Starting phenix.real_space_refine on Fri Sep 27 05:00:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bte_30177/09_2024/7bte_30177.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bte_30177/09_2024/7bte_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_30177/09_2024/7bte_30177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bte_30177/09_2024/7bte_30177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bte_30177/09_2024/7bte_30177.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bte_30177/09_2024/7bte_30177.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 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. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.81, per 1000 atoms: 0.59 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.7 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... Secondary structure from input PDB file: 95 helices and 24 sheets defined 47.0% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 51 through 57 Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.679A pdb=" N GLU A 96 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.655A pdb=" N ARG A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.850A pdb=" N ILE A 171 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 200 through 213 removed outlier: 4.091A pdb=" N ILE A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.645A pdb=" N SER A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 269 through 280 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 285 through 290 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.532A pdb=" N THR A 300 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 313 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) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.568A pdb=" N GLY A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.880A pdb=" N GLN A 350 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.649A pdb=" N GLU A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'C' and resid 423 through 429 removed outlier: 3.525A pdb=" N LYS C 429 " --> pdb=" O GLU C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 459 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 480 through 494 removed outlier: 3.761A pdb=" N ARG C 484 " --> pdb=" O PRO C 480 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 486 " --> pdb=" O ALA C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 514 removed outlier: 3.559A pdb=" N SER C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 removed outlier: 3.883A pdb=" N ILE C 543 " --> pdb=" O PRO C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 565 removed outlier: 3.567A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) 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) removed outlier: 3.811A pdb=" N GLY C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 584 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 590 through 600 removed outlier: 3.779A pdb=" N SER C 600 " --> pdb=" O ALA C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 636 removed outlier: 4.190A pdb=" N LEU C 629 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Proline residue: C 632 - end of helix removed outlier: 3.522A pdb=" N GLY C 636 " --> pdb=" O SER C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 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 654 through 662 removed outlier: 3.979A pdb=" N ARG C 658 " --> pdb=" O ASP C 654 " (cutoff:3.500A) 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) Processing helix chain 'C' and resid 669 through 673 removed outlier: 3.690A pdb=" N MET C 673 " --> pdb=" O GLY C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 687 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) Processing helix chain 'C' and resid 702 through 704 No H-bonds generated for 'chain 'C' and resid 702 through 704' Processing helix chain 'C' and resid 705 through 716 removed outlier: 3.586A pdb=" N GLY C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 715 " --> pdb=" O GLY C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 732 removed outlier: 3.744A pdb=" N GLU C 732 " --> pdb=" O GLN C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 741 Processing helix chain 'E' and resid 795 through 801 Processing helix chain 'E' and resid 818 through 831 removed outlier: 3.641A pdb=" N MET E 822 " --> pdb=" O ASN E 818 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR E 831 " --> pdb=" O HIS E 827 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 841 removed outlier: 3.642A pdb=" N GLU E 840 " --> pdb=" O ALA E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 852 through 866 removed outlier: 3.857A pdb=" N ARG E 856 " --> pdb=" O PRO E 852 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE E 862 " --> pdb=" O LYS E 858 " (cutoff:3.500A) Processing helix chain 'E' and resid 878 through 886 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 921 through 935 removed outlier: 3.569A pdb=" N THR E 934 " --> pdb=" O MET E 930 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU E 935 " --> pdb=" O LYS E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 957 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 962 through 970 removed outlier: 3.668A pdb=" N ALA E 968 " --> pdb=" O GLU E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 997 through 1003 Processing helix chain 'E' and resid 1013 through 1023 removed outlier: 4.822A pdb=" N TYR E1019 " --> pdb=" O HIS E1015 " (cutoff:3.500A) Processing helix chain 'E' and resid 1029 through 1034 Processing helix chain 'E' and resid 1041 through 1045 Processing helix chain 'E' and resid 1048 through 1058 removed outlier: 3.616A pdb=" N MET E1053 " --> pdb=" O ILE E1049 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN E1054 " --> pdb=" O ALA E1050 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR E1058 " --> pdb=" O GLN E1054 " (cutoff:3.500A) Processing helix chain 'E' and resid 1074 through 1076 No H-bonds generated for 'chain 'E' and resid 1074 through 1076' Processing helix chain 'E' and resid 1077 through 1087 Processing helix chain 'E' and resid 1090 through 1095 removed outlier: 3.516A pdb=" N GLN E1094 " --> pdb=" O THR E1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 1099 through 1106 removed outlier: 3.682A pdb=" N GLU E1104 " --> pdb=" O GLN E1100 " (cutoff:3.500A) Processing helix chain 'E' and resid 1109 through 1114 removed outlier: 3.785A pdb=" N LYS E1113 " --> pdb=" O ILE E1109 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS E1114 " --> pdb=" O VAL E1110 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1109 through 1114' Processing helix chain 'G' and resid 1167 through 1173 removed outlier: 3.546A pdb=" N LYS G1173 " --> pdb=" O GLU G1169 " (cutoff:3.500A) Processing helix chain 'G' and resid 1190 through 1205 removed outlier: 3.832A pdb=" N MET G1194 " --> pdb=" O ASN G1190 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR G1203 " --> pdb=" O HIS G1199 " (cutoff:3.500A) Processing helix chain 'G' and resid 1209 through 1213 Processing helix chain 'G' and resid 1224 through 1238 removed outlier: 3.780A pdb=" N ARG G1228 " --> pdb=" O PRO G1224 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE G1234 " --> pdb=" O LYS G1230 " (cutoff:3.500A) Processing helix chain 'G' and resid 1250 through 1258 removed outlier: 3.540A pdb=" N SER G1257 " --> pdb=" O SER G1253 " (cutoff:3.500A) Processing helix chain 'G' and resid 1293 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 1314 through 1329 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) removed outlier: 3.516A pdb=" N CYS G1329 " --> pdb=" O LYS G1325 " (cutoff:3.500A) Processing helix chain 'G' and resid 1334 through 1344 removed outlier: 3.663A pdb=" N SER G1344 " --> pdb=" O ALA G1340 " (cutoff:3.500A) Processing helix chain 'G' and resid 1369 through 1380 Proline residue: G1376 - end of helix Processing helix chain 'G' and resid 1385 through 1395 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) Processing helix chain 'G' and resid 1401 through 1406 Processing helix chain 'G' and resid 1413 through 1417 Processing helix chain 'G' and resid 1418 through 1419 No H-bonds generated for 'chain 'G' and resid 1418 through 1419' Processing helix chain 'G' and resid 1420 through 1433 removed outlier: 3.794A pdb=" N ARG G1424 " --> pdb=" O GLY G1420 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLN G1426 " --> pdb=" O ALA G1422 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G1432 " --> pdb=" O GLU G1428 " (cutoff:3.500A) Processing helix chain 'G' and resid 1446 through 1448 No H-bonds generated for 'chain 'G' and resid 1446 through 1448' Processing helix chain 'G' and resid 1449 through 1461 Processing helix chain 'G' and resid 1471 through 1478 Processing helix chain 'G' and resid 1479 through 1485 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 1545 removed outlier: 3.597A pdb=" N LYS I1545 " --> pdb=" O GLU I1541 " (cutoff:3.500A) Processing helix chain 'I' and resid 1562 through 1577 removed outlier: 3.973A pdb=" N MET I1566 " --> pdb=" O ASN I1562 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE I1569 " --> pdb=" O ASP I1565 " (cutoff:3.500A) Processing helix chain 'I' and resid 1581 through 1585 Processing helix chain 'I' and resid 1596 through 1610 removed outlier: 3.856A pdb=" N ARG I1600 " --> pdb=" O PRO I1596 " (cutoff:3.500A) 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 1630 Processing helix chain 'I' and resid 1655 through 1659 removed outlier: 3.933A pdb=" N ILE I1659 " --> pdb=" O PRO I1656 " (cutoff:3.500A) Processing helix chain 'I' and resid 1665 through 1681 removed outlier: 3.862A pdb=" N LEU I1669 " --> pdb=" O ALA I1665 " (cutoff:3.500A) 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) removed outlier: 3.578A pdb=" N GLY I1681 " --> pdb=" O LEU I1677 " (cutoff:3.500A) Processing helix chain 'I' and resid 1686 through 1701 removed outlier: 3.657A pdb=" N ARG I1690 " --> pdb=" O THR I1686 " (cutoff:3.500A) 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) removed outlier: 3.768A pdb=" N CYS I1701 " --> pdb=" O LYS I1697 " (cutoff:3.500A) Processing helix chain 'I' and resid 1706 through 1716 removed outlier: 3.828A pdb=" N GLU I1710 " --> pdb=" O ASP I1706 " (cutoff:3.500A) Processing helix chain 'I' and resid 1741 through 1751 Proline residue: I1748 - end of helix Processing helix chain 'I' and resid 1757 through 1767 removed outlier: 4.678A pdb=" N TYR I1763 " --> pdb=" O HIS I1759 " (cutoff:3.500A) Processing helix chain 'I' and resid 1773 through 1778 Processing helix chain 'I' and resid 1785 through 1791 removed outlier: 3.559A pdb=" N THR I1788 " --> pdb=" O GLY I1785 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR I1790 " --> pdb=" O THR I1787 " (cutoff:3.500A) Proline residue: I1791 - end of helix Processing helix chain 'I' and resid 1792 through 1804 removed outlier: 3.686A pdb=" N MET I1797 " --> pdb=" O ILE I1793 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN I1798 " --> pdb=" O ALA I1794 " (cutoff:3.500A) Processing helix chain 'I' and resid 1818 through 1820 No H-bonds generated for 'chain 'I' and resid 1818 through 1820' Processing helix chain 'I' and resid 1821 through 1833 removed outlier: 4.038A pdb=" N GLY I1827 " --> pdb=" O VAL I1823 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER I1828 " --> pdb=" O TRP I1824 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE I1829 " --> pdb=" O ILE I1825 " (cutoff:3.500A) Processing helix chain 'I' and resid 1834 through 1839 removed outlier: 3.711A pdb=" N GLN I1838 " --> pdb=" O THR I1835 " (cutoff:3.500A) Processing helix chain 'I' and resid 1842 through 1850 Processing helix chain 'I' and resid 1851 through 1857 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 2 through 14 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=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 3.588A pdb=" N PHE A 27 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 4 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA3, 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=AA4, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 294 removed outlier: 5.919A pdb=" N ASN A 293 " --> pdb=" O ILE A 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 397 through 400 removed outlier: 3.637A pdb=" N PHE C 399 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU C 376 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C 500 " --> pdb=" O ILE C 725 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 725 " --> pdb=" O MET C 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 439 through 440 Processing sheet with id=AA8, 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) removed outlier: 5.771A pdb=" N ASN C 665 " --> pdb=" O ILE C 698 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 608 through 609 Processing sheet with id=AB1, 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: 6.468A pdb=" N LEU E 748 " --> pdb=" O LEU E 844 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR E 846 " --> pdb=" O LEU E 748 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N CYS E 750 " --> pdb=" O THR E 846 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 811 through 812 Processing sheet with id=AB3, 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=AB4, first strand: chain 'E' and resid 980 through 981 Processing sheet with id=AB5, first strand: chain 'G' and resid 1141 through 1144 removed outlier: 3.957A pdb=" N LYS G1130 " --> pdb=" O ASP G1123 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU G1120 " --> pdb=" O LEU G1216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 1183 through 1184 removed outlier: 3.507A pdb=" N ILE G1187 " --> pdb=" O GLU G1184 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 1243 through 1244 removed outlier: 3.852A pdb=" N MET G1244 " --> pdb=" O ILE G1469 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE G1469 " --> pdb=" O MET G1244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 1262 through 1263 Processing sheet with id=AB9, first strand: chain 'G' and resid 1352 through 1353 Processing sheet with id=AC1, first strand: chain 'G' and resid 1409 through 1410 removed outlier: 5.608A pdb=" N ASN G1409 " --> pdb=" O ILE G1442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'I' and resid 1513 through 1516 removed outlier: 3.722A pdb=" N PHE I1515 " --> pdb=" O VAL I1501 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS I1502 " --> pdb=" O ASP I1495 " (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) Processing sheet with id=AC3, first strand: chain 'I' and resid 1537 through 1538 removed outlier: 3.533A pdb=" N VAL I1519 " --> pdb=" O LYS I1552 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 1555 through 1556 removed outlier: 3.517A pdb=" N ILE I1559 " --> pdb=" O GLU I1556 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 1634 through 1639 Processing sheet with id=AC6, first strand: chain 'I' and resid 1723 through 1725 499 hydrogen bonds defined for protein. 1251 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: 5.33 Time building geometry restraints manager: 3.87 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: 0.00 - 1.67: 19895 1.67 - 3.34: 504 3.34 - 5.02: 86 5.02 - 6.69: 29 6.69 - 8.36: 7 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: 11212 3.06 - 3.67: 21734 3.67 - 4.29: 31289 4.29 - 4.90: 50514 Nonbonded interactions: 114897 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 114892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.390 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 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= 0.403 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 : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.67 % Favored : 87.33 % Rotamer: Outliers : 13.76 % Allowed : 12.48 % Favored : 73.76 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 454 HIS 0.004 0.001 HIS C 529 PHE 0.017 0.001 PHE L 10 TYR 0.010 0.001 TYR I1763 ARG 0.004 0.001 ARG E 996 *********************** 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 : 1.712 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: A 6 CYS cc_start: 0.8321 (p) cc_final: 0.8096 (p) REVERT: A 33 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8163 (mtp85) REVERT: A 120 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8948 (m-10) REVERT: A 180 ASP cc_start: 0.8991 (m-30) cc_final: 0.8786 (t70) REVERT: A 223 MET cc_start: 0.9228 (mmm) cc_final: 0.8991 (tpp) REVERT: A 263 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8797 (pt) REVERT: A 289 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9331 (mt) REVERT: C 415 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8395 (tpt) REVERT: C 487 MET cc_start: 0.9341 (ttm) cc_final: 0.9131 (ttm) REVERT: C 535 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: C 544 MET cc_start: 0.8624 (mmm) cc_final: 0.8057 (mmt) REVERT: C 561 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9433 (tp) REVERT: C 595 MET cc_start: 0.9255 (mmm) cc_final: 0.8855 (mmm) REVERT: C 684 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: E 839 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8665 (pm20) REVERT: E 920 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9337 (tt) REVERT: E 1045 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8539 (tpp) REVERT: G 1179 LEU cc_start: 0.9412 (mt) cc_final: 0.9176 (mp) REVERT: G 1211 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8542 (pm20) REVERT: G 1438 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8329 (ttpp) REVERT: I 1498 SER cc_start: 0.9404 (OUTLIER) cc_final: 0.9197 (p) REVERT: I 1583 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: I 1661 ARG cc_start: 0.9428 (OUTLIER) cc_final: 0.8798 (ttt90) REVERT: I 1664 LEU cc_start: 0.9298 (tp) cc_final: 0.9045 (tt) REVERT: I 1668 ASP cc_start: 0.8983 (m-30) cc_final: 0.8689 (t0) REVERT: I 1725 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8674 (pp20) REVERT: I 1796 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.8122 (tmt90) REVERT: I 1804 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9404 (pp) REVERT: M 10 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7675 (m-80) REVERT: N 9 LYS cc_start: 0.9409 (tppp) cc_final: 0.9101 (tptp) outliers start: 216 outliers final: 119 residues processed: 313 average time/residue: 0.2490 time to fit residues: 118.4932 Evaluate side-chains 240 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 101 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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: 6.9990 chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 0.0370 chunk 147 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 HIS E 902 ASN G1200 HIS G1223 ASN G1249 GLN ** G1273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1274 ASN G1408 ASN I1572 HIS I1576 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15129 Z= 0.206 Angle : 0.673 6.365 20521 Z= 0.338 Chirality : 0.047 0.234 2290 Planarity : 0.005 0.038 2617 Dihedral : 6.889 105.438 2111 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.13 % Allowed : 2.68 % Favored : 97.20 % 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: -3.21 (0.18), residues: 1878 helix: -1.71 (0.18), residues: 682 sheet: -2.55 (0.28), residues: 301 loop : -2.22 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 75 HIS 0.006 0.001 HIS A 83 PHE 0.012 0.001 PHE A 27 TYR 0.019 0.001 TYR E 883 ARG 0.006 0.001 ARG G1447 *********************** 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 141 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 MET cc_start: 0.8845 (tpp) cc_final: 0.8560 (tpp) REVERT: C 463 ARG cc_start: 0.8430 (mpp-170) cc_final: 0.8037 (mtm-85) REVERT: C 487 MET cc_start: 0.9327 (ttm) cc_final: 0.9114 (ttm) REVERT: C 544 MET cc_start: 0.8701 (mmm) cc_final: 0.8101 (mmt) REVERT: C 548 LEU cc_start: 0.9446 (tp) cc_final: 0.9065 (tt) REVERT: C 681 MET cc_start: 0.8989 (mmt) cc_final: 0.8665 (mmt) REVERT: C 717 LEU cc_start: 0.9326 (tp) cc_final: 0.8947 (tt) REVERT: E 1023 MET cc_start: 0.9170 (mmm) cc_final: 0.8803 (mmm) REVERT: G 1235 MET cc_start: 0.9147 (tpt) cc_final: 0.8732 (tpp) REVERT: G 1339 MET cc_start: 0.8762 (tmm) cc_final: 0.7720 (tmm) REVERT: I 1607 MET cc_start: 0.8925 (mmm) cc_final: 0.8644 (mmm) REVERT: I 1664 LEU cc_start: 0.9249 (tp) cc_final: 0.8815 (tt) REVERT: I 1668 ASP cc_start: 0.8958 (m-30) cc_final: 0.8579 (t0) REVERT: I 1711 MET cc_start: 0.8988 (mmm) cc_final: 0.8627 (tpp) REVERT: L 1 MET cc_start: 0.6054 (mtp) cc_final: 0.5514 (mtm) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.2459 time to fit residues: 54.0660 Evaluate side-chains 109 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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: 1.9990 chunk 52 optimal weight: 0.9980 chunk 142 optimal weight: 0.1980 chunk 116 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 171 optimal weight: 0.5980 chunk 184 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 752 ASN ** E 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1273 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15129 Z= 0.207 Angle : 0.621 6.511 20521 Z= 0.302 Chirality : 0.045 0.178 2290 Planarity : 0.004 0.036 2617 Dihedral : 6.485 105.992 2111 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.24 % 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: -2.46 (0.19), residues: 1878 helix: -1.05 (0.19), residues: 690 sheet: -2.35 (0.29), residues: 299 loop : -1.75 (0.22), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 75 HIS 0.005 0.001 HIS A 83 PHE 0.013 0.001 PHE M 10 TYR 0.019 0.001 TYR A 194 ARG 0.003 0.000 ARG E 917 *********************** 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 126 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.9132 (mmm) cc_final: 0.8914 (tpp) REVERT: A 301 MET cc_start: 0.8808 (tpp) cc_final: 0.8545 (tpp) REVERT: C 463 ARG cc_start: 0.8397 (mpp-170) cc_final: 0.8037 (mtm-85) REVERT: C 487 MET cc_start: 0.9458 (ttm) cc_final: 0.9117 (ttm) REVERT: C 544 MET cc_start: 0.8620 (mmm) cc_final: 0.7918 (mmt) REVERT: E 967 MET cc_start: 0.9263 (tpp) cc_final: 0.8690 (tpp) REVERT: E 1023 MET cc_start: 0.9227 (mmm) cc_final: 0.8934 (mmm) REVERT: G 1235 MET cc_start: 0.9095 (tpt) cc_final: 0.8521 (tpp) REVERT: G 1244 MET cc_start: 0.8648 (ppp) cc_final: 0.8358 (ppp) REVERT: G 1339 MET cc_start: 0.8932 (tmm) cc_final: 0.7842 (tmm) REVERT: G 1417 MET cc_start: 0.8832 (tpp) cc_final: 0.8316 (tpp) REVERT: I 1664 LEU cc_start: 0.9228 (tp) cc_final: 0.8778 (tt) REVERT: I 1668 ASP cc_start: 0.8967 (m-30) cc_final: 0.8584 (t0) REVERT: L 1 MET cc_start: 0.6126 (mtp) cc_final: 0.5670 (mtm) outliers start: 1 outliers final: 1 residues processed: 126 average time/residue: 0.2384 time to fit residues: 47.5276 Evaluate side-chains 104 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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: 10.0000 chunk 88 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 181 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS C 380 ASN C 479 ASN C 620 ASN C 665 ASN E 752 ASN ** E 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1036 ASN ** E1111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1525 GLN I1621 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 15129 Z= 0.490 Angle : 0.788 12.586 20521 Z= 0.388 Chirality : 0.051 0.261 2290 Planarity : 0.005 0.043 2617 Dihedral : 6.907 102.488 2111 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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: -1.14 (0.19), residues: 696 sheet: -2.16 (0.30), residues: 296 loop : -1.84 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 454 HIS 0.007 0.001 HIS I1855 PHE 0.020 0.002 PHE M 10 TYR 0.032 0.002 TYR C 566 ARG 0.003 0.001 ARG C 484 *********************** 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 109 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.9208 (mmm) cc_final: 0.8954 (tpp) REVERT: C 450 MET cc_start: 0.9085 (tpp) cc_final: 0.8503 (tmm) REVERT: C 463 ARG cc_start: 0.8594 (mpp-170) cc_final: 0.8066 (mtm-85) REVERT: C 544 MET cc_start: 0.8693 (mmm) cc_final: 0.8041 (mmt) REVERT: C 595 MET cc_start: 0.9255 (tpp) cc_final: 0.8637 (tpp) REVERT: E 967 MET cc_start: 0.9263 (tpp) cc_final: 0.8812 (tpp) REVERT: E 1023 MET cc_start: 0.9322 (mmm) cc_final: 0.8943 (mmm) REVERT: G 1417 MET cc_start: 0.8821 (tpp) cc_final: 0.8315 (tpp) REVERT: I 1566 MET cc_start: 0.8986 (ttp) cc_final: 0.8750 (tmm) REVERT: I 1668 ASP cc_start: 0.9013 (m-30) cc_final: 0.8691 (t0) REVERT: N 1 MET cc_start: 0.8775 (mmm) cc_final: 0.8533 (mmm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2464 time to fit residues: 42.5957 Evaluate side-chains 96 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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: 6.9990 chunk 103 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 135 optimal weight: 0.0070 chunk 74 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 799 GLN E1015 HIS ** I1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15129 Z= 0.178 Angle : 0.620 8.268 20521 Z= 0.299 Chirality : 0.045 0.186 2290 Planarity : 0.004 0.045 2617 Dihedral : 6.345 104.461 2111 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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: -2.00 (0.20), residues: 1878 helix: -0.74 (0.20), residues: 711 sheet: -1.98 (0.30), residues: 303 loop : -1.45 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 454 HIS 0.007 0.001 HIS G1387 PHE 0.009 0.001 PHE G1236 TYR 0.022 0.001 TYR C 566 ARG 0.004 0.000 ARG G1402 *********************** 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 121 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.9233 (mmm) cc_final: 0.8802 (mmm) REVERT: A 301 MET cc_start: 0.8678 (mmt) cc_final: 0.8303 (mmm) REVERT: C 487 MET cc_start: 0.9345 (ttm) cc_final: 0.8933 (ttm) REVERT: C 595 MET cc_start: 0.9270 (tpp) cc_final: 0.8668 (tpp) REVERT: E 967 MET cc_start: 0.9227 (tpp) cc_final: 0.8798 (tpp) REVERT: E 1023 MET cc_start: 0.9199 (mmm) cc_final: 0.8873 (mmm) REVERT: E 1053 MET cc_start: 0.9213 (tpt) cc_final: 0.8893 (tpp) REVERT: G 1199 HIS cc_start: 0.8537 (t-90) cc_final: 0.8318 (t70) REVERT: G 1235 MET cc_start: 0.9104 (tpt) cc_final: 0.8682 (tpp) REVERT: G 1244 MET cc_start: 0.8835 (ppp) cc_final: 0.8445 (ppp) REVERT: G 1339 MET cc_start: 0.8811 (tmm) cc_final: 0.7792 (tmm) REVERT: I 1571 HIS cc_start: 0.8802 (t-90) cc_final: 0.8241 (t-90) REVERT: I 1664 LEU cc_start: 0.9176 (tt) cc_final: 0.8590 (tt) REVERT: I 1668 ASP cc_start: 0.8905 (m-30) cc_final: 0.8668 (t70) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2733 time to fit residues: 50.5123 Evaluate side-chains 100 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.691 ------------------------------------------------------------------------------- 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: 7.9990 chunk 163 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 84 optimal weight: 0.2980 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 380 ASN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN E 851 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 15129 Z= 0.429 Angle : 0.751 11.395 20521 Z= 0.365 Chirality : 0.050 0.294 2290 Planarity : 0.004 0.042 2617 Dihedral : 6.594 102.793 2111 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: -2.00 (0.20), residues: 1878 helix: -0.77 (0.20), residues: 697 sheet: -1.95 (0.31), residues: 298 loop : -1.45 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 826 HIS 0.008 0.001 HIS I1855 PHE 0.012 0.002 PHE C 623 TYR 0.027 0.002 TYR C 566 ARG 0.004 0.000 ARG A 286 *********************** 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 112 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 MET cc_start: 0.8727 (mmt) cc_final: 0.8372 (mmm) REVERT: C 463 ARG cc_start: 0.8462 (mpp-170) cc_final: 0.7962 (mtm-85) REVERT: C 487 MET cc_start: 0.9367 (ttm) cc_final: 0.9094 (ttm) REVERT: C 595 MET cc_start: 0.9239 (tpp) cc_final: 0.8782 (tpt) REVERT: E 967 MET cc_start: 0.9243 (tpp) cc_final: 0.8858 (tpp) REVERT: E 1023 MET cc_start: 0.9221 (mmm) cc_final: 0.8833 (mmm) REVERT: G 1199 HIS cc_start: 0.8599 (t-90) cc_final: 0.8372 (t70) REVERT: G 1235 MET cc_start: 0.9140 (tpt) cc_final: 0.8555 (tpp) REVERT: G 1339 MET cc_start: 0.8858 (tmm) cc_final: 0.7750 (tmm) REVERT: G 1417 MET cc_start: 0.8500 (tpp) cc_final: 0.7879 (tpp) REVERT: I 1566 MET cc_start: 0.8884 (tmm) cc_final: 0.8684 (tmm) REVERT: I 1668 ASP cc_start: 0.8973 (m-30) cc_final: 0.8689 (t70) REVERT: I 1711 MET cc_start: 0.8965 (tpp) cc_final: 0.8330 (tpp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2599 time to fit residues: 45.4424 Evaluate side-chains 96 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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: 0.8980 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** I1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15129 Z= 0.153 Angle : 0.621 9.927 20521 Z= 0.296 Chirality : 0.044 0.245 2290 Planarity : 0.004 0.044 2617 Dihedral : 6.111 103.646 2111 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -1.63 (0.20), residues: 1878 helix: -0.50 (0.20), residues: 712 sheet: -1.86 (0.29), residues: 323 loop : -1.12 (0.24), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I1570 HIS 0.006 0.001 HIS G1387 PHE 0.010 0.001 PHE M 10 TYR 0.019 0.001 TYR C 566 ARG 0.003 0.000 ARG C 564 *********************** 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 114 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 487 MET cc_start: 0.9355 (ttm) cc_final: 0.9140 (ttm) REVERT: C 681 MET cc_start: 0.8855 (mmt) cc_final: 0.8632 (mmm) REVERT: E 967 MET cc_start: 0.9249 (tpp) cc_final: 0.8869 (tpp) REVERT: E 1023 MET cc_start: 0.9155 (mmm) cc_final: 0.8783 (mmm) REVERT: E 1053 MET cc_start: 0.9133 (tpt) cc_final: 0.8710 (mmm) REVERT: G 1199 HIS cc_start: 0.8432 (t-90) cc_final: 0.8161 (t70) REVERT: G 1235 MET cc_start: 0.9105 (tpt) cc_final: 0.8587 (tpp) REVERT: I 1566 MET cc_start: 0.8774 (tmm) cc_final: 0.8569 (tmm) REVERT: I 1668 ASP cc_start: 0.8907 (m-30) cc_final: 0.8661 (t70) REVERT: I 1711 MET cc_start: 0.8857 (tpp) cc_final: 0.8176 (tpp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2481 time to fit residues: 44.3094 Evaluate side-chains 100 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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: 10.0000 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 164 optimal weight: 0.4980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15129 Z= 0.241 Angle : 0.647 8.366 20521 Z= 0.309 Chirality : 0.046 0.220 2290 Planarity : 0.004 0.044 2617 Dihedral : 6.033 101.924 2111 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -1.53 (0.21), residues: 1878 helix: -0.44 (0.20), residues: 704 sheet: -1.76 (0.30), residues: 317 loop : -1.07 (0.23), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 826 HIS 0.006 0.001 HIS G1387 PHE 0.010 0.001 PHE A 251 TYR 0.018 0.001 TYR C 566 ARG 0.003 0.000 ARG A 286 *********************** 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 109 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 463 ARG cc_start: 0.8358 (mpp-170) cc_final: 0.8012 (mtm-85) REVERT: C 487 MET cc_start: 0.9361 (ttm) cc_final: 0.9077 (ttm) REVERT: C 681 MET cc_start: 0.8913 (mmt) cc_final: 0.8676 (tpt) REVERT: E 967 MET cc_start: 0.9240 (tpp) cc_final: 0.8847 (tpp) REVERT: E 1023 MET cc_start: 0.9207 (mmm) cc_final: 0.8851 (mmm) REVERT: E 1053 MET cc_start: 0.9179 (tpt) cc_final: 0.8751 (mmm) REVERT: G 1199 HIS cc_start: 0.8444 (t-90) cc_final: 0.8244 (t70) REVERT: G 1339 MET cc_start: 0.8844 (tmm) cc_final: 0.7800 (tmm) REVERT: I 1668 ASP cc_start: 0.8962 (m-30) cc_final: 0.8639 (t70) REVERT: I 1711 MET cc_start: 0.8833 (tpp) cc_final: 0.8123 (tpp) REVERT: M 1 MET cc_start: 0.8946 (pmm) cc_final: 0.8692 (pmm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2430 time to fit residues: 42.0531 Evaluate side-chains 98 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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: 0.4980 chunk 158 optimal weight: 0.1980 chunk 168 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 152 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8805 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15129 Z= 0.151 Angle : 0.611 8.525 20521 Z= 0.290 Chirality : 0.044 0.200 2290 Planarity : 0.004 0.045 2617 Dihedral : 5.838 100.561 2111 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.21), residues: 1878 helix: -0.29 (0.20), residues: 704 sheet: -1.71 (0.29), residues: 326 loop : -0.92 (0.24), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I1570 HIS 0.006 0.001 HIS G1387 PHE 0.008 0.001 PHE A 219 TYR 0.015 0.001 TYR C 566 ARG 0.002 0.000 ARG I1661 *********************** 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 108 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 463 ARG cc_start: 0.8341 (mpp-170) cc_final: 0.7973 (mtm-85) REVERT: C 487 MET cc_start: 0.9377 (ttm) cc_final: 0.9138 (ttm) REVERT: C 595 MET cc_start: 0.9310 (tpp) cc_final: 0.8632 (tpp) REVERT: C 693 MET cc_start: 0.5527 (mmt) cc_final: 0.5322 (mmt) REVERT: C 702 GLU cc_start: 0.8517 (pm20) cc_final: 0.8207 (pm20) REVERT: E 967 MET cc_start: 0.9194 (tpp) cc_final: 0.8825 (tpp) REVERT: E 1023 MET cc_start: 0.9095 (mmm) cc_final: 0.8803 (mmm) REVERT: E 1053 MET cc_start: 0.9199 (tpt) cc_final: 0.8802 (tpp) REVERT: G 1199 HIS cc_start: 0.8355 (t-90) cc_final: 0.8109 (t70) REVERT: G 1235 MET cc_start: 0.9136 (tpt) cc_final: 0.8597 (tpp) REVERT: I 1566 MET cc_start: 0.8801 (tmm) cc_final: 0.8567 (tmm) REVERT: I 1668 ASP cc_start: 0.8926 (m-30) cc_final: 0.8621 (t70) REVERT: I 1711 MET cc_start: 0.8818 (tpp) cc_final: 0.8176 (tpp) REVERT: M 1 MET cc_start: 0.8860 (pmm) cc_final: 0.8642 (pmm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2513 time to fit residues: 43.1948 Evaluate side-chains 99 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.652 ------------------------------------------------------------------------------- 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: 0.7980 chunk 84 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 187 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 158 optimal weight: 0.0670 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8810 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15129 Z= 0.170 Angle : 0.615 8.840 20521 Z= 0.292 Chirality : 0.045 0.396 2290 Planarity : 0.004 0.046 2617 Dihedral : 5.708 98.112 2111 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.28 (0.21), residues: 1878 helix: -0.23 (0.20), residues: 704 sheet: -1.64 (0.29), residues: 327 loop : -0.90 (0.24), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I1570 HIS 0.006 0.001 HIS G1387 PHE 0.008 0.001 PHE A 251 TYR 0.014 0.001 TYR C 566 ARG 0.003 0.000 ARG A 252 ********************** 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 110 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLN cc_start: 0.8539 (tt0) cc_final: 0.8209 (tm-30) REVERT: C 463 ARG cc_start: 0.8364 (mpp-170) cc_final: 0.7983 (mtm-85) REVERT: C 487 MET cc_start: 0.9376 (ttm) cc_final: 0.9129 (ttm) REVERT: C 595 MET cc_start: 0.9325 (tpp) cc_final: 0.8623 (tpp) REVERT: C 651 MET cc_start: 0.9166 (mmm) cc_final: 0.8705 (tpp) REVERT: C 702 GLU cc_start: 0.8540 (pm20) cc_final: 0.8218 (pm20) REVERT: E 967 MET cc_start: 0.9166 (tpp) cc_final: 0.8819 (tpp) REVERT: E 1023 MET cc_start: 0.9153 (mmm) cc_final: 0.8788 (mmm) REVERT: G 1235 MET cc_start: 0.9099 (tpt) cc_final: 0.8556 (tpp) REVERT: I 1566 MET cc_start: 0.8805 (tmm) cc_final: 0.8569 (tmm) REVERT: I 1668 ASP cc_start: 0.8949 (m-30) cc_final: 0.8632 (t70) REVERT: I 1711 MET cc_start: 0.8823 (tpp) cc_final: 0.8194 (tpp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2641 time to fit residues: 46.3529 Evaluate side-chains 99 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.858 ------------------------------------------------------------------------------- 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: 2.9990 chunk 137 optimal weight: 0.0000 chunk 22 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 153 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN I1759 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.050684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.041875 restraints weight = 58690.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.043300 restraints weight = 32023.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.044290 restraints weight = 20584.642| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15129 Z= 0.129 Angle : 0.598 9.216 20521 Z= 0.281 Chirality : 0.044 0.354 2290 Planarity : 0.004 0.046 2617 Dihedral : 5.491 94.413 2111 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.18 (0.21), residues: 1878 helix: -0.14 (0.20), residues: 703 sheet: -1.52 (0.29), residues: 327 loop : -0.89 (0.24), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I1570 HIS 0.007 0.001 HIS G1387 PHE 0.008 0.001 PHE I1836 TYR 0.011 0.001 TYR C 566 ARG 0.002 0.000 ARG I1661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2373.27 seconds wall clock time: 43 minutes 44.08 seconds (2624.08 seconds total)