Starting phenix.real_space_refine on Sat Feb 17 17:12:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emt_28264/02_2024/8emt_28264_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emt_28264/02_2024/8emt_28264.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emt_28264/02_2024/8emt_28264_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emt_28264/02_2024/8emt_28264_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emt_28264/02_2024/8emt_28264_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emt_28264/02_2024/8emt_28264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emt_28264/02_2024/8emt_28264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emt_28264/02_2024/8emt_28264_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emt_28264/02_2024/8emt_28264_updated.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.037 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: 7 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 8 7.16 5 P 6 5.49 5 S 171 5.16 5 C 12240 2.51 5 N 3335 2.21 5 O 3570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "B GLU 967": "OE1" <-> "OE2" Residue "B ASP 1148": "OD1" <-> "OD2" Residue "B PHE 1280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 958": "OE1" <-> "OE2" Residue "A PHE 1280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19332 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 9447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1221, 9447 Classifications: {'peptide': 1221} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1158} Chain breaks: 4 Chain: "A" Number of atoms: 9707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1254, 9707 Classifications: {'peptide': 1254} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1190} Chain breaks: 4 Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 89 Unusual residues: {'FAD': 1, 'FES': 2, 'MOS': 1, 'MTE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 89 Unusual residues: {'FAD': 1, 'FES': 2, 'MOS': 1, 'MTE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 855 SG CYS B 117 54.928 50.138 116.375 1.00 61.96 S ATOM 1095 SG CYS B 149 53.302 47.883 118.820 1.00 71.13 S ATOM 1112 SG CYS B 151 50.029 45.394 115.970 1.00 69.97 S ATOM 322 SG CYS B 44 45.753 60.550 117.595 1.00 68.49 S ATOM 344 SG CYS B 49 48.927 58.720 116.463 1.00 67.67 S ATOM 359 SG CYS B 52 51.321 62.668 114.149 1.00 58.88 S ATOM 538 SG CYS B 74 48.079 64.046 114.821 1.00 66.92 S ATOM 10313 SG CYS A 117 40.053 48.999 61.454 1.00 51.01 S ATOM 10553 SG CYS A 149 40.156 46.599 58.682 1.00 58.00 S ATOM 10570 SG CYS A 151 42.608 45.029 61.866 1.00 56.11 S ATOM 10292 SG CYS A 114 42.878 46.222 65.286 1.00 52.85 S ATOM 10570 SG CYS A 151 42.608 45.029 61.866 1.00 56.11 S ATOM 9780 SG CYS A 44 47.593 59.447 59.236 1.00 62.23 S ATOM 9802 SG CYS A 49 45.173 56.899 60.169 1.00 59.14 S ATOM 9817 SG CYS A 52 42.216 61.714 62.462 1.00 55.85 S ATOM 9996 SG CYS A 74 45.397 62.955 61.780 1.00 63.04 S Time building chain proxies: 11.14, per 1000 atoms: 0.58 Number of scatterers: 19332 At special positions: 0 Unit cell: (93.96, 109.08, 173.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mo 2 41.97 Fe 8 26.01 S 171 16.00 P 6 15.00 O 3570 8.00 N 3335 7.00 C 12240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.22 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A3001 " pdb="FE1 FES A3001 " - pdb=" SG CYS A 117 " pdb="FE2 FES A3001 " - pdb=" SG CYS A 114 " pdb="FE1 FES A3001 " - pdb=" SG CYS A 149 " pdb="FE2 FES A3001 " - pdb=" SG CYS A 151 " pdb=" FES A3002 " pdb="FE2 FES A3002 " - pdb=" SG CYS A 52 " pdb="FE1 FES A3002 " - pdb=" SG CYS A 44 " pdb="FE2 FES A3002 " - pdb=" SG CYS A 74 " pdb="FE1 FES A3002 " - pdb=" SG CYS A 49 " pdb=" FES B3001 " pdb="FE1 FES B3001 " - pdb=" SG CYS B 149 " pdb="FE2 FES B3001 " - pdb=" SG CYS B 151 " pdb="FE1 FES B3001 " - pdb=" SG CYS B 117 " pdb=" FES B3002 " pdb="FE2 FES B3002 " - pdb=" SG CYS B 52 " pdb="FE1 FES B3002 " - pdb=" SG CYS B 49 " pdb="FE1 FES B3002 " - pdb=" SG CYS B 44 " pdb="FE2 FES B3002 " - pdb=" SG CYS B 74 " Number of angles added : 24 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4538 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 23 sheets defined 32.3% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 118 through 131 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 155 through 163 removed outlier: 4.190A pdb=" N THR B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 249 through 257 Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 312 through 324 removed outlier: 4.002A pdb=" N GLN B 324 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 341 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 394 through 397 No H-bonds generated for 'chain 'B' and resid 394 through 397' Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 487 through 500 removed outlier: 4.656A pdb=" N ASN B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 537 removed outlier: 4.045A pdb=" N ILE B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 630 through 633 No H-bonds generated for 'chain 'B' and resid 630 through 633' Processing helix chain 'B' and resid 683 through 692 removed outlier: 4.096A pdb=" N ARG B 692 " --> pdb=" O ARG B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 728 through 734 Processing helix chain 'B' and resid 778 through 789 Processing helix chain 'B' and resid 812 through 827 Processing helix chain 'B' and resid 838 through 844 Processing helix chain 'B' and resid 884 through 894 removed outlier: 4.324A pdb=" N GLY B 890 " --> pdb=" O ILE B 887 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 893 " --> pdb=" O GLY B 890 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET B 894 " --> pdb=" O LEU B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 943 Processing helix chain 'B' and resid 947 through 952 Processing helix chain 'B' and resid 971 through 983 Processing helix chain 'B' and resid 986 through 997 Processing helix chain 'B' and resid 1022 through 1024 No H-bonds generated for 'chain 'B' and resid 1022 through 1024' Processing helix chain 'B' and resid 1051 through 1063 Processing helix chain 'B' and resid 1067 through 1069 No H-bonds generated for 'chain 'B' and resid 1067 through 1069' Processing helix chain 'B' and resid 1091 through 1115 removed outlier: 3.636A pdb=" N LEU B1110 " --> pdb=" O LEU B1106 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU B1111 " --> pdb=" O LEU B1107 " (cutoff:3.500A) Proline residue: B1112 - end of helix Processing helix chain 'B' and resid 1122 through 1131 Processing helix chain 'B' and resid 1197 through 1216 Processing helix chain 'B' and resid 1241 through 1243 No H-bonds generated for 'chain 'B' and resid 1241 through 1243' Processing helix chain 'B' and resid 1262 through 1264 No H-bonds generated for 'chain 'B' and resid 1262 through 1264' Processing helix chain 'B' and resid 1274 through 1293 removed outlier: 3.928A pdb=" N VAL B1279 " --> pdb=" O GLY B1276 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1314 Processing helix chain 'B' and resid 1320 through 1322 No H-bonds generated for 'chain 'B' and resid 1320 through 1322' Processing helix chain 'A' and resid 28 through 33 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 101 through 108 removed outlier: 3.546A pdb=" N ALA A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 155 through 163 removed outlier: 3.835A pdb=" N THR A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 249 through 258 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 328 through 341 removed outlier: 4.061A pdb=" N GLN A 332 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET A 333 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 334 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS A 335 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 336 " --> pdb=" O MET A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.836A pdb=" N VAL A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 398 removed outlier: 3.636A pdb=" N SER A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 398' Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 487 through 500 Processing helix chain 'A' and resid 512 through 537 removed outlier: 3.532A pdb=" N ILE A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 592 No H-bonds generated for 'chain 'A' and resid 589 through 592' Processing helix chain 'A' and resid 630 through 633 No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 649 through 651 No H-bonds generated for 'chain 'A' and resid 649 through 651' Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.632A pdb=" N ARG A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 711 Processing helix chain 'A' and resid 728 through 734 removed outlier: 4.008A pdb=" N PHE A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS A 733 " --> pdb=" O ASP A 729 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 728 through 734' Processing helix chain 'A' and resid 778 through 788 Processing helix chain 'A' and resid 793 through 795 No H-bonds generated for 'chain 'A' and resid 793 through 795' Processing helix chain 'A' and resid 812 through 827 removed outlier: 3.866A pdb=" N VAL A 820 " --> pdb=" O ILE A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 844 Processing helix chain 'A' and resid 885 through 892 Processing helix chain 'A' and resid 925 through 942 Processing helix chain 'A' and resid 947 through 954 Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 986 through 996 Processing helix chain 'A' and resid 1021 through 1023 No H-bonds generated for 'chain 'A' and resid 1021 through 1023' Processing helix chain 'A' and resid 1051 through 1062 Processing helix chain 'A' and resid 1067 through 1069 No H-bonds generated for 'chain 'A' and resid 1067 through 1069' Processing helix chain 'A' and resid 1091 through 1115 removed outlier: 3.736A pdb=" N ARG A1109 " --> pdb=" O THR A1105 " (cutoff:3.500A) Proline residue: A1112 - end of helix Processing helix chain 'A' and resid 1122 through 1131 Processing helix chain 'A' and resid 1197 through 1216 Processing helix chain 'A' and resid 1272 through 1291 removed outlier: 3.731A pdb=" N GLY A1276 " --> pdb=" O GLY A1272 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS A1277 " --> pdb=" O VAL A1273 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER A1278 " --> pdb=" O PHE A1274 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A1280 " --> pdb=" O GLY A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1314 Processing helix chain 'A' and resid 1318 through 1322 Processing sheet with id= A, first strand: chain 'B' and resid 7 through 11 Processing sheet with id= B, first strand: chain 'B' and resid 65 through 72 removed outlier: 3.790A pdb=" N ARG B 65 " --> pdb=" O ASN B 60 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 234 through 236 Processing sheet with id= D, first strand: chain 'B' and resid 297 through 300 removed outlier: 3.582A pdb=" N ILE B 410 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 382 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN B 380 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL B 414 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR B 378 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 388 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 423 through 430 removed outlier: 3.723A pdb=" N VAL B 441 " --> pdb=" O GLN B 430 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 641 through 643 removed outlier: 3.593A pdb=" N VAL B 675 " --> pdb=" O VAL B 615 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL B 615 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA B 677 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR B 613 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU B 679 " --> pdb=" O PHE B 611 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N PHE B 611 " --> pdb=" O LEU B 679 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 721 through 725 removed outlier: 6.138A pdb=" N GLY B 858 " --> pdb=" O LEU B 866 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU B 868 " --> pdb=" O LYS B 856 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS B 856 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N MET B 870 " --> pdb=" O LYS B 854 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS B 854 " --> pdb=" O MET B 870 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N HIS B 872 " --> pdb=" O LEU B 852 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 852 " --> pdb=" O HIS B 872 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 832 through 835 Processing sheet with id= I, first strand: chain 'B' and resid 959 through 961 Processing sheet with id= J, first strand: chain 'B' and resid 1003 through 1016 removed outlier: 4.349A pdb=" N TYR B1164 " --> pdb=" O ASP B1190 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B1184 " --> pdb=" O GLU B1170 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLU B1172 " --> pdb=" O ASN B1182 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASN B1182 " --> pdb=" O GLU B1172 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP B1174 " --> pdb=" O HIS B1180 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS B1180 " --> pdb=" O ASP B1174 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B1251 " --> pdb=" O ILE B1187 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET B1189 " --> pdb=" O ALA B1251 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 1137 through 1142 Processing sheet with id= L, first strand: chain 'B' and resid 1148 through 1150 Processing sheet with id= M, first strand: chain 'B' and resid 622 through 628 removed outlier: 6.965A pdb=" N VAL B 696 " --> pdb=" O VAL B 625 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B 627 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS B 694 " --> pdb=" O ILE B 627 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 7 through 11 Processing sheet with id= O, first strand: chain 'A' and resid 65 through 72 removed outlier: 4.463A pdb=" N ARG A 65 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 234 through 237 Processing sheet with id= Q, first strand: chain 'A' and resid 303 through 307 removed outlier: 6.803A pdb=" N ASN A 380 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL A 414 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR A 378 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 458 through 464 removed outlier: 6.799A pdb=" N GLN A 430 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN A 442 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE A 428 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A 444 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER A 426 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG A 446 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE A 424 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 638 through 642 removed outlier: 7.074A pdb=" N LEU A 679 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE A 641 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA A 677 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 676 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 833 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL A 835 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE A 614 " --> pdb=" O VAL A 835 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 721 through 725 removed outlier: 6.377A pdb=" N LEU A 868 " --> pdb=" O ARG A 904 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ARG A 906 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N MET A 870 " --> pdb=" O ARG A 906 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TRP A 908 " --> pdb=" O MET A 870 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS A 872 " --> pdb=" O TRP A 908 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N CYS A 910 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER A 874 " --> pdb=" O CYS A 910 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 867 " --> pdb=" O GLY A 858 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 1137 through 1142 Processing sheet with id= V, first strand: chain 'A' and resid 1148 through 1150 Processing sheet with id= W, first strand: chain 'A' and resid 1247 through 1252 removed outlier: 3.719A pdb=" N MET A1189 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A1179 " --> pdb=" O ASP A1174 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU A1170 " --> pdb=" O ILE A1183 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR A1185 " --> pdb=" O CYS A1168 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS A1168 " --> pdb=" O THR A1185 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A1187 " --> pdb=" O ALA A1166 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A1166 " --> pdb=" O ILE A1187 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET A1189 " --> pdb=" O TYR A1164 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR A1164 " --> pdb=" O MET A1189 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A1016 " --> pdb=" O GLU A1160 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE A1162 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE A1014 " --> pdb=" O PHE A1162 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR A1164 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A1012 " --> pdb=" O TYR A1164 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA A1166 " --> pdb=" O VAL A1010 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A1010 " --> pdb=" O ALA A1166 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS A1168 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA A1008 " --> pdb=" O CYS A1168 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU A1170 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY A1006 " --> pdb=" O GLU A1170 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU A1172 " --> pdb=" O LYS A1004 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS A1004 " --> pdb=" O GLU A1172 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1854 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: 7.49 Time building geometry restraints manager: 8.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.45: 8272 1.45 - 1.68: 11196 1.68 - 1.92: 248 1.92 - 2.16: 0 2.16 - 2.39: 18 Bond restraints: 19734 Sorted by residual: bond pdb=" C3' MTE B3003 " pdb=" O3' MTE B3003 " ideal model delta sigma weight residual 1.697 1.424 0.273 2.00e-02 2.50e+03 1.87e+02 bond pdb=" C3' MTE A3003 " pdb=" O3' MTE A3003 " ideal model delta sigma weight residual 1.697 1.426 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C1' MTE A3003 " pdb=" C2' MTE A3003 " ideal model delta sigma weight residual 1.559 1.332 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1' MTE B3003 " pdb=" C2' MTE B3003 " ideal model delta sigma weight residual 1.559 1.333 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C10 MTE A3003 " pdb=" N8 MTE A3003 " ideal model delta sigma weight residual 1.555 1.340 0.215 2.00e-02 2.50e+03 1.15e+02 ... (remaining 19729 not shown) Histogram of bond angle deviations from ideal: 75.36 - 87.11: 8 87.11 - 98.85: 8 98.85 - 110.59: 5927 110.59 - 122.34: 17560 122.34 - 134.08: 3196 Bond angle restraints: 26699 Sorted by residual: angle pdb=" N ASP B 862 " pdb=" CA ASP B 862 " pdb=" C ASP B 862 " ideal model delta sigma weight residual 113.15 107.20 5.95 1.19e+00 7.06e-01 2.50e+01 angle pdb=" N GLY A 386 " pdb=" CA GLY A 386 " pdb=" C GLY A 386 " ideal model delta sigma weight residual 111.63 117.20 -5.57 1.15e+00 7.56e-01 2.35e+01 angle pdb=" N ASN B 402 " pdb=" CA ASN B 402 " pdb=" C ASN B 402 " ideal model delta sigma weight residual 111.28 116.48 -5.20 1.09e+00 8.42e-01 2.27e+01 angle pdb=" CA GLU A 409 " pdb=" CB GLU A 409 " pdb=" CG GLU A 409 " ideal model delta sigma weight residual 114.10 122.92 -8.82 2.00e+00 2.50e-01 1.95e+01 angle pdb=" CA PRO A 702 " pdb=" N PRO A 702 " pdb=" CD PRO A 702 " ideal model delta sigma weight residual 112.00 106.35 5.65 1.40e+00 5.10e-01 1.63e+01 ... (remaining 26694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.23: 11157 22.23 - 44.47: 709 44.47 - 66.70: 86 66.70 - 88.93: 23 88.93 - 111.17: 1 Dihedral angle restraints: 11976 sinusoidal: 4897 harmonic: 7079 Sorted by residual: dihedral pdb=" CA LEU B 344 " pdb=" C LEU B 344 " pdb=" N ALA B 345 " pdb=" CA ALA B 345 " ideal model delta harmonic sigma weight residual 180.00 -155.20 -24.80 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA PHE B 751 " pdb=" C PHE B 751 " pdb=" N TYR B 752 " pdb=" CA TYR B 752 " ideal model delta harmonic sigma weight residual 180.00 155.61 24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA LEU B 884 " pdb=" C LEU B 884 " pdb=" N PHE B 885 " pdb=" CA PHE B 885 " ideal model delta harmonic sigma weight residual -180.00 -158.12 -21.88 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 11973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2245 0.056 - 0.113: 622 0.113 - 0.169: 104 0.169 - 0.226: 10 0.226 - 0.282: 3 Chirality restraints: 2984 Sorted by residual: chirality pdb=" CA LYS B 399 " pdb=" N LYS B 399 " pdb=" C LYS B 399 " pdb=" CB LYS B 399 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB VAL B 735 " pdb=" CA VAL B 735 " pdb=" CG1 VAL B 735 " pdb=" CG2 VAL B 735 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA GLU A 409 " pdb=" N GLU A 409 " pdb=" C GLU A 409 " pdb=" CB GLU A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2981 not shown) Planarity restraints: 3411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 262 " 0.045 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO A 263 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 428 " -0.013 2.00e-02 2.50e+03 1.81e-02 5.74e+00 pdb=" CG PHE A 428 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 428 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 428 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 428 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 428 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 428 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 100 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO B 101 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " -0.033 5.00e-02 4.00e+02 ... (remaining 3408 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1637 2.74 - 3.28: 19069 3.28 - 3.82: 31706 3.82 - 4.36: 38437 4.36 - 4.90: 65773 Nonbonded interactions: 156622 Sorted by model distance: nonbonded pdb=" O CYS B 980 " pdb=" OG SER B 984 " model vdw 2.197 2.440 nonbonded pdb=" OG SER A1169 " pdb=" OG SER A1278 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR B1033 " pdb=" O THR A1077 " model vdw 2.212 2.440 nonbonded pdb=" OE1 GLU B1218 " pdb=" OH TYR B1236 " model vdw 2.241 2.440 nonbonded pdb=" O ASP A 783 " pdb=" OG SER A 787 " model vdw 2.256 2.440 ... (remaining 156617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 166 or resid 215 through 538 or resid 547 or res \ id 580 through 646 or resid 662 through 710 or resid 719 through 1336 or resid 3 \ 001 through 3005)) selection = (chain 'B' and (resid 6 through 578 or resid 580 through 1336 or resid 3001 thro \ ugh 3005)) } 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=0.63 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.730 Check model and map are aligned: 0.330 Set scattering table: 0.230 Process input model: 58.740 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 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 : 0.008 0.273 19734 Z= 0.563 Angle : 0.863 11.678 26699 Z= 0.452 Chirality : 0.053 0.282 2984 Planarity : 0.006 0.069 3411 Dihedral : 14.327 111.166 7438 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.14 % Allowed : 0.77 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.16), residues: 2455 helix: -0.69 (0.17), residues: 840 sheet: -0.62 (0.21), residues: 537 loop : -1.87 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 422 HIS 0.008 0.002 HIS B1052 PHE 0.041 0.003 PHE A 428 TYR 0.019 0.002 TYR B 82 ARG 0.015 0.001 ARG A 848 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 287 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 436 ASN cc_start: 0.7250 (t0) cc_final: 0.6902 (t160) REVERT: B 528 LEU cc_start: 0.8235 (mp) cc_final: 0.7964 (mm) REVERT: B 532 GLN cc_start: 0.7455 (tm-30) cc_final: 0.7151 (tp-100) REVERT: B 603 MET cc_start: 0.6729 (ptt) cc_final: 0.6517 (ptm) REVERT: B 720 GLU cc_start: 0.6083 (mp0) cc_final: 0.5783 (mp0) REVERT: B 888 GLU cc_start: 0.6663 (mp0) cc_final: 0.6252 (mp0) REVERT: B 1297 HIS cc_start: 0.6429 (m170) cc_final: 0.6137 (p-80) REVERT: B 1331 TYR cc_start: 0.5579 (t80) cc_final: 0.5104 (t80) REVERT: A 277 PHE cc_start: 0.7832 (m-80) cc_final: 0.7564 (m-80) REVERT: A 551 SER cc_start: 0.6360 (p) cc_final: 0.6025 (t) outliers start: 3 outliers final: 1 residues processed: 290 average time/residue: 1.3678 time to fit residues: 445.1022 Evaluate side-chains 216 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 7.9990 chunk 187 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 126 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 ASN B1084 ASN A 363 HIS ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 ASN ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19734 Z= 0.197 Angle : 0.615 9.867 26699 Z= 0.313 Chirality : 0.044 0.199 2984 Planarity : 0.005 0.050 3411 Dihedral : 7.233 95.998 2786 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.44 % Allowed : 11.05 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2455 helix: -0.25 (0.18), residues: 839 sheet: -0.43 (0.22), residues: 508 loop : -1.71 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 243 HIS 0.004 0.001 HIS B1052 PHE 0.016 0.002 PHE B 9 TYR 0.015 0.001 TYR A 126 ARG 0.008 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 244 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.5759 (ttt) REVERT: B 436 ASN cc_start: 0.7283 (t0) cc_final: 0.6900 (t160) REVERT: B 720 GLU cc_start: 0.6060 (mp0) cc_final: 0.5815 (mp0) REVERT: B 758 MET cc_start: 0.5375 (ptp) cc_final: 0.5170 (ptp) REVERT: B 1297 HIS cc_start: 0.6295 (m170) cc_final: 0.5954 (p-80) REVERT: B 1331 TYR cc_start: 0.5508 (t80) cc_final: 0.5152 (t80) REVERT: A 255 PHE cc_start: 0.5989 (OUTLIER) cc_final: 0.5666 (m-80) REVERT: A 277 PHE cc_start: 0.7865 (m-80) cc_final: 0.7626 (m-80) REVERT: A 352 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7554 (ptp) REVERT: A 1175 CYS cc_start: 0.4908 (m) cc_final: 0.4333 (m) outliers start: 30 outliers final: 8 residues processed: 254 average time/residue: 1.2584 time to fit residues: 363.6715 Evaluate side-chains 219 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 1106 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 352 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 186 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 222 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 180 optimal weight: 0.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS A 363 HIS A 849 HIS ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 HIS A1182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19734 Z= 0.203 Angle : 0.606 11.056 26699 Z= 0.305 Chirality : 0.044 0.175 2984 Planarity : 0.004 0.048 3411 Dihedral : 7.025 88.134 2786 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.15 % Allowed : 13.88 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2455 helix: -0.05 (0.18), residues: 832 sheet: -0.46 (0.22), residues: 531 loop : -1.62 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 977 HIS 0.007 0.001 HIS B1052 PHE 0.017 0.002 PHE B 9 TYR 0.013 0.001 TYR A 126 ARG 0.006 0.000 ARG A 848 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 233 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.5830 (ttt) REVERT: B 333 MET cc_start: 0.4760 (OUTLIER) cc_final: 0.4485 (ttt) REVERT: B 436 ASN cc_start: 0.7181 (t0) cc_final: 0.6941 (t160) REVERT: B 504 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7145 (mt) REVERT: B 720 GLU cc_start: 0.6173 (mp0) cc_final: 0.5966 (mp0) REVERT: B 1237 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7003 (ttmm) REVERT: B 1297 HIS cc_start: 0.6278 (m170) cc_final: 0.5929 (p-80) REVERT: A 223 MET cc_start: 0.4742 (ptt) cc_final: 0.4536 (ptt) REVERT: A 255 PHE cc_start: 0.5955 (OUTLIER) cc_final: 0.5635 (m-80) REVERT: A 277 PHE cc_start: 0.7920 (m-80) cc_final: 0.7673 (m-80) REVERT: A 1175 CYS cc_start: 0.4860 (m) cc_final: 0.4325 (m) outliers start: 45 outliers final: 17 residues processed: 253 average time/residue: 1.2658 time to fit residues: 364.4608 Evaluate side-chains 232 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 210 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 994 GLU Chi-restraints excluded: chain B residue 1106 LEU Chi-restraints excluded: chain B residue 1237 LYS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 1041 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 363 HIS A 430 GLN ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19734 Z= 0.218 Angle : 0.605 10.759 26699 Z= 0.305 Chirality : 0.044 0.177 2984 Planarity : 0.004 0.048 3411 Dihedral : 6.936 83.129 2786 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.58 % Allowed : 16.36 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.17), residues: 2455 helix: 0.00 (0.18), residues: 833 sheet: -0.43 (0.22), residues: 529 loop : -1.63 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 977 HIS 0.006 0.001 HIS B1052 PHE 0.044 0.002 PHE B 777 TYR 0.025 0.001 TYR A 964 ARG 0.010 0.000 ARG B 978 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 228 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.5912 (ttt) REVERT: B 380 ASN cc_start: 0.5963 (OUTLIER) cc_final: 0.5471 (m-40) REVERT: B 436 ASN cc_start: 0.7231 (t0) cc_final: 0.6996 (t160) REVERT: B 720 GLU cc_start: 0.6301 (mp0) cc_final: 0.6031 (mp0) REVERT: B 1237 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6961 (ttmm) REVERT: B 1297 HIS cc_start: 0.6312 (m170) cc_final: 0.5948 (p-80) REVERT: A 255 PHE cc_start: 0.5969 (OUTLIER) cc_final: 0.5643 (m-80) REVERT: A 430 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7303 (tm130) REVERT: A 511 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7713 (mtmm) REVERT: A 1175 CYS cc_start: 0.4895 (m) cc_final: 0.4367 (m) outliers start: 54 outliers final: 24 residues processed: 251 average time/residue: 1.2587 time to fit residues: 359.4965 Evaluate side-chains 242 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 994 GLU Chi-restraints excluded: chain B residue 1085 ILE Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1237 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1189 MET Chi-restraints excluded: chain A residue 1317 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 177 optimal weight: 0.0470 chunk 98 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 121 optimal weight: 0.3980 chunk 214 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 overall best weight: 2.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 ASN A 363 HIS ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19734 Z= 0.342 Angle : 0.696 10.575 26699 Z= 0.353 Chirality : 0.047 0.200 2984 Planarity : 0.005 0.052 3411 Dihedral : 7.333 85.698 2786 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.40 % Allowed : 17.85 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2455 helix: -0.35 (0.18), residues: 838 sheet: -0.66 (0.22), residues: 534 loop : -1.79 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 977 HIS 0.008 0.001 HIS B1052 PHE 0.039 0.002 PHE B 777 TYR 0.017 0.002 TYR A 851 ARG 0.017 0.001 ARG B 978 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 222 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5491 (tt) REVERT: B 436 ASN cc_start: 0.7309 (t0) cc_final: 0.7109 (t160) REVERT: B 504 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7159 (mt) REVERT: B 532 GLN cc_start: 0.7447 (tm-30) cc_final: 0.7160 (tp-100) REVERT: B 596 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6789 (mt-10) REVERT: B 720 GLU cc_start: 0.6329 (mp0) cc_final: 0.6048 (mp0) REVERT: B 1237 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.6957 (ttmm) REVERT: B 1297 HIS cc_start: 0.6455 (m170) cc_final: 0.6023 (p-80) REVERT: A 241 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.5681 (ttp) REVERT: A 255 PHE cc_start: 0.6078 (OUTLIER) cc_final: 0.5878 (m-80) REVERT: A 382 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5994 (tp) REVERT: A 423 GLU cc_start: 0.6780 (tt0) cc_final: 0.6152 (tt0) REVERT: A 445 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6834 (mpp) REVERT: A 483 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7139 (mmp80) REVERT: A 511 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7769 (mtmm) REVERT: A 859 PHE cc_start: 0.5838 (p90) cc_final: 0.5363 (p90) REVERT: A 1175 CYS cc_start: 0.5334 (m) cc_final: 0.4775 (m) outliers start: 71 outliers final: 31 residues processed: 263 average time/residue: 1.2439 time to fit residues: 374.6015 Evaluate side-chains 250 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 210 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 981 MET Chi-restraints excluded: chain B residue 994 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1237 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1277 CYS Chi-restraints excluded: chain A residue 1317 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS A 430 GLN ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19734 Z= 0.307 Angle : 0.674 10.234 26699 Z= 0.341 Chirality : 0.046 0.198 2984 Planarity : 0.005 0.053 3411 Dihedral : 7.231 82.356 2786 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.54 % Allowed : 18.66 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2455 helix: -0.36 (0.18), residues: 832 sheet: -0.70 (0.21), residues: 537 loop : -1.77 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 977 HIS 0.007 0.001 HIS B1052 PHE 0.033 0.002 PHE B 777 TYR 0.018 0.002 TYR A 851 ARG 0.011 0.001 ARG B 978 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 221 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 225 MET cc_start: 0.2782 (pp-130) cc_final: 0.2575 (pp-130) REVERT: B 331 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7339 (p) REVERT: B 382 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5444 (tt) REVERT: B 394 GLU cc_start: 0.7721 (tt0) cc_final: 0.7420 (tt0) REVERT: B 532 GLN cc_start: 0.7436 (tm-30) cc_final: 0.7164 (tp-100) REVERT: B 596 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6887 (mt-10) REVERT: B 720 GLU cc_start: 0.6330 (mp0) cc_final: 0.6052 (mp0) REVERT: B 1237 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6860 (ttmm) REVERT: B 1297 HIS cc_start: 0.6567 (m170) cc_final: 0.6218 (p-80) REVERT: A 382 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.6013 (tp) REVERT: A 423 GLU cc_start: 0.6821 (tt0) cc_final: 0.6185 (tt0) REVERT: A 445 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6862 (mpp) REVERT: A 483 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7135 (mmp80) REVERT: A 851 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6356 (t80) REVERT: A 859 PHE cc_start: 0.5856 (p90) cc_final: 0.5359 (p90) REVERT: A 1175 CYS cc_start: 0.5278 (m) cc_final: 0.4749 (m) outliers start: 74 outliers final: 36 residues processed: 263 average time/residue: 1.2352 time to fit residues: 370.4347 Evaluate side-chains 253 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 994 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1085 ILE Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1237 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 851 TYR Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1277 CYS Chi-restraints excluded: chain A residue 1317 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 174 optimal weight: 0.3980 chunk 135 optimal weight: 0.9990 chunk 201 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 238 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS A 430 GLN ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19734 Z= 0.232 Angle : 0.631 9.917 26699 Z= 0.317 Chirality : 0.044 0.184 2984 Planarity : 0.005 0.062 3411 Dihedral : 6.956 78.265 2786 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.06 % Allowed : 19.62 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2455 helix: -0.16 (0.18), residues: 831 sheet: -0.62 (0.22), residues: 535 loop : -1.70 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 977 HIS 0.006 0.001 HIS B1052 PHE 0.029 0.002 PHE B 777 TYR 0.016 0.001 TYR A 851 ARG 0.016 0.000 ARG B 978 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 225 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.5886 (ttt) REVERT: B 331 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7232 (p) REVERT: B 382 LEU cc_start: 0.5887 (OUTLIER) cc_final: 0.5370 (tt) REVERT: B 394 GLU cc_start: 0.7679 (tt0) cc_final: 0.7343 (tt0) REVERT: B 532 GLN cc_start: 0.7401 (tm-30) cc_final: 0.7125 (tp-100) REVERT: B 720 GLU cc_start: 0.6192 (mp0) cc_final: 0.5930 (mp0) REVERT: B 870 MET cc_start: 0.5428 (OUTLIER) cc_final: 0.5217 (mmm) REVERT: B 1047 MET cc_start: 0.7162 (ptt) cc_final: 0.6922 (ptp) REVERT: B 1237 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6989 (ttmm) REVERT: B 1297 HIS cc_start: 0.6555 (m170) cc_final: 0.6222 (p-80) REVERT: A 98 ARG cc_start: 0.6888 (mtp-110) cc_final: 0.6412 (ttt-90) REVERT: A 423 GLU cc_start: 0.6753 (tt0) cc_final: 0.6106 (tt0) REVERT: A 483 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7085 (mmp80) REVERT: A 511 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7681 (mtmm) REVERT: A 851 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6350 (t80) REVERT: A 859 PHE cc_start: 0.5667 (p90) cc_final: 0.5203 (p90) REVERT: A 1175 CYS cc_start: 0.5107 (m) cc_final: 0.4654 (m) outliers start: 64 outliers final: 29 residues processed: 265 average time/residue: 1.2154 time to fit residues: 367.4272 Evaluate side-chains 250 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 214 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 870 MET Chi-restraints excluded: chain B residue 981 MET Chi-restraints excluded: chain B residue 994 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1085 ILE Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1237 LYS Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 483 ARG Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 851 TYR Chi-restraints excluded: chain A residue 932 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1277 CYS Chi-restraints excluded: chain A residue 1317 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 216 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 147 ASN A 363 HIS ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19734 Z= 0.180 Angle : 0.603 11.601 26699 Z= 0.301 Chirality : 0.043 0.170 2984 Planarity : 0.004 0.051 3411 Dihedral : 6.620 72.854 2786 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.01 % Allowed : 21.48 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2455 helix: 0.09 (0.18), residues: 832 sheet: -0.51 (0.22), residues: 536 loop : -1.61 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 422 HIS 0.005 0.001 HIS B1052 PHE 0.025 0.001 PHE B 526 TYR 0.015 0.001 TYR A1161 ARG 0.013 0.000 ARG B 978 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 226 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 MET cc_start: 0.6380 (ttp) cc_final: 0.6060 (tmm) REVERT: B 331 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7151 (p) REVERT: B 382 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5548 (tt) REVERT: B 394 GLU cc_start: 0.7548 (tt0) cc_final: 0.7243 (tt0) REVERT: B 720 GLU cc_start: 0.6314 (mp0) cc_final: 0.6103 (mp0) REVERT: B 870 MET cc_start: 0.5377 (OUTLIER) cc_final: 0.5175 (mmm) REVERT: B 1047 MET cc_start: 0.7148 (ptt) cc_final: 0.6931 (ptp) REVERT: B 1297 HIS cc_start: 0.6537 (m170) cc_final: 0.6187 (p-80) REVERT: A 98 ARG cc_start: 0.6764 (mtp-110) cc_final: 0.6370 (ttt-90) REVERT: A 255 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.5937 (m-80) REVERT: A 511 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7723 (mtmm) REVERT: A 725 TYR cc_start: 0.5468 (t80) cc_final: 0.5230 (t80) REVERT: A 859 PHE cc_start: 0.5697 (p90) cc_final: 0.5186 (p90) REVERT: A 1175 CYS cc_start: 0.4743 (m) cc_final: 0.4362 (m) outliers start: 42 outliers final: 21 residues processed: 251 average time/residue: 1.2304 time to fit residues: 352.8851 Evaluate side-chains 241 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 870 MET Chi-restraints excluded: chain B residue 994 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1085 ILE Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1212 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 221 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 174 optimal weight: 0.0170 chunk 68 optimal weight: 0.0980 chunk 200 optimal weight: 0.5980 chunk 209 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 234 optimal weight: 4.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 972 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19734 Z= 0.154 Angle : 0.595 12.105 26699 Z= 0.293 Chirality : 0.042 0.153 2984 Planarity : 0.004 0.052 3411 Dihedral : 6.213 67.649 2786 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.24 % Allowed : 22.58 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2455 helix: 0.36 (0.19), residues: 827 sheet: -0.31 (0.22), residues: 532 loop : -1.54 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 422 HIS 0.004 0.001 HIS B1052 PHE 0.026 0.001 PHE A 428 TYR 0.014 0.001 TYR B 527 ARG 0.010 0.000 ARG B 978 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7044 (p) REVERT: B 436 ASN cc_start: 0.7169 (t0) cc_final: 0.6963 (t160) REVERT: B 720 GLU cc_start: 0.6268 (mp0) cc_final: 0.6039 (mp0) REVERT: B 955 MET cc_start: 0.6725 (ttm) cc_final: 0.6158 (tpp) REVERT: B 1297 HIS cc_start: 0.6475 (m170) cc_final: 0.6032 (p-80) REVERT: B 1331 TYR cc_start: 0.5947 (t80) cc_final: 0.5684 (t80) REVERT: A 98 ARG cc_start: 0.6766 (mtp-110) cc_final: 0.6416 (ttt-90) REVERT: A 121 MET cc_start: 0.6938 (mtt) cc_final: 0.6686 (mtt) REVERT: A 511 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7699 (mtmm) REVERT: A 725 TYR cc_start: 0.5412 (t80) cc_final: 0.5194 (t80) REVERT: A 859 PHE cc_start: 0.5519 (p90) cc_final: 0.5125 (p90) REVERT: A 1175 CYS cc_start: 0.4348 (m) cc_final: 0.4066 (m) REVERT: A 1322 MET cc_start: 0.5172 (ptm) cc_final: 0.4960 (ptm) outliers start: 26 outliers final: 12 residues processed: 253 average time/residue: 1.2339 time to fit residues: 356.6343 Evaluate side-chains 227 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 214 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 994 GLU Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 752 TYR Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1085 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 246 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN A 363 HIS ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19734 Z= 0.262 Angle : 0.654 11.247 26699 Z= 0.325 Chirality : 0.045 0.188 2984 Planarity : 0.005 0.091 3411 Dihedral : 6.670 76.411 2786 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.48 % Allowed : 22.58 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2455 helix: 0.18 (0.18), residues: 832 sheet: -0.44 (0.21), residues: 536 loop : -1.55 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 422 HIS 0.006 0.001 HIS B1052 PHE 0.033 0.002 PHE A 428 TYR 0.025 0.002 TYR A 964 ARG 0.019 0.000 ARG B 978 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 225 MET cc_start: 0.2857 (ppp) cc_final: 0.2542 (pp-130) REVERT: B 331 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7119 (p) REVERT: B 382 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5475 (tt) REVERT: B 394 GLU cc_start: 0.7591 (tt0) cc_final: 0.7248 (tt0) REVERT: B 436 ASN cc_start: 0.7245 (t0) cc_final: 0.7027 (t160) REVERT: B 532 GLN cc_start: 0.7453 (tm-30) cc_final: 0.7136 (tp-100) REVERT: B 1297 HIS cc_start: 0.6571 (m170) cc_final: 0.6098 (p-80) REVERT: A 98 ARG cc_start: 0.6783 (mtp-110) cc_final: 0.6388 (ttt-90) REVERT: A 382 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.5916 (mm) REVERT: A 511 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7734 (mtmm) REVERT: A 720 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: A 725 TYR cc_start: 0.5560 (t80) cc_final: 0.5348 (t80) REVERT: A 859 PHE cc_start: 0.5710 (p90) cc_final: 0.5373 (p90) REVERT: A 1175 CYS cc_start: 0.4892 (m) cc_final: 0.4502 (m) outliers start: 31 outliers final: 20 residues processed: 238 average time/residue: 1.2517 time to fit residues: 340.5309 Evaluate side-chains 236 residues out of total 2090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 994 GLU Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 752 TYR Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain A residue 1055 MET Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1212 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.0570 chunk 172 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.136303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.117374 restraints weight = 41493.854| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.34 r_work: 0.3895 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19734 Z= 0.199 Angle : 0.630 10.855 26699 Z= 0.311 Chirality : 0.044 0.214 2984 Planarity : 0.004 0.080 3411 Dihedral : 6.560 75.561 2786 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.48 % Allowed : 22.82 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2455 helix: 0.23 (0.18), residues: 829 sheet: -0.40 (0.22), residues: 530 loop : -1.55 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 422 HIS 0.005 0.001 HIS B1052 PHE 0.034 0.002 PHE A 428 TYR 0.014 0.001 TYR A 851 ARG 0.018 0.000 ARG B 978 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6806.32 seconds wall clock time: 122 minutes 22.84 seconds (7342.84 seconds total)