Starting phenix.real_space_refine on Tue Jul 7 02:10:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7en2_31200/07_2026/7en2_31200_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7en2_31200/07_2026/7en2_31200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7en2_31200/07_2026/7en2_31200_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7en2_31200/07_2026/7en2_31200_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7en2_31200/07_2026/7en2_31200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7en2_31200/07_2026/7en2_31200.map" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 68 5.16 5 C 13237 2.51 5 N 3883 2.21 5 O 3817 1.98 5 H 21010 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42019 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 20290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 20290 Classifications: {'peptide': 1321} Link IDs: {'PCIS': 1, 'PTRANS': 83, 'TRANS': 1236} Chain breaks: 1 Chain: "B" Number of atoms: 21641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 21641 Classifications: {'peptide': 1410} Link IDs: {'PCIS': 1, 'PTRANS': 87, 'TRANS': 1321} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'AMP%rna2p': 1, 'PNS': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'AMP%rna2p': 1, 'PNS': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C28 PNS A1501 " occ=0.00 ... (19 atoms not shown) pdb=" S44 PNS A1501 " occ=0.00 Time building chain proxies: 5.90, per 1000 atoms: 0.14 Number of scatterers: 42019 At special positions: 0 Unit cell: (145, 158, 133, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 4 15.00 O 3817 8.00 N 3883 7.00 C 13237 6.00 H 21010 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.0 seconds 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5044 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 23 sheets defined 47.7% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.507A pdb=" N ALA A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 183 through 187 removed outlier: 4.247A pdb=" N THR A 186 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 206 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 240 through 257 Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 268 through 295 removed outlier: 4.269A pdb=" N ALA A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 removed outlier: 4.303A pdb=" N ILE A 313 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 343 through 360 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 403 through 422 removed outlier: 3.657A pdb=" N ASP A 420 " --> pdb=" O HIS A 416 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 457 through 464 Processing helix chain 'A' and resid 504 through 523 Processing helix chain 'A' and resid 534 through 547 removed outlier: 3.537A pdb=" N GLN A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 567 Processing helix chain 'A' and resid 582 through 599 Processing helix chain 'A' and resid 614 through 627 Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.797A pdb=" N LEU A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 698 through 702 Processing helix chain 'A' and resid 711 through 726 removed outlier: 3.637A pdb=" N LEU A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 752 removed outlier: 3.865A pdb=" N PHE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 766 Processing helix chain 'A' and resid 768 through 780 Processing helix chain 'A' and resid 787 through 797 removed outlier: 3.689A pdb=" N LEU A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 797 " --> pdb=" O MET A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 826 Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 906 through 913 removed outlier: 3.597A pdb=" N SER A 910 " --> pdb=" O ASP A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 1008 through 1027 removed outlier: 3.895A pdb=" N ALA A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 removed outlier: 6.496A pdb=" N LEU A1031 " --> pdb=" O GLU A1028 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU A1032 " --> pdb=" O ALA A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1047 Processing helix chain 'A' and resid 1048 through 1053 Processing helix chain 'A' and resid 1057 through 1064 removed outlier: 3.768A pdb=" N ARG A1061 " --> pdb=" O ASP A1057 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY A1064 " --> pdb=" O LEU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1083 removed outlier: 3.556A pdb=" N GLY A1083 " --> pdb=" O GLY A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1092 removed outlier: 3.813A pdb=" N LEU A1091 " --> pdb=" O PRO A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1103 Processing helix chain 'A' and resid 1107 through 1117 Processing helix chain 'A' and resid 1120 through 1125 Processing helix chain 'A' and resid 1140 through 1143 Processing helix chain 'A' and resid 1144 through 1149 Processing helix chain 'A' and resid 1162 through 1172 Processing helix chain 'A' and resid 1181 through 1185 Processing helix chain 'A' and resid 1189 through 1191 No H-bonds generated for 'chain 'A' and resid 1189 through 1191' Processing helix chain 'A' and resid 1208 through 1219 removed outlier: 3.703A pdb=" N GLY A1212 " --> pdb=" O ALA A1208 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1242 Processing helix chain 'A' and resid 1243 through 1246 Processing helix chain 'A' and resid 1248 through 1252 Processing helix chain 'A' and resid 1254 through 1265 Processing helix chain 'A' and resid 1291 through 1301 Processing helix chain 'A' and resid 1304 through 1308 Processing helix chain 'A' and resid 1327 through 1338 Processing helix chain 'A' and resid 1353 through 1368 Processing helix chain 'A' and resid 1377 through 1383 Processing helix chain 'A' and resid 1384 through 1400 removed outlier: 3.544A pdb=" N ARG A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1409 Processing helix chain 'A' and resid 1413 through 1423 removed outlier: 4.192A pdb=" N ARG A1419 " --> pdb=" O ALA A1415 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS A1420 " --> pdb=" O GLY A1416 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A1423 " --> pdb=" O ARG A1419 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 24 Processing helix chain 'B' and resid 26 through 32 Processing helix chain 'B' and resid 45 through 59 removed outlier: 3.871A pdb=" N TYR B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 70 removed outlier: 3.561A pdb=" N LEU B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 Processing helix chain 'B' and resid 108 through 118 removed outlier: 3.685A pdb=" N ARG B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 156 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 240 through 257 Processing helix chain 'B' and resid 258 through 261 removed outlier: 3.550A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 261' Processing helix chain 'B' and resid 268 through 293 removed outlier: 3.561A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 343 through 360 Processing helix chain 'B' and resid 403 through 422 removed outlier: 3.980A pdb=" N ASP B 420 " --> pdb=" O HIS B 416 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 457 through 464 Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 534 through 546 Processing helix chain 'B' and resid 557 through 567 removed outlier: 3.558A pdb=" N PHE B 561 " --> pdb=" O HIS B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 599 Processing helix chain 'B' and resid 614 through 627 Processing helix chain 'B' and resid 639 through 650 removed outlier: 3.558A pdb=" N LEU B 645 " --> pdb=" O ALA B 641 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 648 " --> pdb=" O ARG B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'B' and resid 698 through 702 Processing helix chain 'B' and resid 711 through 726 removed outlier: 4.247A pdb=" N LEU B 724 " --> pdb=" O ALA B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 754 Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 768 through 779 Processing helix chain 'B' and resid 787 through 796 removed outlier: 3.560A pdb=" N LEU B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 826 removed outlier: 4.713A pdb=" N GLY B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 906 through 913 removed outlier: 3.970A pdb=" N ARG B 912 " --> pdb=" O GLU B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 965 Processing helix chain 'B' and resid 1008 through 1027 removed outlier: 4.006A pdb=" N ALA B1012 " --> pdb=" O PHE B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1033 removed outlier: 6.149A pdb=" N LEU B1031 " --> pdb=" O GLU B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1048 removed outlier: 4.409A pdb=" N ARG B1040 " --> pdb=" O GLY B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1062 removed outlier: 4.202A pdb=" N LEU B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG B1062 " --> pdb=" O GLU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1083 Processing helix chain 'B' and resid 1089 through 1093 removed outlier: 3.558A pdb=" N ASP B1093 " --> pdb=" O LEU B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1102 Processing helix chain 'B' and resid 1107 through 1117 removed outlier: 3.636A pdb=" N ALA B1111 " --> pdb=" O ASP B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1125 Processing helix chain 'B' and resid 1140 through 1143 Processing helix chain 'B' and resid 1144 through 1149 Processing helix chain 'B' and resid 1162 through 1172 Processing helix chain 'B' and resid 1182 through 1185 Processing helix chain 'B' and resid 1189 through 1191 No H-bonds generated for 'chain 'B' and resid 1189 through 1191' Processing helix chain 'B' and resid 1208 through 1219 removed outlier: 3.560A pdb=" N GLY B1212 " --> pdb=" O ALA B1208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B1214 " --> pdb=" O ARG B1210 " (cutoff:3.500A) Processing helix chain 'B' and resid 1237 through 1245 Processing helix chain 'B' and resid 1254 through 1265 Processing helix chain 'B' and resid 1274 through 1279 removed outlier: 3.802A pdb=" N ILE B1278 " --> pdb=" O ARG B1274 " (cutoff:3.500A) Processing helix chain 'B' and resid 1291 through 1303 Processing helix chain 'B' and resid 1304 through 1308 Processing helix chain 'B' and resid 1327 through 1340 Processing helix chain 'B' and resid 1353 through 1368 Processing helix chain 'B' and resid 1377 through 1382 Processing helix chain 'B' and resid 1384 through 1400 removed outlier: 3.547A pdb=" N ALA B1393 " --> pdb=" O THR B1389 " (cutoff:3.500A) Processing helix chain 'B' and resid 1404 through 1409 Processing helix chain 'B' and resid 1413 through 1423 removed outlier: 4.236A pdb=" N ARG B1419 " --> pdb=" O ALA B1415 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS B1420 " --> pdb=" O GLY B1416 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU B1421 " --> pdb=" O LEU B1417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 182 removed outlier: 3.575A pdb=" N LEU A 230 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 325 removed outlier: 4.061A pdb=" N ARG A 485 " --> pdb=" O ASN A 449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 372 Processing sheet with id=AA5, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.646A pdb=" N VAL A 580 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ALA A 572 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU A 733 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG A 732 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASN A 785 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 734 " --> pdb=" O ASN A 785 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TRP A 784 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER A 813 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 786 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL A 810 " --> pdb=" O HIS A 836 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU A 838 " --> pdb=" O VAL A 810 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A 812 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 835 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG A 867 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 630 through 634 removed outlier: 6.444A pdb=" N VAL A 607 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU A 634 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL A 609 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 654 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 691 through 696 Processing sheet with id=AA8, first strand: chain 'A' and resid 872 through 877 removed outlier: 3.599A pdb=" N GLY A 896 " --> pdb=" O ARG A 921 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG A 921 " --> pdb=" O GLY A 896 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 872 through 877 removed outlier: 4.649A pdb=" N ASP A 927 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ARG A 928 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 946 through 948 removed outlier: 4.010A pdb=" N VAL A 947 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 969 through 976 removed outlier: 3.506A pdb=" N SER A 971 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A 984 " --> pdb=" O ARG A1311 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N TRP A1313 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA A 986 " --> pdb=" O TRP A1313 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1177 through 1178 removed outlier: 6.096A pdb=" N LEU A1128 " --> pdb=" O GLU A1154 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N THR A1156 " --> pdb=" O LEU A1128 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A1130 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A1129 " --> pdb=" O ARG A1196 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE A1198 " --> pdb=" O ARG A1129 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA A1131 " --> pdb=" O ILE A1198 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N PHE A1200 " --> pdb=" O ALA A1131 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASP A1195 " --> pdb=" O ARG A1225 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU A1227 " --> pdb=" O ASP A1195 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL A1197 " --> pdb=" O LEU A1227 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A1229 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER A1199 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N LEU A1231 " --> pdb=" O SER A1199 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A1230 " --> pdb=" O ALA A1279 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP A1273 " --> pdb=" O LEU A1280 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU A1282 " --> pdb=" O CYS A1271 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N CYS A1271 " --> pdb=" O GLU A1282 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A1284 " --> pdb=" O PRO A1269 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 105 through 106 Processing sheet with id=AB5, first strand: chain 'B' and resid 179 through 183 Processing sheet with id=AB6, first strand: chain 'B' and resid 318 through 325 removed outlier: 5.751A pdb=" N VAL B 445 " --> pdb=" O HIS B 481 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU B 483 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA B 447 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ARG B 485 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N ASN B 449 " --> pdb=" O ARG B 485 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 364 through 372 Processing sheet with id=AB8, first strand: chain 'B' and resid 579 through 581 removed outlier: 7.093A pdb=" N ALA B 572 " --> pdb=" O LEU B 758 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 733 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN B 785 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL B 810 " --> pdb=" O HIS B 836 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU B 838 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU B 812 " --> pdb=" O LEU B 838 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 835 " --> pdb=" O VAL B 853 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN B 849 " --> pdb=" O GLY B 839 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 867 " --> pdb=" O LEU B 850 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 630 through 633 removed outlier: 6.344A pdb=" N VAL B 607 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 606 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE B 656 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU B 608 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 691 through 696 removed outlier: 3.743A pdb=" N GLY B 902 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 872 through 877 removed outlier: 6.596A pdb=" N GLY B 890 " --> pdb=" O ASP B 927 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP B 927 " --> pdb=" O GLY B 890 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 892 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 896 " --> pdb=" O ARG B 921 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ARG B 921 " --> pdb=" O GLY B 896 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 872 through 877 removed outlier: 6.596A pdb=" N GLY B 890 " --> pdb=" O ASP B 927 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP B 927 " --> pdb=" O GLY B 890 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 892 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 896 " --> pdb=" O ARG B 921 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ARG B 921 " --> pdb=" O GLY B 896 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N GLY B 926 " --> pdb=" O ARG B 942 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ARG B 942 " --> pdb=" O GLY B 926 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG B 928 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 969 through 976 removed outlier: 3.625A pdb=" N SER B 971 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TRP B1313 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 986 " --> pdb=" O TRP B1313 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1177 through 1180 removed outlier: 4.066A pdb=" N GLU B1159 " --> pdb=" O GLN B1179 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG B1129 " --> pdb=" O ARG B1196 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE B1198 " --> pdb=" O ARG B1129 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA B1131 " --> pdb=" O ILE B1198 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE B1200 " --> pdb=" O ALA B1131 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP B1195 " --> pdb=" O ARG B1225 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU B1227 " --> pdb=" O ASP B1195 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL B1197 " --> pdb=" O LEU B1227 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL B1229 " --> pdb=" O VAL B1197 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER B1199 " --> pdb=" O VAL B1229 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B1280 " --> pdb=" O LEU B1272 " (cutoff:3.500A) 1009 hydrogen bonds defined for protein. 2859 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: 11.56 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.08: 6706 1.08 - 1.27: 17834 1.27 - 1.46: 6642 1.46 - 1.65: 11183 1.65 - 1.84: 93 Bond restraints: 42458 Sorted by residual: bond pdb=" CZ3 TRP A 184 " pdb=" HZ3 TRP A 184 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" N GLY B 487 " pdb=" H GLY B 487 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" CZ2 TRP A1140 " pdb=" HZ2 TRP A1140 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" CD1 TRP A 847 " pdb=" HD1 TRP A 847 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" CD2 TYR A1206 " pdb=" HD2 TYR A1206 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.59e+01 ... (remaining 42453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.38: 76373 7.38 - 14.75: 444 14.75 - 22.13: 2 22.13 - 29.51: 1 29.51 - 36.88: 5 Bond angle restraints: 76825 Sorted by residual: angle pdb=" N ALA B 84 " pdb=" CA ALA B 84 " pdb=" HA ALA B 84 " ideal model delta sigma weight residual 110.00 73.12 36.88 3.00e+00 1.11e-01 1.51e+02 angle pdb=" N GLN A 518 " pdb=" CA GLN A 518 " pdb=" HA GLN A 518 " ideal model delta sigma weight residual 110.00 76.52 33.48 3.00e+00 1.11e-01 1.25e+02 angle pdb=" C ALA B 84 " pdb=" CA ALA B 84 " pdb=" HA ALA B 84 " ideal model delta sigma weight residual 109.00 77.10 31.90 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CB GLN A 518 " pdb=" CA GLN A 518 " pdb=" HA GLN A 518 " ideal model delta sigma weight residual 109.00 77.61 31.39 3.00e+00 1.11e-01 1.10e+02 angle pdb=" C GLN A 518 " pdb=" CA GLN A 518 " pdb=" HA GLN A 518 " ideal model delta sigma weight residual 109.00 79.04 29.96 3.00e+00 1.11e-01 9.97e+01 ... (remaining 76820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.79: 18462 26.79 - 53.59: 964 53.59 - 80.38: 368 80.38 - 107.18: 18 107.18 - 133.97: 2 Dihedral angle restraints: 19814 sinusoidal: 11004 harmonic: 8810 Sorted by residual: dihedral pdb=" C ARG B1274 " pdb=" N ARG B1274 " pdb=" CA ARG B1274 " pdb=" CB ARG B1274 " ideal model delta harmonic sigma weight residual -122.60 -141.26 18.66 0 2.50e+00 1.60e-01 5.57e+01 dihedral pdb=" N ARG B1274 " pdb=" C ARG B1274 " pdb=" CA ARG B1274 " pdb=" CB ARG B1274 " ideal model delta harmonic sigma weight residual 122.80 141.12 -18.32 0 2.50e+00 1.60e-01 5.37e+01 dihedral pdb=" C GLN A 518 " pdb=" N GLN A 518 " pdb=" CA GLN A 518 " pdb=" CB GLN A 518 " ideal model delta harmonic sigma weight residual -122.60 -139.09 16.49 0 2.50e+00 1.60e-01 4.35e+01 ... (remaining 19811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 2880 0.151 - 0.302: 360 0.302 - 0.453: 21 0.453 - 0.604: 3 0.604 - 0.755: 2 Chirality restraints: 3266 Sorted by residual: chirality pdb=" CA ARG B1274 " pdb=" N ARG B1274 " pdb=" C ARG B1274 " pdb=" CB ARG B1274 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA GLN A 518 " pdb=" N GLN A 518 " pdb=" C GLN A 518 " pdb=" CB GLN A 518 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA ARG A1274 " pdb=" N ARG A1274 " pdb=" C ARG A1274 " pdb=" CB ARG A1274 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.42e+00 ... (remaining 3263 not shown) Planarity restraints: 6442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.402 2.00e-02 2.50e+03 1.56e-01 9.74e+02 pdb=" CG TRP A 816 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " 0.151 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " 0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " -0.102 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " 0.071 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.087 2.00e-02 2.50e+03 pdb=" HD1 TRP A 816 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TRP A 816 " 0.197 2.00e-02 2.50e+03 pdb=" HE3 TRP A 816 " 0.144 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 816 " -0.182 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 816 " 0.189 2.00e-02 2.50e+03 pdb=" HH2 TRP A 816 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1273 " -0.379 2.00e-02 2.50e+03 1.30e-01 6.73e+02 pdb=" CG TRP A1273 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A1273 " 0.094 2.00e-02 2.50e+03 pdb=" CD2 TRP A1273 " 0.111 2.00e-02 2.50e+03 pdb=" NE1 TRP A1273 " 0.140 2.00e-02 2.50e+03 pdb=" CE2 TRP A1273 " 0.084 2.00e-02 2.50e+03 pdb=" CE3 TRP A1273 " 0.094 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1273 " -0.053 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1273 " 0.063 2.00e-02 2.50e+03 pdb=" CH2 TRP A1273 " -0.040 2.00e-02 2.50e+03 pdb=" HD1 TRP A1273 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 TRP A1273 " 0.048 2.00e-02 2.50e+03 pdb=" HE3 TRP A1273 " 0.080 2.00e-02 2.50e+03 pdb=" HZ2 TRP A1273 " -0.178 2.00e-02 2.50e+03 pdb=" HZ3 TRP A1273 " 0.052 2.00e-02 2.50e+03 pdb=" HH2 TRP A1273 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AMP A1502 " -0.377 2.00e-02 2.50e+03 1.55e-01 6.58e+02 pdb=" C2 AMP A1502 " 0.056 2.00e-02 2.50e+03 pdb=" C4 AMP A1502 " 0.119 2.00e-02 2.50e+03 pdb=" C5 AMP A1502 " 0.063 2.00e-02 2.50e+03 pdb=" C6 AMP A1502 " -0.038 2.00e-02 2.50e+03 pdb=" C8 AMP A1502 " 0.128 2.00e-02 2.50e+03 pdb=" N1 AMP A1502 " -0.069 2.00e-02 2.50e+03 pdb=" N3 AMP A1502 " 0.148 2.00e-02 2.50e+03 pdb=" N6 AMP A1502 " -0.200 2.00e-02 2.50e+03 pdb=" N7 AMP A1502 " 0.074 2.00e-02 2.50e+03 pdb=" N9 AMP A1502 " 0.096 2.00e-02 2.50e+03 ... (remaining 6439 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 3324 2.16 - 2.77: 78013 2.77 - 3.38: 134216 3.38 - 3.99: 178335 3.99 - 4.60: 260722 Nonbonded interactions: 654610 Sorted by model distance: nonbonded pdb=" OE2 GLU A1015 " pdb=" HG SER A1235 " model vdw 1.555 2.450 nonbonded pdb=" HG1 THR A 474 " pdb=" OD2 ASP A 480 " model vdw 1.572 2.450 nonbonded pdb=" HG1 THR B 343 " pdb=" O26 PNS B1501 " model vdw 1.584 2.450 nonbonded pdb=" OD2 ASP B1134 " pdb=" HG SER B1199 " model vdw 1.591 2.450 nonbonded pdb=" OE2 GLU A 843 " pdb=" HH TYR A 903 " model vdw 1.592 2.450 ... (remaining 654605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 98 through 1502) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.290 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 37.110 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.013 0.234 21450 Z= 0.861 Angle : 1.995 15.387 29212 Z= 1.304 Chirality : 0.103 0.755 3266 Planarity : 0.024 0.361 3888 Dihedral : 15.861 133.971 7921 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.17 % Favored : 92.32 % Rotamer: Outliers : 2.21 % Allowed : 6.57 % Favored : 91.23 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.14), residues: 2721 helix: -2.17 (0.12), residues: 1118 sheet: -1.61 (0.23), residues: 409 loop : -1.36 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 901 TYR 0.224 0.034 TYR B 51 PHE 0.097 0.023 PHE B1200 TRP 0.260 0.038 TRP A1273 HIS 0.025 0.005 HIS B 711 Details of bonding type rmsd/Z covalent geometry : bond 0.01284 / 0.84 (21448) covalent geometry : angle 1.99490 / 1.30 (29212) hydrogen bonds : bond 0.14915 / 10.10 ( 994) hydrogen bonds : angle 8.86584 / 6.41 ( 2859) Misc. bond : bond 0.20089 / 9.90 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1248 ARG cc_start: 0.8011 (mmp80) cc_final: 0.7221 (ptt90) REVERT: B 381 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7000 (mp) REVERT: B 471 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8216 (mt) REVERT: B 850 LEU cc_start: 0.8884 (tt) cc_final: 0.8654 (tt) REVERT: B 1000 MET cc_start: 0.4471 (tmm) cc_final: 0.3504 (ppp) REVERT: B 1105 LEU cc_start: 0.5711 (mp) cc_final: 0.5318 (mp) REVERT: B 1402 ARG cc_start: 0.4549 (OUTLIER) cc_final: 0.4287 (mmt180) outliers start: 46 outliers final: 21 residues processed: 279 average time/residue: 0.4235 time to fit residues: 168.2890 Evaluate side-chains 159 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1109 ARG Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1402 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 919 GLN A1099 GLN B 205 HIS B 449 ASN ** B 916 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.076808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.058712 restraints weight = 300743.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.059830 restraints weight = 124022.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.060859 restraints weight = 75282.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.061440 restraints weight = 57557.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.061730 restraints weight = 50701.397| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 21450 Z= 0.310 Angle : 0.878 8.310 29212 Z= 0.456 Chirality : 0.044 0.480 3266 Planarity : 0.008 0.122 3888 Dihedral : 10.210 138.299 3133 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.73 % Favored : 94.19 % Rotamer: Outliers : 2.64 % Allowed : 9.68 % Favored : 87.68 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.15), residues: 2721 helix: -1.17 (0.14), residues: 1135 sheet: -2.09 (0.22), residues: 433 loop : -1.21 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 314 TYR 0.031 0.002 TYR A 114 PHE 0.028 0.003 PHE B 560 TRP 0.023 0.002 TRP B 535 HIS 0.010 0.003 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.31 (21448) covalent geometry : angle 0.87775 / 0.46 (29212) hydrogen bonds : bond 0.06340 / 4.22 ( 994) hydrogen bonds : angle 7.10436 / 5.11 ( 2859) Misc. bond : bond 0.00226 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 137 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.7527 (mmm) cc_final: 0.7222 (mmm) REVERT: A 481 HIS cc_start: 0.8788 (OUTLIER) cc_final: 0.8232 (t70) REVERT: A 783 LEU cc_start: 0.8901 (tt) cc_final: 0.8224 (mp) REVERT: A 791 LEU cc_start: 0.9251 (tp) cc_final: 0.9018 (tt) REVERT: A 1248 ARG cc_start: 0.8394 (mmp80) cc_final: 0.7254 (ptt90) REVERT: B 381 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6869 (mp) REVERT: B 471 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8225 (tt) REVERT: B 1000 MET cc_start: 0.4637 (tmm) cc_final: 0.3775 (ppp) REVERT: B 1105 LEU cc_start: 0.6753 (mp) cc_final: 0.6504 (mt) outliers start: 55 outliers final: 42 residues processed: 184 average time/residue: 0.4196 time to fit residues: 111.3285 Evaluate side-chains 152 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1109 ARG Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1261 ASP Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1384 ASP Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 50 optimal weight: 5.9990 chunk 245 optimal weight: 30.0000 chunk 76 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 ASN ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.075992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.057489 restraints weight = 298592.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.058898 restraints weight = 125434.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.059883 restraints weight = 75976.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.060513 restraints weight = 58491.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.060754 restraints weight = 51164.266| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21450 Z= 0.255 Angle : 0.759 7.541 29212 Z= 0.396 Chirality : 0.041 0.452 3266 Planarity : 0.007 0.087 3888 Dihedral : 8.983 113.461 3123 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.73 % Favored : 93.24 % Rotamer: Outliers : 2.49 % Allowed : 11.36 % Favored : 86.15 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.16), residues: 2721 helix: -0.47 (0.15), residues: 1123 sheet: -2.19 (0.22), residues: 448 loop : -1.09 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 826 TYR 0.020 0.002 TYR A 290 PHE 0.022 0.002 PHE B 372 TRP 0.021 0.002 TRP B 14 HIS 0.007 0.002 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.25 (21448) covalent geometry : angle 0.75891 / 0.40 (29212) hydrogen bonds : bond 0.05341 / 3.58 ( 994) hydrogen bonds : angle 6.58292 / 4.73 ( 2859) Misc. bond : bond 0.00066 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 125 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8308 (ptp-110) REVERT: A 223 MET cc_start: 0.7532 (mmm) cc_final: 0.7270 (mmm) REVERT: A 1246 ASP cc_start: 0.8132 (t0) cc_final: 0.7374 (t0) REVERT: A 1248 ARG cc_start: 0.8429 (mmp80) cc_final: 0.7207 (ptt90) REVERT: B 471 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8425 (tt) REVERT: B 988 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 1000 MET cc_start: 0.4776 (tmm) cc_final: 0.4066 (ppp) outliers start: 52 outliers final: 44 residues processed: 169 average time/residue: 0.3718 time to fit residues: 93.5558 Evaluate side-chains 146 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 99 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1261 ASP Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 111 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 241 optimal weight: 20.0000 chunk 135 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 199 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 HIS ** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.077390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.058804 restraints weight = 297276.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.060230 restraints weight = 124364.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.061300 restraints weight = 74710.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.061915 restraints weight = 57586.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.062115 restraints weight = 50720.845| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 21450 Z= 0.159 Angle : 0.674 7.178 29212 Z= 0.343 Chirality : 0.040 0.423 3266 Planarity : 0.006 0.056 3888 Dihedral : 8.144 80.755 3113 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.03 % Favored : 94.93 % Rotamer: Outliers : 2.25 % Allowed : 12.08 % Favored : 85.67 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2721 helix: 0.12 (0.15), residues: 1119 sheet: -2.03 (0.23), residues: 426 loop : -0.84 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1104 TYR 0.021 0.002 TYR A 290 PHE 0.024 0.002 PHE A 560 TRP 0.019 0.001 TRP B 14 HIS 0.006 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (21448) covalent geometry : angle 0.67353 / 0.34 (29212) hydrogen bonds : bond 0.04525 / 3.01 ( 994) hydrogen bonds : angle 6.15727 / 4.42 ( 2859) Misc. bond : bond 0.00072 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8145 (ptp-110) REVERT: A 223 MET cc_start: 0.7571 (mmm) cc_final: 0.7297 (mmm) REVERT: A 793 MET cc_start: 0.8115 (ttp) cc_final: 0.7889 (mtm) REVERT: A 1246 ASP cc_start: 0.8060 (t0) cc_final: 0.7378 (t0) REVERT: A 1248 ARG cc_start: 0.8647 (mmp80) cc_final: 0.7291 (ptt90) REVERT: A 1267 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7706 (mt) REVERT: A 1363 TRP cc_start: 0.6858 (m-10) cc_final: 0.6171 (m-10) REVERT: B 393 LEU cc_start: 0.9033 (tp) cc_final: 0.8833 (tt) REVERT: B 471 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8372 (tt) REVERT: B 757 SER cc_start: 0.8710 (OUTLIER) cc_final: 0.8318 (p) REVERT: B 1000 MET cc_start: 0.4734 (tmm) cc_final: 0.4149 (ppp) REVERT: B 1364 GLU cc_start: 0.8727 (tt0) cc_final: 0.8282 (mm-30) outliers start: 47 outliers final: 33 residues processed: 163 average time/residue: 0.3859 time to fit residues: 93.7902 Evaluate side-chains 141 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1117 GLU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1384 ASP Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 209 optimal weight: 7.9990 chunk 253 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 200 optimal weight: 0.2980 chunk 12 optimal weight: 6.9990 chunk 229 optimal weight: 20.0000 chunk 249 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.075770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.057485 restraints weight = 299337.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.058853 restraints weight = 124899.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.059846 restraints weight = 74488.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.060450 restraints weight = 57560.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.060661 restraints weight = 50549.342| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21450 Z= 0.273 Angle : 0.705 6.934 29212 Z= 0.365 Chirality : 0.040 0.453 3266 Planarity : 0.006 0.055 3888 Dihedral : 7.619 78.535 3103 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.06 % Favored : 92.91 % Rotamer: Outliers : 2.59 % Allowed : 12.80 % Favored : 84.61 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.16), residues: 2721 helix: 0.19 (0.15), residues: 1119 sheet: -2.25 (0.22), residues: 453 loop : -0.84 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 320 TYR 0.016 0.002 TYR A 290 PHE 0.021 0.002 PHE B 560 TRP 0.019 0.002 TRP B 535 HIS 0.007 0.002 HIS B1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.27 (21448) covalent geometry : angle 0.70502 / 0.36 (29212) hydrogen bonds : bond 0.04774 / 3.16 ( 994) hydrogen bonds : angle 6.18202 / 4.45 ( 2859) Misc. bond : bond 0.00067 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8023 (ptp-110) REVERT: A 1246 ASP cc_start: 0.8064 (t0) cc_final: 0.7377 (t0) REVERT: A 1248 ARG cc_start: 0.8694 (mmp80) cc_final: 0.7383 (ptt90) REVERT: A 1267 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7738 (mt) REVERT: B 757 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8315 (p) REVERT: B 1000 MET cc_start: 0.4771 (tmm) cc_final: 0.4203 (ppp) REVERT: B 1364 GLU cc_start: 0.8750 (tt0) cc_final: 0.8295 (mm-30) REVERT: B 1405 MET cc_start: 0.1500 (tmm) cc_final: 0.0554 (ttm) outliers start: 54 outliers final: 40 residues processed: 151 average time/residue: 0.3535 time to fit residues: 81.3955 Evaluate side-chains 142 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1117 GLU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1384 ASP Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 134 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 221 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.077049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.058634 restraints weight = 297757.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.059996 restraints weight = 121991.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.061045 restraints weight = 73042.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.061611 restraints weight = 56199.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.061826 restraints weight = 49698.894| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21450 Z= 0.157 Angle : 0.645 7.372 29212 Z= 0.327 Chirality : 0.039 0.438 3266 Planarity : 0.005 0.054 3888 Dihedral : 7.270 73.422 3101 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.73 % Favored : 94.23 % Rotamer: Outliers : 2.44 % Allowed : 13.23 % Favored : 84.32 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2721 helix: 0.45 (0.16), residues: 1117 sheet: -2.25 (0.23), residues: 437 loop : -0.66 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 320 TYR 0.020 0.001 TYR A 290 PHE 0.020 0.002 PHE A 560 TRP 0.019 0.001 TRP B 535 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (21448) covalent geometry : angle 0.64541 / 0.33 (29212) hydrogen bonds : bond 0.04257 / 2.83 ( 994) hydrogen bonds : angle 5.94201 / 4.27 ( 2859) Misc. bond : bond 0.00034 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7962 (ptp-110) REVERT: A 399 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7918 (pt0) REVERT: A 1246 ASP cc_start: 0.8020 (t0) cc_final: 0.7357 (t0) REVERT: A 1248 ARG cc_start: 0.8674 (mmp80) cc_final: 0.7429 (ptt90) REVERT: A 1267 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7755 (mt) REVERT: A 1363 TRP cc_start: 0.6972 (m-10) cc_final: 0.6320 (m-10) REVERT: B 757 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8290 (p) REVERT: B 1000 MET cc_start: 0.4851 (tmm) cc_final: 0.4350 (ppp) REVERT: B 1020 ARG cc_start: 0.5946 (OUTLIER) cc_final: 0.5730 (ttp-110) REVERT: B 1364 GLU cc_start: 0.8746 (tt0) cc_final: 0.8293 (mm-30) REVERT: B 1405 MET cc_start: 0.1496 (tmm) cc_final: 0.0466 (ttm) outliers start: 51 outliers final: 37 residues processed: 156 average time/residue: 0.4033 time to fit residues: 94.7099 Evaluate side-chains 146 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1117 GLU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1020 ARG Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1384 ASP Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 227 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 181 optimal weight: 0.4980 chunk 15 optimal weight: 9.9990 chunk 194 optimal weight: 0.8980 chunk 265 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 229 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 HIS ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.076032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.057675 restraints weight = 295815.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.059084 restraints weight = 123955.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.060076 restraints weight = 73801.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.060660 restraints weight = 57311.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.060939 restraints weight = 50476.307| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21450 Z= 0.207 Angle : 0.653 7.551 29212 Z= 0.332 Chirality : 0.039 0.446 3266 Planarity : 0.005 0.055 3888 Dihedral : 7.128 72.202 3101 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.06 % Favored : 92.91 % Rotamer: Outliers : 2.49 % Allowed : 13.37 % Favored : 84.13 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.17), residues: 2721 helix: 0.54 (0.16), residues: 1127 sheet: -2.32 (0.22), residues: 450 loop : -0.68 (0.20), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.022 0.002 TYR B 693 PHE 0.021 0.002 PHE B 323 TRP 0.019 0.001 TRP B 535 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 (21448) covalent geometry : angle 0.65306 / 0.33 (29212) hydrogen bonds : bond 0.04289 / 2.84 ( 994) hydrogen bonds : angle 5.90387 / 4.24 ( 2859) Misc. bond : bond 0.00044 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 109 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7898 (pp20) REVERT: A 1246 ASP cc_start: 0.8018 (t0) cc_final: 0.7425 (t0) REVERT: A 1248 ARG cc_start: 0.8677 (mmp80) cc_final: 0.7531 (ptt90) REVERT: A 1267 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7761 (mt) REVERT: A 1363 TRP cc_start: 0.6997 (m-10) cc_final: 0.6391 (m-10) REVERT: B 158 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8198 (tpp) REVERT: B 1000 MET cc_start: 0.4785 (tmm) cc_final: 0.4240 (ppp) REVERT: B 1148 LEU cc_start: 0.7761 (tt) cc_final: 0.7501 (tp) REVERT: B 1364 GLU cc_start: 0.8763 (tt0) cc_final: 0.8282 (mm-30) outliers start: 52 outliers final: 40 residues processed: 154 average time/residue: 0.3611 time to fit residues: 84.4958 Evaluate side-chains 145 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1315 LEU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1384 ASP Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 65 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 239 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 226 optimal weight: 20.0000 chunk 241 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 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 = 0.3918 r_free = 0.3918 target = 0.074723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.056242 restraints weight = 299362.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.057510 restraints weight = 124750.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.058492 restraints weight = 74432.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.059083 restraints weight = 57387.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.059352 restraints weight = 50501.822| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 21450 Z= 0.302 Angle : 0.720 8.491 29212 Z= 0.372 Chirality : 0.041 0.447 3266 Planarity : 0.007 0.109 3888 Dihedral : 7.233 77.784 3101 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.83 % Favored : 92.14 % Rotamer: Outliers : 2.68 % Allowed : 13.66 % Favored : 83.65 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.16), residues: 2721 helix: 0.33 (0.15), residues: 1125 sheet: -2.43 (0.23), residues: 449 loop : -0.92 (0.19), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1020 TYR 0.023 0.002 TYR B 693 PHE 0.022 0.002 PHE B 560 TRP 0.018 0.002 TRP B 535 HIS 0.007 0.002 HIS B 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.30 (21448) covalent geometry : angle 0.72046 / 0.37 (29212) hydrogen bonds : bond 0.04716 / 3.12 ( 994) hydrogen bonds : angle 6.09788 / 4.39 ( 2859) Misc. bond : bond 0.00050 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 104 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7920 (pp20) REVERT: A 1246 ASP cc_start: 0.8040 (t0) cc_final: 0.7360 (t0) REVERT: A 1248 ARG cc_start: 0.8698 (mmp80) cc_final: 0.7508 (ptt90) REVERT: A 1267 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7752 (mt) REVERT: B 220 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8729 (tp) REVERT: B 371 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8209 (tt) REVERT: B 988 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8114 (mp) REVERT: B 1000 MET cc_start: 0.4771 (tmm) cc_final: 0.4269 (ppp) REVERT: B 1364 GLU cc_start: 0.8760 (tt0) cc_final: 0.8288 (mm-30) outliers start: 56 outliers final: 44 residues processed: 150 average time/residue: 0.3635 time to fit residues: 83.0923 Evaluate side-chains 149 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 100 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 983 SER Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1384 ASP Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 169 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 142 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 238 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 168 optimal weight: 0.2980 chunk 244 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 ASN ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 HIS A1099 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.077281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.058822 restraints weight = 293414.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.060308 restraints weight = 122684.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.061336 restraints weight = 72792.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.061947 restraints weight = 56222.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.062220 restraints weight = 49309.923| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21450 Z= 0.125 Angle : 0.631 7.770 29212 Z= 0.315 Chirality : 0.040 0.438 3266 Planarity : 0.005 0.055 3888 Dihedral : 6.748 66.161 3098 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.88 % Favored : 94.08 % Rotamer: Outliers : 1.87 % Allowed : 14.43 % Favored : 83.70 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2721 helix: 0.66 (0.16), residues: 1126 sheet: -2.33 (0.23), residues: 438 loop : -0.67 (0.20), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 320 TYR 0.022 0.002 TYR A 290 PHE 0.033 0.002 PHE A 216 TRP 0.021 0.001 TRP B 535 HIS 0.004 0.001 HIS B 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (21448) covalent geometry : angle 0.63149 / 0.32 (29212) hydrogen bonds : bond 0.03906 / 2.61 ( 994) hydrogen bonds : angle 5.75874 / 4.14 ( 2859) Misc. bond : bond 0.00017 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7993 (pp20) REVERT: A 876 VAL cc_start: 0.8784 (t) cc_final: 0.8575 (m) REVERT: A 1246 ASP cc_start: 0.8102 (t0) cc_final: 0.7534 (t0) REVERT: A 1248 ARG cc_start: 0.8625 (mmp80) cc_final: 0.7523 (ptt90) REVERT: A 1267 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7708 (mt) REVERT: A 1363 TRP cc_start: 0.6955 (m-10) cc_final: 0.6321 (m-10) REVERT: B 757 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8209 (p) REVERT: B 1000 MET cc_start: 0.4687 (tmm) cc_final: 0.4247 (ppp) REVERT: B 1364 GLU cc_start: 0.8771 (tt0) cc_final: 0.8285 (mm-30) REVERT: B 1405 MET cc_start: 0.1589 (tmm) cc_final: 0.0629 (ttm) outliers start: 39 outliers final: 34 residues processed: 148 average time/residue: 0.3773 time to fit residues: 84.9752 Evaluate side-chains 148 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1315 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1384 ASP Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 46 optimal weight: 0.8980 chunk 255 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.076980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.058356 restraints weight = 295098.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.059727 restraints weight = 124010.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.060816 restraints weight = 74313.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.061394 restraints weight = 57278.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.061602 restraints weight = 50596.281| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21450 Z= 0.143 Angle : 0.622 8.478 29212 Z= 0.312 Chirality : 0.039 0.438 3266 Planarity : 0.005 0.054 3888 Dihedral : 6.426 53.674 3092 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.79 % Rotamer: Outliers : 1.73 % Allowed : 14.62 % Favored : 83.65 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2721 helix: 0.77 (0.16), residues: 1133 sheet: -2.34 (0.23), residues: 446 loop : -0.59 (0.20), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 320 TYR 0.018 0.002 TYR A 290 PHE 0.018 0.002 PHE A 560 TRP 0.019 0.001 TRP B 535 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (21448) covalent geometry : angle 0.62230 / 0.31 (29212) hydrogen bonds : bond 0.03860 / 2.57 ( 994) hydrogen bonds : angle 5.71842 / 4.11 ( 2859) Misc. bond : bond 0.00025 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7949 (pp20) REVERT: A 1246 ASP cc_start: 0.8116 (t0) cc_final: 0.7578 (t0) REVERT: A 1248 ARG cc_start: 0.8632 (mmp80) cc_final: 0.7537 (ptt90) REVERT: A 1267 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7738 (mt) REVERT: A 1363 TRP cc_start: 0.7039 (m-10) cc_final: 0.6399 (m-10) REVERT: B 757 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8175 (p) REVERT: B 1000 MET cc_start: 0.4709 (tmm) cc_final: 0.4319 (ppp) REVERT: B 1364 GLU cc_start: 0.8762 (tt0) cc_final: 0.8289 (mm-30) REVERT: B 1405 MET cc_start: 0.1615 (tmm) cc_final: 0.0636 (ttm) outliers start: 36 outliers final: 32 residues processed: 143 average time/residue: 0.3817 time to fit residues: 81.5942 Evaluate side-chains 145 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1315 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1384 ASP Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 240 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 204 optimal weight: 0.0770 chunk 268 optimal weight: 30.0000 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 ASN ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.075692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.057267 restraints weight = 298728.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.058642 restraints weight = 124915.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.059648 restraints weight = 74629.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.060215 restraints weight = 57641.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.060389 restraints weight = 50867.973| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21450 Z= 0.241 Angle : 0.660 8.123 29212 Z= 0.336 Chirality : 0.040 0.442 3266 Planarity : 0.006 0.055 3888 Dihedral : 6.479 54.247 3092 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.72 % Favored : 92.25 % Rotamer: Outliers : 1.87 % Allowed : 14.38 % Favored : 83.75 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2721 helix: 0.68 (0.16), residues: 1137 sheet: -2.31 (0.23), residues: 452 loop : -0.75 (0.20), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 320 TYR 0.015 0.002 TYR A 290 PHE 0.016 0.002 PHE B 560 TRP 0.017 0.001 TRP B 535 HIS 0.005 0.001 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.24 (21448) covalent geometry : angle 0.66037 / 0.34 (29212) hydrogen bonds : bond 0.04203 / 2.78 ( 994) hydrogen bonds : angle 5.81761 / 4.19 ( 2859) Misc. bond : bond 0.00050 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6437.82 seconds wall clock time: 110 minutes 23.95 seconds (6623.95 seconds total)