.7995 (mm-40) REVERT: A 1261 GLN cc_start: 0.8302 (tt0) cc_final: 0.7998 (tp40) REVERT: B 153 ILE cc_start: 0.7444 (mt) cc_final: 0.7085 (mt) REVERT: B 154 THR cc_start: 0.7216 (OUTLIER) cc_final: 0.6704 (p) REVERT: B 499 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7557 (tt0) REVERT: B 516 ASN cc_start: 0.7642 (m-40) cc_final: 0.7432 (m-40) REVERT: B 662 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8344 (tpp) REVERT: B 741 LYS cc_start: 0.7431 (pptt) cc_final: 0.6930 (pptt) REVERT: B 817 MET cc_start: 0.7583 (mmm) cc_final: 0.7335 (mmm) REVERT: B 873 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6573 (tp30) REVERT: B 876 ARG cc_start: 0.7392 (ttp-170) cc_final: 0.7112 (ttp80) REVERT: B 992 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.6875 (mmt) REVERT: B 1004 GLN cc_start: 0.7920 (mt0) cc_final: 0.7331 (mm110) REVERT: B 1208 ARG cc_start: 0.8213 (ttt-90) cc_final: 0.7839 (ttt90) REVERT: B 1259 GLN cc_start: 0.8464 (mm-40) cc_final: 0.7901 (mm-40) outliers start: 37 outliers final: 21 residues processed: 215 average time/residue: 1.5690 time to fit residues: 374.0320 Evaluate side-chains 204 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 569 ARG Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 738 ASN Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 992 MET Chi-restraints excluded: chain B residue 1079 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 246 optimal weight: 9.9990 chunk 236 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.158660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112220 restraints weight = 61736.661| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.81 r_work: 0.2942 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 0.031 19669 Z= 0.116 Angle : 0.505 10.908 26742 Z= 0.258 Chirality : 0.049 1.352 2981 Planarity : 0.005 0.058 3510 Dihedral : 4.028 33.494 2734 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.80 % Allowed : 16.77 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2515 helix: 1.60 (0.18), residues: 858 sheet: 0.14 (0.26), residues: 366 loop : -1.00 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 876 TYR 0.012 0.001 TYR B1237 PHE 0.014 0.001 PHE B1251 TRP 0.012 0.001 TRP A1177 HIS 0.005 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00287 (19669) covalent geometry : angle 0.50514 (26742) hydrogen bonds : bond 0.03571 ( 768) hydrogen bonds : angle 4.60912 ( 2238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8765 (pt) cc_final: 0.8119 (mt) REVERT: A 281 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8682 (ttt180) REVERT: A 382 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7365 (ttt180) REVERT: A 499 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7641 (tt0) REVERT: A 602 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7757 (tt0) REVERT: A 606 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7105 (pt0) REVERT: A 662 MET cc_start: 0.8520 (ttm) cc_final: 0.8165 (tpp) REVERT: A 1004 GLN cc_start: 0.7937 (mt0) cc_final: 0.7167 (mp-120) REVERT: A 1020 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: A 1208 ARG cc_start: 0.8414 (tmt170) cc_final: 0.8114 (ttt-90) REVERT: A 1259 GLN cc_start: 0.8387 (mm110) cc_final: 0.8020 (mm-40) REVERT: A 1261 GLN cc_start: 0.8338 (tt0) cc_final: 0.8062 (tp40) REVERT: B 153 ILE cc_start: 0.7482 (mt) cc_final: 0.7120 (mt) REVERT: B 154 THR cc_start: 0.7213 (OUTLIER) cc_final: 0.6702 (p) REVERT: B 499 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7592 (tt0) REVERT: B 563 GLU cc_start: 0.7925 (mp0) cc_final: 0.7231 (mm-30) REVERT: B 662 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8412 (tpp) REVERT: B 741 LYS cc_start: 0.7386 (pptt) cc_final: 0.6888 (pptt) REVERT: B 817 MET cc_start: 0.7668 (mmm) cc_final: 0.7400 (mmm) REVERT: B 873 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6585 (tp30) REVERT: B 876 ARG cc_start: 0.7430 (ttp-170) cc_final: 0.7145 (ttp80) REVERT: B 1004 GLN cc_start: 0.7950 (mt0) cc_final: 0.7239 (mp-120) REVERT: B 1150 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.6524 (tpt) REVERT: B 1208 ARG cc_start: 0.8240 (ttt-90) cc_final: 0.7915 (ttt90) REVERT: B 1259 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7919 (mm-40) outliers start: 37 outliers final: 23 residues processed: 207 average time/residue: 1.5988 time to fit residues: 367.7342 Evaluate side-chains 206 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 569 ARG Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 738 ASN Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1150 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 180 optimal weight: 0.3980 chunk 224 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 70 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 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.158845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112946 restraints weight = 61277.450| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.77 r_work: 0.2964 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19669 Z= 0.109 Angle : 0.499 10.940 26742 Z= 0.253 Chirality : 0.049 1.353 2981 Planarity : 0.005 0.043 3510 Dihedral : 3.952 33.590 2734 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.26 % Allowed : 17.11 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2515 helix: 1.67 (0.19), residues: 861 sheet: 0.17 (0.26), residues: 364 loop : -1.00 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1099 TYR 0.012 0.001 TYR A1237 PHE 0.013 0.001 PHE B1251 TRP 0.012 0.001 TRP A1177 HIS 0.004 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00269 (19669) covalent geometry : angle 0.49875 (26742) hydrogen bonds : bond 0.03426 ( 768) hydrogen bonds : angle 4.52220 ( 2238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8642 (pt) cc_final: 0.8170 (mt) REVERT: A 382 ARG cc_start: 0.8017 (mtt-85) cc_final: 0.7152 (ttt180) REVERT: A 499 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7487 (tt0) REVERT: A 602 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7684 (tt0) REVERT: A 606 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7042 (pt0) REVERT: A 662 MET cc_start: 0.8375 (ttm) cc_final: 0.7989 (tpp) REVERT: A 1004 GLN cc_start: 0.7846 (mt0) cc_final: 0.7072 (mp-120) REVERT: A 1020 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: A 1208 ARG cc_start: 0.8324 (tmt170) cc_final: 0.8008 (ttt-90) REVERT: A 1259 GLN cc_start: 0.8231 (mm110) cc_final: 0.7826 (mm-40) REVERT: A 1261 GLN cc_start: 0.8273 (tt0) cc_final: 0.7942 (tp40) REVERT: B 153 ILE cc_start: 0.7423 (mt) cc_final: 0.7061 (mt) REVERT: B 154 THR cc_start: 0.7014 (OUTLIER) cc_final: 0.6529 (p) REVERT: B 499 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7437 (tt0) REVERT: B 563 GLU cc_start: 0.7938 (mp0) cc_final: 0.7218 (mm-30) REVERT: B 662 MET cc_start: 0.8560 (ttp) cc_final: 0.8277 (tpp) REVERT: B 741 LYS cc_start: 0.7350 (pptt) cc_final: 0.6837 (pptt) REVERT: B 817 MET cc_start: 0.7612 (mmm) cc_final: 0.7303 (mmm) REVERT: B 873 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6387 (tp30) REVERT: B 876 ARG cc_start: 0.7351 (ttp-170) cc_final: 0.7089 (ttp80) REVERT: B 1004 GLN cc_start: 0.7867 (mt0) cc_final: 0.7069 (mp-120) REVERT: B 1208 ARG cc_start: 0.8102 (ttt-90) cc_final: 0.7793 (ttt90) REVERT: B 1259 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7728 (mm-40) outliers start: 26 outliers final: 23 residues processed: 201 average time/residue: 1.5792 time to fit residues: 352.9631 Evaluate side-chains 199 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 569 ARG Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 738 ASN Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 148 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN B1261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112494 restraints weight = 61524.070| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.76 r_work: 0.2986 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19669 Z= 0.122 Angle : 0.507 10.849 26742 Z= 0.258 Chirality : 0.049 1.345 2981 Planarity : 0.005 0.071 3510 Dihedral : 3.965 33.769 2734 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.46 % Allowed : 16.92 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2515 helix: 1.67 (0.18), residues: 861 sheet: 0.15 (0.26), residues: 364 loop : -1.00 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 876 TYR 0.012 0.001 TYR B1237 PHE 0.014 0.001 PHE B1251 TRP 0.012 0.001 TRP A1177 HIS 0.005 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00304 (19669) covalent geometry : angle 0.50671 (26742) hydrogen bonds : bond 0.03546 ( 768) hydrogen bonds : angle 4.51904 ( 2238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8663 (pt) cc_final: 0.8207 (mt) REVERT: A 281 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8677 (ttt180) REVERT: A 382 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7226 (ttt180) REVERT: A 499 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7560 (tt0) REVERT: A 571 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8593 (mtpt) REVERT: A 602 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7740 (tt0) REVERT: A 606 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7075 (pt0) REVERT: A 662 MET cc_start: 0.8421 (ttm) cc_final: 0.8084 (tpp) REVERT: A 1004 GLN cc_start: 0.7899 (mt0) cc_final: 0.7230 (mm110) REVERT: A 1020 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: A 1208 ARG cc_start: 0.8372 (tmt170) cc_final: 0.8063 (ttt-90) REVERT: A 1229 HIS cc_start: 0.7449 (m90) cc_final: 0.7236 (m-70) REVERT: A 1259 GLN cc_start: 0.8288 (mm110) cc_final: 0.7881 (mm-40) REVERT: A 1261 GLN cc_start: 0.8329 (tt0) cc_final: 0.8018 (tp40) REVERT: B 153 ILE cc_start: 0.7525 (mt) cc_final: 0.7155 (mt) REVERT: B 154 THR cc_start: 0.7068 (OUTLIER) cc_final: 0.6572 (p) REVERT: B 499 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7519 (tt0) REVERT: B 563 GLU cc_start: 0.7804 (mp0) cc_final: 0.7168 (mm-30) REVERT: B 662 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8330 (tpp) REVERT: B 741 LYS cc_start: 0.7345 (pptt) cc_final: 0.6803 (pptt) REVERT: B 817 MET cc_start: 0.7661 (mmm) cc_final: 0.7352 (mmm) REVERT: B 873 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6499 (tp30) REVERT: B 1004 GLN cc_start: 0.7857 (mt0) cc_final: 0.7126 (mp-120) REVERT: B 1208 ARG cc_start: 0.8156 (ttt-90) cc_final: 0.7880 (ttt90) REVERT: B 1229 HIS cc_start: 0.7496 (m90) cc_final: 0.7274 (m-70) REVERT: B 1259 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7909 (mm-40) outliers start: 30 outliers final: 22 residues processed: 208 average time/residue: 1.5726 time to fit residues: 363.8907 Evaluate side-chains 200 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 569 ARG Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 738 ASN Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 91 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN A 550 ASN B 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109426 restraints weight = 61672.940| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.78 r_work: 0.2913 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19669 Z= 0.212 Angle : 0.580 10.321 26742 Z= 0.300 Chirality : 0.052 1.298 2981 Planarity : 0.006 0.047 3510 Dihedral : 4.256 34.136 2733 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.25 % Favored : 95.71 % Rotamer: Outliers : 1.51 % Allowed : 16.87 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.17), residues: 2515 helix: 1.39 (0.18), residues: 854 sheet: 0.02 (0.26), residues: 371 loop : -1.09 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1099 TYR 0.015 0.002 TYR B1237 PHE 0.017 0.002 PHE A 403 TRP 0.010 0.001 TRP A1177 HIS 0.009 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00540 (19669) covalent geometry : angle 0.58045 (26742) hydrogen bonds : bond 0.04598 ( 768) hydrogen bonds : angle 4.74982 ( 2238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8682 (pt) cc_final: 0.8200 (mt) REVERT: A 281 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.6859 (ttp-170) REVERT: A 382 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7174 (ttt180) REVERT: A 499 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7503 (tt0) REVERT: A 571 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8575 (mtpt) REVERT: A 602 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7696 (tt0) REVERT: A 662 MET cc_start: 0.8392 (ttm) cc_final: 0.8084 (tpp) REVERT: A 1004 GLN cc_start: 0.7873 (mt0) cc_final: 0.7113 (mp-120) REVERT: A 1020 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: A 1208 ARG cc_start: 0.8341 (tmt170) cc_final: 0.7698 (ttt90) REVERT: A 1229 HIS cc_start: 0.7402 (m90) cc_final: 0.7183 (m-70) REVERT: A 1261 GLN cc_start: 0.8438 (tt0) cc_final: 0.8094 (tp40) REVERT: B 153 ILE cc_start: 0.7541 (mt) cc_final: 0.7164 (mt) REVERT: B 154 THR cc_start: 0.7079 (OUTLIER) cc_final: 0.6574 (p) REVERT: B 499 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7516 (tt0) REVERT: B 563 GLU cc_start: 0.7821 (mp0) cc_final: 0.7183 (mm-30) REVERT: B 741 LYS cc_start: 0.7472 (pptt) cc_final: 0.6904 (pptt) REVERT: B 817 MET cc_start: 0.7669 (mmm) cc_final: 0.7359 (mmm) REVERT: B 873 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6124 (mm-30) REVERT: B 992 MET cc_start: 0.8078 (mmt) cc_final: 0.7809 (mtt) REVERT: B 1004 GLN cc_start: 0.7837 (mt0) cc_final: 0.7111 (mp-120) REVERT: B 1150 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.6421 (tpt) REVERT: B 1208 ARG cc_start: 0.8122 (ttt-90) cc_final: 0.7836 (ttt90) REVERT: B 1229 HIS cc_start: 0.7460 (m90) cc_final: 0.7243 (m-70) REVERT: B 1259 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7853 (mm-40) outliers start: 31 outliers final: 24 residues processed: 203 average time/residue: 1.6370 time to fit residues: 368.4012 Evaluate side-chains 197 residues out of total 2059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 738 ASN Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 1079 THR Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1150 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 185 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 143 optimal weight: 0.1980 chunk 133 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.156340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110286 restraints weight = 61577.079| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.78 r_work: 0.2947 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19669 Z= 0.106 Angle : 0.508 10.910 26742 Z= 0.259 Chirality : 0.049 1.347 2981 Planarity : 0.005 0.078 3510 Dihedral : 4.060 34.199 2733 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.02 % Rotamer: Outliers : 1.31 % Allowed : 17.50 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2515 helix: 1.62 (0.18), residues: 863 sheet: 0.07 (0.26), residues: 365 loop : -1.02 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 876 TYR 0.012 0.001 TYR B1237 PHE 0.014 0.001 PHE B1251 TRP 0.012 0.001 TRP A1177 HIS 0.005 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00262 (19669) covalent geometry : angle 0.50844 (26742) hydrogen bonds : bond 0.03527 ( 768) hydrogen bonds : angle 4.54655 ( 2238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12299.49 seconds wall clock time: 208 minutes 15.83 seconds (12495.83 seconds total)