Starting phenix.real_space_refine (version: dev) on Tue Dec 13 09:23:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bte_30177/12_2022/7bte_30177_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bte_30177/12_2022/7bte_30177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bte_30177/12_2022/7bte_30177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bte_30177/12_2022/7bte_30177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bte_30177/12_2022/7bte_30177_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bte_30177/12_2022/7bte_30177_updated.pdb" } resolution = 4.2 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 ------------------------------------------------------------------------------- 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= 0.010 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 24": "NH1" <-> "NH2" Residue "C ARG 396": "NH1" <-> "NH2" Residue "E ARG 768": "NH1" <-> "NH2" Residue "G ARG 1140": "NH1" <-> "NH2" Residue "G GLU 1169": "OE1" <-> "OE2" Residue "G TYR 1310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1446": "OE1" <-> "OE2" Residue "I ARG 1512": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 14814 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2865 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2873 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2876 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2867 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2870 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 111 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 110 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.85, per 1000 atoms: 0.87 Number of scatterers: 14814 At special positions: 0 Unit cell: (99.36, 81.42, 197.34, 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 108 16.00 P 10 15.00 Mg 5 11.99 O 2828 8.00 N 2512 7.00 C 9351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.98 Conformation dependent library (CDL) restraints added in 3.3 seconds 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3502 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 13 sheets defined 40.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 135 through 141 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 178 through 192 removed outlier: 4.320A pdb=" N THR A 190 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.871A pdb=" N ARG A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.780A pdb=" N TYR A 275 " --> pdb=" O HIS A 271 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 5.785A pdb=" N ALA A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 305 through 315 removed outlier: 5.201A pdb=" N GLN A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 344 removed outlier: 5.801A pdb=" N VAL A 335 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY A 338 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 342 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.880A pdb=" N GLN A 350 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.649A pdb=" N GLU A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'C' and resid 424 through 428 Processing helix chain 'C' and resid 447 through 462 removed outlier: 3.567A pdb=" N ASN C 460 " --> pdb=" O HIS C 456 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 468 No H-bonds generated for 'chain 'C' and resid 466 through 468' Processing helix chain 'C' and resid 481 through 493 removed outlier: 3.589A pdb=" N LYS C 486 " --> pdb=" O ALA C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 513 removed outlier: 3.559A pdb=" N SER C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 550 through 564 removed outlier: 3.723A pdb=" N MET C 558 " --> pdb=" O THR C 554 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR C 562 " --> pdb=" O MET C 558 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU C 563 " --> pdb=" O LYS C 559 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG C 564 " --> pdb=" O ILE C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 583 removed outlier: 3.532A pdb=" N GLU C 575 " --> pdb=" O THR C 571 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 576 " --> pdb=" O ALA C 572 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG C 578 " --> pdb=" O ARG C 574 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS C 583 " --> pdb=" O ASP C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 599 Processing helix chain 'C' and resid 625 through 630 removed outlier: 4.190A pdb=" N LEU C 629 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 635 Processing helix chain 'C' and resid 642 through 652 removed outlier: 4.996A pdb=" N TYR C 647 " --> pdb=" O HIS C 643 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 650 " --> pdb=" O THR C 646 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS C 652 " --> pdb=" O ASN C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 663 removed outlier: 4.416A pdb=" N LYS C 659 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASP C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ALA C 663 " --> pdb=" O LYS C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 672 No H-bonds generated for 'chain 'C' and resid 670 through 672' Processing helix chain 'C' and resid 677 through 688 removed outlier: 3.602A pdb=" N MET C 681 " --> pdb=" O ILE C 677 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN C 682 " --> pdb=" O ALA C 678 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR C 686 " --> pdb=" O GLN C 682 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 715 removed outlier: 5.620A pdb=" N VAL C 707 " --> pdb=" O LYS C 704 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY C 710 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 714 " --> pdb=" O GLY C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 731 Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'E' and resid 796 through 800 Processing helix chain 'E' and resid 819 through 834 removed outlier: 3.770A pdb=" N TYR E 831 " --> pdb=" O HIS E 827 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU E 833 " --> pdb=" O THR E 829 " (cutoff:3.500A) Processing helix chain 'E' and resid 838 through 840 No H-bonds generated for 'chain 'E' and resid 838 through 840' Processing helix chain 'E' and resid 853 through 865 removed outlier: 4.123A pdb=" N ILE E 862 " --> pdb=" O LYS E 858 " (cutoff:3.500A) Processing helix chain 'E' and resid 879 through 885 removed outlier: 3.560A pdb=" N ALA E 884 " --> pdb=" O LEU E 880 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER E 885 " --> pdb=" O SER E 881 " (cutoff:3.500A) Processing helix chain 'E' and resid 922 through 934 removed outlier: 3.569A pdb=" N THR E 934 " --> pdb=" O MET E 930 " (cutoff:3.500A) Processing helix chain 'E' and resid 943 through 956 removed outlier: 3.736A pdb=" N ILE E 948 " --> pdb=" O ALA E 944 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG E 950 " --> pdb=" O ARG E 946 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP E 951 " --> pdb=" O GLU E 947 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LYS E 955 " --> pdb=" O ASP E 951 " (cutoff:3.500A) Processing helix chain 'E' and resid 963 through 969 removed outlier: 3.668A pdb=" N ALA E 968 " --> pdb=" O GLU E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 998 through 1002 Processing helix chain 'E' and resid 1014 through 1024 removed outlier: 4.822A pdb=" N TYR E1019 " --> pdb=" O HIS E1015 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS E1024 " --> pdb=" O ASN E1020 " (cutoff:3.500A) Processing helix chain 'E' and resid 1030 through 1035 removed outlier: 4.333A pdb=" N ALA E1035 " --> pdb=" O LYS E1031 " (cutoff:3.500A) Processing helix chain 'E' and resid 1042 through 1044 No H-bonds generated for 'chain 'E' and resid 1042 through 1044' Processing helix chain 'E' and resid 1048 through 1060 removed outlier: 3.857A pdb=" N ARG E1052 " --> pdb=" O ILE E1049 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N MET E1053 " --> pdb=" O ALA E1050 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE E1057 " --> pdb=" O GLN E1054 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR E1058 " --> pdb=" O LYS E1055 " (cutoff:3.500A) Processing helix chain 'E' and resid 1075 through 1086 removed outlier: 5.670A pdb=" N VAL E1079 " --> pdb=" O LYS E1076 " (cutoff:3.500A) Processing helix chain 'E' and resid 1091 through 1094 removed outlier: 3.516A pdb=" N GLN E1094 " --> pdb=" O THR E1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1091 through 1094' Processing helix chain 'E' and resid 1099 through 1105 removed outlier: 3.682A pdb=" N GLU E1104 " --> pdb=" O GLN E1100 " (cutoff:3.500A) Processing helix chain 'E' and resid 1107 through 1113 removed outlier: 3.632A pdb=" N VAL E1110 " --> pdb=" O PRO E1107 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS E1111 " --> pdb=" O SER E1108 " (cutoff:3.500A) Processing helix chain 'G' and resid 1168 through 1172 Processing helix chain 'G' and resid 1191 through 1204 removed outlier: 3.618A pdb=" N TYR G1203 " --> pdb=" O HIS G1199 " (cutoff:3.500A) Processing helix chain 'G' and resid 1210 through 1212 No H-bonds generated for 'chain 'G' and resid 1210 through 1212' Processing helix chain 'G' and resid 1225 through 1237 removed outlier: 3.740A pdb=" N ILE G1234 " --> pdb=" O LYS G1230 " (cutoff:3.500A) Processing helix chain 'G' and resid 1251 through 1257 removed outlier: 3.540A pdb=" N SER G1257 " --> pdb=" O SER G1253 " (cutoff:3.500A) Processing helix chain 'G' and resid 1294 through 1307 removed outlier: 3.897A pdb=" N ASP G1299 " --> pdb=" O ARG G1295 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR G1306 " --> pdb=" O MET G1302 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU G1307 " --> pdb=" O LYS G1303 " (cutoff:3.500A) Processing helix chain 'G' and resid 1315 through 1328 removed outlier: 3.645A pdb=" N ILE G1320 " --> pdb=" O ALA G1316 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU G1326 " --> pdb=" O ARG G1322 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS G1327 " --> pdb=" O ASP G1323 " (cutoff:3.500A) Processing helix chain 'G' and resid 1335 through 1343 Processing helix chain 'G' and resid 1370 through 1374 Processing helix chain 'G' and resid 1376 through 1379 Processing helix chain 'G' and resid 1386 through 1396 removed outlier: 4.036A pdb=" N TYR G1391 " --> pdb=" O HIS G1387 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE G1394 " --> pdb=" O THR G1390 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS G1396 " --> pdb=" O ASN G1392 " (cutoff:3.500A) Processing helix chain 'G' and resid 1402 through 1407 removed outlier: 4.050A pdb=" N ALA G1407 " --> pdb=" O LYS G1403 " (cutoff:3.500A) Processing helix chain 'G' and resid 1414 through 1416 No H-bonds generated for 'chain 'G' and resid 1414 through 1416' Processing helix chain 'G' and resid 1419 through 1432 removed outlier: 4.038A pdb=" N ALA G1422 " --> pdb=" O PRO G1419 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP G1423 " --> pdb=" O GLY G1420 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG G1424 " --> pdb=" O ILE G1421 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N MET G1425 " --> pdb=" O ALA G1422 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU G1428 " --> pdb=" O MET G1425 " (cutoff:3.500A) Processing helix chain 'G' and resid 1447 through 1460 removed outlier: 5.842A pdb=" N VAL G1451 " --> pdb=" O LYS G1448 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY G1455 " --> pdb=" O TRP G1452 " (cutoff:3.500A) Processing helix chain 'G' and resid 1471 through 1477 Processing helix chain 'G' and resid 1479 through 1484 removed outlier: 3.538A pdb=" N VAL G1482 " --> pdb=" O PRO G1479 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS G1483 " --> pdb=" O SER G1480 " (cutoff:3.500A) Processing helix chain 'I' and resid 1539 through 1544 Processing helix chain 'I' and resid 1563 through 1576 removed outlier: 3.567A pdb=" N ILE I1569 " --> pdb=" O ASP I1565 " (cutoff:3.500A) Processing helix chain 'I' and resid 1582 through 1584 No H-bonds generated for 'chain 'I' and resid 1582 through 1584' Processing helix chain 'I' and resid 1597 through 1609 removed outlier: 3.681A pdb=" N GLU I1601 " --> pdb=" O LYS I1597 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS I1602 " --> pdb=" O ALA I1598 " (cutoff:3.500A) Processing helix chain 'I' and resid 1621 through 1629 Processing helix chain 'I' and resid 1656 through 1658 No H-bonds generated for 'chain 'I' and resid 1656 through 1658' Processing helix chain 'I' and resid 1666 through 1680 removed outlier: 3.944A pdb=" N THR I1678 " --> pdb=" O MET I1674 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU I1679 " --> pdb=" O LYS I1675 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG I1680 " --> pdb=" O ILE I1676 " (cutoff:3.500A) Processing helix chain 'I' and resid 1687 through 1700 removed outlier: 3.549A pdb=" N GLU I1691 " --> pdb=" O THR I1687 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE I1692 " --> pdb=" O ALA I1688 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS I1699 " --> pdb=" O ASP I1695 " (cutoff:3.500A) Processing helix chain 'I' and resid 1707 through 1715 Processing helix chain 'I' and resid 1740 through 1746 removed outlier: 3.900A pdb=" N THR I1744 " --> pdb=" O ARG I1740 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU I1745 " --> pdb=" O CYS I1741 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE I1746 " --> pdb=" O PRO I1742 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1740 through 1746' Processing helix chain 'I' and resid 1748 through 1750 No H-bonds generated for 'chain 'I' and resid 1748 through 1750' Processing helix chain 'I' and resid 1758 through 1768 removed outlier: 4.678A pdb=" N TYR I1763 " --> pdb=" O HIS I1759 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS I1768 " --> pdb=" O ASN I1764 " (cutoff:3.500A) Processing helix chain 'I' and resid 1774 through 1779 removed outlier: 4.012A pdb=" N ALA I1779 " --> pdb=" O LYS I1775 " (cutoff:3.500A) Processing helix chain 'I' and resid 1786 through 1789 Processing helix chain 'I' and resid 1792 through 1804 removed outlier: 3.746A pdb=" N ARG I1796 " --> pdb=" O ILE I1793 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET I1797 " --> pdb=" O ALA I1794 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS I1799 " --> pdb=" O ARG I1796 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE I1801 " --> pdb=" O GLN I1798 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR I1802 " --> pdb=" O LYS I1799 " (cutoff:3.500A) Processing helix chain 'I' and resid 1819 through 1832 removed outlier: 5.831A pdb=" N VAL I1823 " --> pdb=" O LYS I1820 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY I1826 " --> pdb=" O VAL I1823 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU I1830 " --> pdb=" O GLY I1827 " (cutoff:3.500A) Processing helix chain 'I' and resid 1835 through 1838 removed outlier: 3.711A pdb=" N GLN I1838 " --> pdb=" O THR I1835 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1835 through 1838' Processing helix chain 'I' and resid 1843 through 1849 Processing helix chain 'I' and resid 1851 through 1856 removed outlier: 3.502A pdb=" N VAL I1854 " --> pdb=" O PRO I1851 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS I1855 " --> pdb=" O SER I1852 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 4.791A pdb=" N LYS N 8 " --> pdb=" O ALA N 4 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS N 9 " --> pdb=" O ASP N 5 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE N 13 " --> pdb=" O LYS N 9 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.588A pdb=" N PHE A 27 " --> pdb=" O VAL A 13 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 101 Processing sheet with id= C, first strand: chain 'A' and resid 146 through 150 removed outlier: 4.016A pdb=" N VAL A 148 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 159 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A 150 " --> pdb=" O HIS A 157 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.637A pdb=" N PHE C 399 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 471 through 473 Processing sheet with id= F, first strand: chain 'C' and resid 529 through 533 removed outlier: 3.627A pdb=" N VAL C 531 " --> pdb=" O VAL C 520 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL C 520 " --> pdb=" O VAL C 531 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 666 " --> pdb=" O ILE C 519 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 769 through 772 removed outlier: 3.537A pdb=" N PHE E 771 " --> pdb=" O VAL E 757 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N CYS E 750 " --> pdb=" O PRO E 842 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU E 844 " --> pdb=" O CYS E 750 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 890 through 892 removed outlier: 3.820A pdb=" N VAL E 892 " --> pdb=" O VAL E 903 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL E 903 " --> pdb=" O VAL E 892 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 1215 through 1217 removed outlier: 6.526A pdb=" N LEU G1120 " --> pdb=" O LEU G1216 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS G1130 " --> pdb=" O ASP G1123 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 1616 through 1620 removed outlier: 6.988A pdb=" N THR I1587 " --> pdb=" O TYR I1617 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ALA I1619 " --> pdb=" O THR I1587 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU I1589 " --> pdb=" O ALA I1619 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU I1492 " --> pdb=" O LEU I1588 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR I1590 " --> pdb=" O LEU I1492 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N CYS I1494 " --> pdb=" O THR I1590 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS I1502 " --> pdb=" O ASP I1495 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE I1515 " --> pdb=" O VAL I1501 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'I' and resid 1518 through 1522 removed outlier: 3.533A pdb=" N VAL I1519 " --> pdb=" O LYS I1552 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 1634 through 1639 Processing sheet with id= M, first strand: chain 'I' and resid 1723 through 1725 385 hydrogen bonds defined for protein. 891 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: 5.28 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4833 1.34 - 1.46: 2984 1.46 - 1.57: 7106 1.57 - 1.69: 15 1.69 - 1.81: 191 Bond restraints: 15129 Sorted by residual: bond pdb=" CA GLN A 133 " pdb=" C GLN A 133 " ideal model delta sigma weight residual 1.522 1.475 0.047 1.72e-02 3.38e+03 7.44e+00 bond pdb=" CA GLN E 877 " pdb=" C GLN E 877 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.80e-02 3.09e+03 5.68e+00 bond pdb=" C LEU G1432 " pdb=" N ALA G1433 " ideal model delta sigma weight residual 1.327 1.261 0.066 2.86e-02 1.22e+03 5.36e+00 bond pdb=" C4 ADP G1502 " pdb=" C5 ADP G1502 " ideal model delta sigma weight residual 1.490 1.459 0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C MET A 301 " pdb=" N TYR A 302 " ideal model delta sigma weight residual 1.340 1.254 0.086 5.87e-02 2.90e+02 2.15e+00 ... (remaining 15124 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.60: 585 106.60 - 114.03: 8861 114.03 - 121.47: 7630 121.47 - 128.90: 3344 128.90 - 136.34: 101 Bond angle restraints: 20521 Sorted by residual: angle pdb=" C GLY C 410 " pdb=" N VAL C 411 " pdb=" CA VAL C 411 " ideal model delta sigma weight residual 122.96 119.76 3.20 9.50e-01 1.11e+00 1.14e+01 angle pdb=" C GLY I1642 " pdb=" N VAL I1643 " pdb=" CA VAL I1643 " ideal model delta sigma weight residual 121.97 127.20 -5.23 1.80e+00 3.09e-01 8.45e+00 angle pdb=" C GLY A 304 " pdb=" N ILE A 305 " pdb=" CA ILE A 305 " ideal model delta sigma weight residual 121.97 127.08 -5.11 1.80e+00 3.09e-01 8.04e+00 angle pdb=" C GLY C 676 " pdb=" N ILE C 677 " pdb=" CA ILE C 677 " ideal model delta sigma weight residual 121.97 127.02 -5.05 1.80e+00 3.09e-01 7.87e+00 angle pdb=" C ILE C 698 " pdb=" N ALA C 699 " pdb=" CA ALA C 699 " ideal model delta sigma weight residual 122.28 119.86 2.42 8.80e-01 1.29e+00 7.54e+00 ... (remaining 20516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.51: 8480 22.51 - 45.02: 508 45.02 - 67.53: 108 67.53 - 90.04: 12 90.04 - 112.55: 3 Dihedral angle restraints: 9111 sinusoidal: 3643 harmonic: 5468 Sorted by residual: dihedral pdb=" O1B ADP E1202 " pdb=" O3A ADP E1202 " pdb=" PB ADP E1202 " pdb=" PA ADP E1202 " ideal model delta sinusoidal sigma weight residual -60.00 -172.55 112.55 1 2.00e+01 2.50e-03 3.32e+01 dihedral pdb=" O1B ADP C 802 " pdb=" O3A ADP C 802 " pdb=" PB ADP C 802 " pdb=" PA ADP C 802 " ideal model delta sinusoidal sigma weight residual -60.00 -172.22 112.22 1 2.00e+01 2.50e-03 3.31e+01 dihedral pdb=" O1B ADP G1502 " pdb=" O3A ADP G1502 " pdb=" PB ADP G1502 " pdb=" PA ADP G1502 " ideal model delta sinusoidal sigma weight residual -60.00 -166.30 106.30 1 2.00e+01 2.50e-03 3.07e+01 ... (remaining 9108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1096 0.028 - 0.056: 720 0.056 - 0.085: 291 0.085 - 0.113: 143 0.113 - 0.141: 40 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA ILE I1841 " pdb=" N ILE I1841 " pdb=" C ILE I1841 " pdb=" CB ILE I1841 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" C3' ADP C 802 " pdb=" C2' ADP C 802 " pdb=" C4' ADP C 802 " pdb=" O3' ADP C 802 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" C3' ADP E1202 " pdb=" C2' ADP E1202 " pdb=" C4' ADP E1202 " pdb=" O3' ADP E1202 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 2287 not shown) Planarity restraints: 2617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 9 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C LYS L 9 " 0.044 2.00e-02 2.50e+03 pdb=" O LYS L 9 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE L 10 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 65 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A 66 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 328 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 329 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " 0.021 5.00e-02 4.00e+02 ... (remaining 2614 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 148 2.45 - 3.06: 11266 3.06 - 3.67: 21804 3.67 - 4.29: 31521 4.29 - 4.90: 50614 Nonbonded interactions: 115353 Sorted by model distance: nonbonded pdb="MG MG I1901 " pdb=" O3A ADP I1902 " model vdw 1.835 2.170 nonbonded pdb="MG MG A 401 " pdb=" O1A ADP A 402 " model vdw 1.869 2.170 nonbonded pdb="MG MG G1501 " pdb=" O3B ADP G1502 " model vdw 1.873 2.170 nonbonded pdb="MG MG A 401 " pdb=" O2B ADP A 402 " model vdw 1.940 2.170 nonbonded pdb="MG MG G1501 " pdb=" O3A ADP G1502 " model vdw 1.942 2.170 ... (remaining 115348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 149 or (resid 150 and (name N or name \ CA or name C or name O or name CB )) or resid 151 through 202 or (resid 203 and \ (name N or name CA or name C or name O or name CB )) or resid 204 through 208 or \ (resid 209 through 210 and (name N or name CA or name C or name O or name CB )) \ or resid 211 through 221 or (resid 222 and (name N or name CA or name C or name \ O or name CB )) or resid 223 through 341 or (resid 342 through 343 and (name N \ or name CA or name C or name O or name CB )) or resid 344 or (resid 345 and (nam \ e N or name CA or name C or name O or name CB )) or resid 346 through 370 or res \ id 401 through 402)) selection = (chain 'C' and (resid 373 through 378 or (resid 379 and (name N or name CA or na \ me C or name O or name CB )) or resid 380 through 381 or (resid 382 and (name N \ or name CA or name C or name O or name CB )) or resid 383 through 385 or (resid \ 386 through 387 and (name N or name CA or name C or name O or name CB )) or resi \ d 388 through 521 or (resid 522 and (name N or name CA or name C or name O or na \ me CB )) or resid 523 through 524 or (resid 525 and (name N or name CA or name C \ or name O or name CB )) or resid 526 through 581 or (resid 582 and (name N or n \ ame CA or name C or name O or name CB )) or resid 583 through 593 or (resid 594 \ and (name N or name CA or name C or name O or name CB )) or resid 595 through 67 \ 0 or (resid 671 through 672 and (name N or name CA or name C or name O or name C \ B )) or resid 673 through 713 or (resid 714 through 715 and (name N or name CA o \ r name C or name O or name CB )) or resid 716 or (resid 717 and (name N or name \ CA or name C or name O or name CB )) or resid 718 through 742 or resid 801 throu \ gh 802)) selection = (chain 'E' and (resid 745 through 750 or (resid 751 and (name N or name CA or na \ me C or name O or name CB )) or resid 752 through 753 or (resid 754 and (name N \ or name CA or name C or name O or name CB )) or resid 755 through 757 or (resid \ 758 through 759 and (name N or name CA or name C or name O or name CB )) or resi \ d 760 through 864 or (resid 865 and (name N or name CA or name C or name O or na \ me CB )) or resid 866 through 896 or (resid 897 and (name N or name CA or name C \ or name O or name CB )) or resid 898 through 946 or (resid 947 and (name N or n \ ame CA or name C or name O or name CB )) or resid 948 through 953 or (resid 954 \ and (name N or name CA or name C or name O or name CB )) or resid 955 through 96 \ 5 or (resid 966 and (name N or name CA or name C or name O or name CB )) or resi \ d 967 through 1042 or (resid 1043 through 1044 and (name N or name CA or name C \ or name O or name CB )) or resid 1045 through 1085 or (resid 1086 through 1087 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1088 or (resid \ 1089 and (name N or name CA or name C or name O or name CB )) or resid 1090 thro \ ugh 1114 or resid 1201 through 1202)) selection = (chain 'G' and (resid 1117 through 1125 or (resid 1126 and (name N or name CA or \ name C or name O or name CB )) or resid 1127 through 1129 or (resid 1130 throug \ h 1131 and (name N or name CA or name C or name O or name CB )) or resid 1132 th \ rough 1236 or (resid 1237 and (name N or name CA or name C or name O or name CB \ )) or resid 1238 through 1268 or (resid 1269 and (name N or name CA or name C or \ name O or name CB )) or resid 1270 through 1318 or (resid 1319 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1320 through 1325 or (resid 13 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 1327 throug \ h 1457 or (resid 1458 through 1459 and (name N or name CA or name C or name O or \ name CB )) or resid 1460 or (resid 1461 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1462 through 1486 or resid 1501 through 1502)) selection = (chain 'I' and (resid 1489 through 1497 or (resid 1498 and (name N or name CA or \ name C or name O or name CB )) or resid 1499 through 1608 or (resid 1609 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1610 through 1637 or \ (resid 1638 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 639 through 1640 or (resid 1641 and (name N or name CA or name C or name O or na \ me CB )) or resid 1642 through 1690 or (resid 1691 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1692 through 1696 or (resid 1697 through 16 \ 98 and (name N or name CA or name C or name O or name CB )) or resid 1699 throug \ h 1709 or (resid 1710 and (name N or name CA or name C or name O or name CB )) o \ r resid 1711 through 1786 or (resid 1787 through 1788 and (name N or name CA or \ name C or name O or name CB )) or resid 1789 through 1858 or resid 1901 through \ 1902)) } ncs_group { reference = (chain 'L' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'M' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'N' and resid 1 through 14) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 108 5.16 5 C 9351 2.51 5 N 2512 2.21 5 O 2828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.110 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 8.840 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.000 Process input model: 51.050 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 15129 Z= 0.405 Angle : 0.696 8.359 20521 Z= 0.358 Chirality : 0.046 0.141 2290 Planarity : 0.004 0.039 2617 Dihedral : 15.021 112.551 5609 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.67 % Favored : 87.33 % Rotamer Outliers : 13.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.33 (0.15), residues: 1878 helix: -3.77 (0.12), residues: 667 sheet: -3.10 (0.27), residues: 281 loop : -3.49 (0.18), residues: 930 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 115 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 216 outliers final: 119 residues processed: 313 average time/residue: 0.2679 time to fit residues: 127.8286 Evaluate side-chains 215 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 96 time to evaluate : 1.853 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 0 residues processed: 119 average time/residue: 0.1639 time to fit residues: 36.1571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 0.0050 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 349 GLN ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN C 643 HIS E 752 ASN ** E 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 ASN E1111 HIS G1200 HIS G1223 ASN G1249 GLN ** G1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1364 ASN G1408 ASN I1572 HIS I1576 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 15129 Z= 0.193 Angle : 0.641 7.473 20521 Z= 0.315 Chirality : 0.045 0.229 2290 Planarity : 0.004 0.039 2617 Dihedral : 6.765 101.953 2111 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.18), residues: 1878 helix: -2.14 (0.17), residues: 696 sheet: -2.56 (0.28), residues: 297 loop : -2.42 (0.21), residues: 885 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 138 average time/residue: 0.2633 time to fit residues: 56.4962 Evaluate side-chains 99 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.852 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1511 time to fit residues: 2.9081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 0.0770 chunk 169 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 84 HIS ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 752 ASN ** E 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1273 HIS I1621 GLN I1781 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 15129 Z= 0.344 Angle : 0.682 9.225 20521 Z= 0.330 Chirality : 0.046 0.189 2290 Planarity : 0.004 0.038 2617 Dihedral : 6.730 100.073 2111 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.19), residues: 1878 helix: -1.81 (0.17), residues: 717 sheet: -2.36 (0.30), residues: 284 loop : -2.09 (0.22), residues: 877 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 119 average time/residue: 0.2496 time to fit residues: 47.1583 Evaluate side-chains 98 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1778 time to fit residues: 3.4906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS C 427 GLN ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 752 ASN I1525 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 15129 Z= 0.246 Angle : 0.627 8.568 20521 Z= 0.300 Chirality : 0.045 0.249 2290 Planarity : 0.004 0.034 2617 Dihedral : 6.455 97.322 2111 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.19), residues: 1878 helix: -1.47 (0.18), residues: 694 sheet: -2.12 (0.31), residues: 285 loop : -1.80 (0.22), residues: 899 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.2676 time to fit residues: 51.5188 Evaluate side-chains 95 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.676 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1708 time to fit residues: 2.5225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1036 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.092 15129 Z= 0.510 Angle : 0.791 12.458 20521 Z= 0.382 Chirality : 0.050 0.236 2290 Planarity : 0.005 0.039 2617 Dihedral : 6.995 96.129 2111 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.19), residues: 1878 helix: -1.70 (0.18), residues: 714 sheet: -2.05 (0.32), residues: 269 loop : -1.94 (0.22), residues: 895 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.2617 time to fit residues: 44.6149 Evaluate side-chains 96 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.932 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1803 time to fit residues: 2.8756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 15129 Z= 0.260 Angle : 0.649 10.845 20521 Z= 0.310 Chirality : 0.046 0.301 2290 Planarity : 0.004 0.035 2617 Dihedral : 6.574 95.346 2111 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.19), residues: 1878 helix: -1.41 (0.18), residues: 714 sheet: -1.99 (0.31), residues: 290 loop : -1.65 (0.22), residues: 874 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2635 time to fit residues: 46.0851 Evaluate side-chains 97 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 181 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 15129 Z= 0.146 Angle : 0.593 8.333 20521 Z= 0.280 Chirality : 0.044 0.256 2290 Planarity : 0.003 0.037 2617 Dihedral : 6.011 91.565 2111 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.20), residues: 1878 helix: -1.12 (0.19), residues: 700 sheet: -1.91 (0.30), residues: 301 loop : -1.27 (0.23), residues: 877 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2594 time to fit residues: 47.8813 Evaluate side-chains 100 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.837 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 0.0170 chunk 142 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 overall best weight: 2.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 15129 Z= 0.286 Angle : 0.660 10.295 20521 Z= 0.312 Chirality : 0.045 0.222 2290 Planarity : 0.004 0.035 2617 Dihedral : 6.075 90.907 2111 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.20), residues: 1878 helix: -1.09 (0.19), residues: 706 sheet: -1.76 (0.31), residues: 296 loop : -1.29 (0.23), residues: 876 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2710 time to fit residues: 46.5837 Evaluate side-chains 99 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.141 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 159 optimal weight: 0.7980 chunk 110 optimal weight: 0.0670 chunk 178 optimal weight: 1.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 15129 Z= 0.202 Angle : 0.629 12.196 20521 Z= 0.294 Chirality : 0.044 0.207 2290 Planarity : 0.004 0.036 2617 Dihedral : 5.898 89.619 2111 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.20), residues: 1878 helix: -1.02 (0.19), residues: 711 sheet: -1.66 (0.30), residues: 305 loop : -1.15 (0.23), residues: 862 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2587 time to fit residues: 45.8282 Evaluate side-chains 98 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.926 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 187 optimal weight: 0.0970 chunk 172 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 overall best weight: 3.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 15129 Z= 0.374 Angle : 0.723 11.704 20521 Z= 0.341 Chirality : 0.047 0.207 2290 Planarity : 0.004 0.034 2617 Dihedral : 6.190 91.158 2111 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1878 helix: -1.09 (0.19), residues: 711 sheet: -1.70 (0.31), residues: 291 loop : -1.27 (0.23), residues: 876 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2508 time to fit residues: 43.0066 Evaluate side-chains 98 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.732 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN E 992 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.048847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.040334 restraints weight = 59031.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.041658 restraints weight = 32971.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.042591 restraints weight = 21452.714| |-----------------------------------------------------------------------------| r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 15129 Z= 0.167 Angle : 0.626 11.408 20521 Z= 0.291 Chirality : 0.044 0.382 2290 Planarity : 0.004 0.035 2617 Dihedral : 5.854 89.598 2111 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.20), residues: 1878 helix: -0.97 (0.19), residues: 713 sheet: -1.61 (0.30), residues: 312 loop : -1.12 (0.23), residues: 853 =============================================================================== Job complete usr+sys time: 2318.82 seconds wall clock time: 44 minutes 23.45 seconds (2663.45 seconds total)