Starting phenix.real_space_refine on Mon Apr 8 07:20:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzn_36748/04_2024/8jzn_36748_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzn_36748/04_2024/8jzn_36748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzn_36748/04_2024/8jzn_36748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzn_36748/04_2024/8jzn_36748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzn_36748/04_2024/8jzn_36748_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzn_36748/04_2024/8jzn_36748_updated.pdb" } resolution = 2.47 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= -0.001 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 72 5.16 5 C 8520 2.51 5 N 2042 2.21 5 O 2195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 146": "OE1" <-> "OE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 553": "OD1" <-> "OD2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 617": "OD1" <-> "OD2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 691": "OD1" <-> "OD2" Residue "A PHE 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 739": "OD1" <-> "OD2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "A GLU 832": "OE1" <-> "OE2" Residue "A ASP 837": "OD1" <-> "OD2" Residue "A GLU 859": "OE1" <-> "OE2" Residue "A ASP 890": "OD1" <-> "OD2" Residue "A TYR 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 971": "OE1" <-> "OE2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A GLU 989": "OE1" <-> "OE2" Residue "A GLU 991": "OE1" <-> "OE2" Residue "A PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1016": "OE1" <-> "OE2" Residue "A ASP 1034": "OD1" <-> "OD2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A ASP 1053": "OD1" <-> "OD2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A ASP 1060": "OD1" <-> "OD2" Residue "A GLU 1096": "OE1" <-> "OE2" Residue "A GLU 1121": "OE1" <-> "OE2" Residue "A GLU 1123": "OE1" <-> "OE2" Residue "A TYR 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "A ASP 1222": "OD1" <-> "OD2" Residue "A GLU 1240": "OE1" <-> "OE2" Residue "A ARG 1248": "NH1" <-> "NH2" Residue "A TYR 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1353": "OD1" <-> "OD2" Residue "A PHE 1366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1497": "OE1" <-> "OE2" Residue "A ASP 1505": "OD1" <-> "OD2" Residue "A ASP 1592": "OD1" <-> "OD2" Residue "A PHE 1618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1665": "OE1" <-> "OE2" Residue "A PHE 1667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1778": "NH1" <-> "NH2" Residue "A ARG 1791": "NH1" <-> "NH2" Residue "A TYR 1800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1841": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12831 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1489, 12155 Classifications: {'peptide': 1489} Link IDs: {'PTRANS': 66, 'TRANS': 1422} Chain breaks: 13 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 648 Unusual residues: {'AV0': 2, 'ERG': 14, 'POV': 2} Classifications: {'undetermined': 18} Link IDs: {None: 17} Time building chain proxies: 7.73, per 1000 atoms: 0.60 Number of scatterers: 12831 At special positions: 0 Unit cell: (100.244, 117.127, 135.066, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 2 15.00 O 2195 8.00 N 2042 7.00 C 8520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1345 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A1849 " Time building additional restraints: 5.13 Conformation dependent library (CDL) restraints added in 2.4 seconds 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 5 sheets defined 59.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 149 through 152 No H-bonds generated for 'chain 'A' and resid 149 through 152' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 179 through 196 Processing helix chain 'A' and resid 202 through 213 Processing helix chain 'A' and resid 220 through 228 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.687A pdb=" N GLU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.923A pdb=" N VAL A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 398 removed outlier: 3.964A pdb=" N LEU A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TRP A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 444 through 451 removed outlier: 3.533A pdb=" N THR A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 removed outlier: 3.663A pdb=" N MET A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 489 through 517 removed outlier: 3.726A pdb=" N LEU A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 517 " --> pdb=" O CYS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 551 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 560 through 582 removed outlier: 4.736A pdb=" N VAL A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 615 through 638 removed outlier: 3.545A pdb=" N TRP A 619 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET A 620 " --> pdb=" O ASP A 617 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 624 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 626 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 628 " --> pdb=" O TRP A 625 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 630 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 631 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 632 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR A 633 " --> pdb=" O ALA A 630 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 634 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER A 636 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 638 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 651 removed outlier: 4.714A pdb=" N ASP A 646 " --> pdb=" O SER A 643 " (cutoff:3.500A) Proline residue: A 647 - end of helix removed outlier: 3.518A pdb=" N ILE A 650 " --> pdb=" O PRO A 647 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 651 " --> pdb=" O ILE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 672 through 710 removed outlier: 3.608A pdb=" N ILE A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 689 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.543A pdb=" N TYR A 731 " --> pdb=" O PRO A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 763 removed outlier: 3.916A pdb=" N ALA A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 773 Processing helix chain 'A' and resid 794 through 798 removed outlier: 4.388A pdb=" N SER A 798 " --> pdb=" O PHE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 827 removed outlier: 3.833A pdb=" N SER A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 838 No H-bonds generated for 'chain 'A' and resid 836 through 838' Processing helix chain 'A' and resid 857 through 861 Processing helix chain 'A' and resid 872 through 879 removed outlier: 3.556A pdb=" N GLN A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 898 Processing helix chain 'A' and resid 933 through 946 removed outlier: 3.596A pdb=" N THR A 939 " --> pdb=" O TYR A 935 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 946 " --> pdb=" O TRP A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 970 removed outlier: 4.227A pdb=" N ASN A 959 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER A 961 " --> pdb=" O PHE A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.556A pdb=" N PHE A 979 " --> pdb=" O ILE A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 997 removed outlier: 3.520A pdb=" N GLU A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1012 through 1024 Processing helix chain 'A' and resid 1082 through 1088 Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1109 through 1122 removed outlier: 4.360A pdb=" N LYS A1114 " --> pdb=" O GLU A1110 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A1115 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ARG A1116 " --> pdb=" O CYS A1112 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER A1117 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A1120 " --> pdb=" O ARG A1116 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU A1121 " --> pdb=" O SER A1117 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE A1122 " --> pdb=" O VAL A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1172 through 1186 removed outlier: 3.993A pdb=" N THR A1178 " --> pdb=" O GLN A1174 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A1179 " --> pdb=" O THR A1175 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARG A1182 " --> pdb=" O THR A1178 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1207 removed outlier: 3.547A pdb=" N THR A1206 " --> pdb=" O THR A1202 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A1207 " --> pdb=" O PHE A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1231 No H-bonds generated for 'chain 'A' and resid 1228 through 1231' Processing helix chain 'A' and resid 1268 through 1271 Processing helix chain 'A' and resid 1273 through 1279 Processing helix chain 'A' and resid 1284 through 1293 removed outlier: 3.531A pdb=" N THR A1289 " --> pdb=" O ASP A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1323 removed outlier: 3.599A pdb=" N ASN A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1380 removed outlier: 3.527A pdb=" N TRP A1354 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A1355 " --> pdb=" O ALA A1351 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A1356 " --> pdb=" O VAL A1352 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA A1369 " --> pdb=" O VAL A1365 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE A1370 " --> pdb=" O PHE A1366 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A1371 " --> pdb=" O TRP A1367 " (cutoff:3.500A) Proline residue: A1372 - end of helix Processing helix chain 'A' and resid 1385 through 1396 Processing helix chain 'A' and resid 1438 through 1444 removed outlier: 4.119A pdb=" N SER A1443 " --> pdb=" O SER A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1466 Processing helix chain 'A' and resid 1470 through 1484 removed outlier: 3.809A pdb=" N SER A1478 " --> pdb=" O PHE A1475 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER A1481 " --> pdb=" O SER A1478 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A1484 " --> pdb=" O SER A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1511 removed outlier: 3.610A pdb=" N PHE A1500 " --> pdb=" O TRP A1496 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A1501 " --> pdb=" O GLU A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1564 No H-bonds generated for 'chain 'A' and resid 1561 through 1564' Processing helix chain 'A' and resid 1566 through 1582 Processing helix chain 'A' and resid 1598 through 1622 removed outlier: 3.761A pdb=" N ILE A1602 " --> pdb=" O SER A1598 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A1608 " --> pdb=" O ILE A1604 " (cutoff:3.500A) Proline residue: A1609 - end of helix removed outlier: 3.698A pdb=" N LEU A1617 " --> pdb=" O ASN A1613 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A1619 " --> pdb=" O GLY A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1641 through 1664 removed outlier: 3.645A pdb=" N ILE A1645 " --> pdb=" O VAL A1641 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA A1646 " --> pdb=" O MET A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1693 removed outlier: 3.652A pdb=" N ILE A1674 " --> pdb=" O VAL A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1758 removed outlier: 3.739A pdb=" N GLU A1729 " --> pdb=" O GLN A1725 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A1730 " --> pdb=" O PRO A1726 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A1733 " --> pdb=" O GLU A1729 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A1736 " --> pdb=" O ALA A1732 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A1738 " --> pdb=" O VAL A1734 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A1754 " --> pdb=" O ILE A1750 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A1755 " --> pdb=" O LEU A1751 " (cutoff:3.500A) Proline residue: A1756 - end of helix Processing helix chain 'A' and resid 1764 through 1773 removed outlier: 4.276A pdb=" N MET A1770 " --> pdb=" O PHE A1766 " (cutoff:3.500A) Processing helix chain 'A' and resid 1787 through 1799 removed outlier: 3.949A pdb=" N ARG A1791 " --> pdb=" O LEU A1787 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A1792 " --> pdb=" O LYS A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1822 removed outlier: 3.755A pdb=" N LEU A1806 " --> pdb=" O SER A1802 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A1815 " --> pdb=" O PHE A1811 " (cutoff:3.500A) Proline residue: A1818 - end of helix removed outlier: 3.841A pdb=" N SER A1822 " --> pdb=" O PRO A1818 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 370 through 373 removed outlier: 3.728A pdb=" N ARG A 376 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 778 through 781 Processing sheet with id= C, first strand: chain 'A' and resid 1198 through 1200 removed outlier: 6.410A pdb=" N GLN A1029 " --> pdb=" O VAL A1002 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N MET A1004 " --> pdb=" O GLN A1029 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ALA A1031 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A1068 " --> pdb=" O LEU A1051 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1154 through 1158 Processing sheet with id= E, first strand: chain 'A' and resid 1148 through 1153 removed outlier: 7.024A pdb=" N ARG A1235 " --> pdb=" O ALA A1149 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL A1151 " --> pdb=" O ARG A1235 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LYS A1237 " --> pdb=" O VAL A1151 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ALA A1153 " --> pdb=" O LYS A1237 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYS A1239 " --> pdb=" O ALA A1153 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 536 hydrogen bonds defined for protein. 1542 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: 4.37 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1892 1.31 - 1.43: 3698 1.43 - 1.56: 7258 1.56 - 1.68: 229 1.68 - 1.81: 126 Bond restraints: 13203 Sorted by residual: bond pdb=" C5 ERG A1912 " pdb=" C6 ERG A1912 " ideal model delta sigma weight residual 1.338 1.617 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C5 ERG A1908 " pdb=" C6 ERG A1908 " ideal model delta sigma weight residual 1.338 1.612 -0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C5 ERG A1913 " pdb=" C6 ERG A1913 " ideal model delta sigma weight residual 1.338 1.612 -0.274 2.00e-02 2.50e+03 1.87e+02 bond pdb=" C5 ERG A1915 " pdb=" C6 ERG A1915 " ideal model delta sigma weight residual 1.338 1.611 -0.273 2.00e-02 2.50e+03 1.86e+02 bond pdb=" C5 ERG A1906 " pdb=" C6 ERG A1906 " ideal model delta sigma weight residual 1.338 1.611 -0.273 2.00e-02 2.50e+03 1.86e+02 ... (remaining 13198 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.53: 308 105.53 - 112.70: 7102 112.70 - 119.87: 4520 119.87 - 127.05: 5870 127.05 - 134.22: 178 Bond angle restraints: 17978 Sorted by residual: angle pdb=" N VAL A 705 " pdb=" CA VAL A 705 " pdb=" C VAL A 705 " ideal model delta sigma weight residual 111.90 107.98 3.92 8.10e-01 1.52e+00 2.34e+01 angle pdb=" C14 ERG A1917 " pdb=" C8 ERG A1917 " pdb=" C9 ERG A1917 " ideal model delta sigma weight residual 116.25 102.93 13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C14 ERG A1904 " pdb=" C8 ERG A1904 " pdb=" C9 ERG A1904 " ideal model delta sigma weight residual 116.25 103.29 12.96 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C14 ERG A1909 " pdb=" C8 ERG A1909 " pdb=" C9 ERG A1909 " ideal model delta sigma weight residual 116.25 103.98 12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" N MET A 458 " pdb=" CA MET A 458 " pdb=" C MET A 458 " ideal model delta sigma weight residual 111.14 115.49 -4.35 1.08e+00 8.57e-01 1.62e+01 ... (remaining 17973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 8138 34.37 - 68.74: 434 68.74 - 103.11: 64 103.11 - 137.48: 26 137.48 - 171.85: 3 Dihedral angle restraints: 8665 sinusoidal: 4292 harmonic: 4373 Sorted by residual: dihedral pdb=" CA HIS A1826 " pdb=" C HIS A1826 " pdb=" N LYS A1827 " pdb=" CA LYS A1827 " ideal model delta harmonic sigma weight residual -180.00 -151.86 -28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ALA A 525 " pdb=" C ALA A 525 " pdb=" N GLN A 526 " pdb=" CA GLN A 526 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LEU A1340 " pdb=" C LEU A1340 " pdb=" N VAL A1341 " pdb=" CA VAL A1341 " ideal model delta harmonic sigma weight residual 180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 8662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1924 0.125 - 0.250: 59 0.250 - 0.375: 16 0.375 - 0.500: 6 0.500 - 0.625: 19 Chirality restraints: 2024 Sorted by residual: chirality pdb=" C13 ERG A1905 " pdb=" C12 ERG A1905 " pdb=" C14 ERG A1905 " pdb=" C17 ERG A1905 " both_signs ideal model delta sigma weight residual False -2.93 -2.30 -0.63 2.00e-01 2.50e+01 9.77e+00 chirality pdb=" C13 ERG A1911 " pdb=" C12 ERG A1911 " pdb=" C14 ERG A1911 " pdb=" C17 ERG A1911 " both_signs ideal model delta sigma weight residual False -2.93 -2.30 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" C13 ERG A1916 " pdb=" C12 ERG A1916 " pdb=" C14 ERG A1916 " pdb=" C17 ERG A1916 " both_signs ideal model delta sigma weight residual False -2.93 -2.31 -0.62 2.00e-01 2.50e+01 9.58e+00 ... (remaining 2021 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1036 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO A1037 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A1037 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1037 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1775 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A1776 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A1776 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1776 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 544 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 545 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 545 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 545 " -0.031 5.00e-02 4.00e+02 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 38 2.41 - 3.03: 7363 3.03 - 3.65: 18886 3.65 - 4.28: 30949 4.28 - 4.90: 49503 Nonbonded interactions: 106739 Sorted by model distance: nonbonded pdb=" OAI AV0 A1902 " pdb=" OAS AV0 A1902 " model vdw 1.784 2.440 nonbonded pdb=" OG1 THR A1040 " pdb=" OE1 GLU A1043 " model vdw 2.199 2.440 nonbonded pdb=" O4 AV0 A1902 " pdb=" OAQ AV0 A1902 " model vdw 2.203 2.440 nonbonded pdb=" OE2 GLU A 984 " pdb=" NH1 ARG A 988 " model vdw 2.207 2.520 nonbonded pdb=" OE1 GLU A 661 " pdb=" OG SER A1598 " model vdw 2.216 2.440 ... (remaining 106734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 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: 10.030 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 37.910 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 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 : 0.019 0.279 13203 Z= 1.141 Angle : 1.121 13.317 17978 Z= 0.472 Chirality : 0.084 0.625 2024 Planarity : 0.005 0.067 2147 Dihedral : 21.229 171.849 5831 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.91 % Allowed : 16.42 % Favored : 81.67 % 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: -2.06 (0.20), residues: 1461 helix: -1.58 (0.15), residues: 863 sheet: -0.39 (0.57), residues: 76 loop : -0.77 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 493 HIS 0.010 0.001 HIS A1195 PHE 0.027 0.002 PHE A1657 TYR 0.017 0.002 TYR A1804 ARG 0.021 0.001 ARG A 791 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 1.361 Fit side-chains REVERT: A 601 VAL cc_start: 0.8113 (t) cc_final: 0.7873 (m) REVERT: A 745 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7718 (mptt) REVERT: A 763 ARG cc_start: 0.7699 (mmt180) cc_final: 0.7022 (mtm-85) REVERT: A 791 ARG cc_start: 0.7728 (ptp-110) cc_final: 0.6985 (ptm-80) REVERT: A 1202 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8544 (m) REVERT: A 1770 MET cc_start: 0.6790 (mpt) cc_final: 0.5661 (mmp) outliers start: 25 outliers final: 17 residues processed: 167 average time/residue: 1.4266 time to fit residues: 259.8207 Evaluate side-chains 164 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1154 ARG Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1752 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.7980 chunk 112 optimal weight: 0.0570 chunk 62 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS A 721 ASN A1228 ASN ** A1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13203 Z= 0.183 Angle : 0.635 9.882 17978 Z= 0.304 Chirality : 0.042 0.190 2024 Planarity : 0.005 0.054 2147 Dihedral : 16.073 167.784 2984 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.90 % Allowed : 15.58 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1461 helix: -0.16 (0.17), residues: 876 sheet: 0.37 (0.63), residues: 66 loop : -0.58 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 664 HIS 0.011 0.001 HIS A1195 PHE 0.014 0.001 PHE A1581 TYR 0.013 0.001 TYR A 308 ARG 0.006 0.000 ARG A 791 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 162 time to evaluate : 1.598 Fit side-chains REVERT: A 386 LYS cc_start: 0.8571 (mmmt) cc_final: 0.7986 (mmtt) REVERT: A 533 TRP cc_start: 0.7208 (t60) cc_final: 0.5891 (m100) REVERT: A 741 GLU cc_start: 0.5644 (OUTLIER) cc_final: 0.5393 (pt0) REVERT: A 745 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7575 (mptt) REVERT: A 763 ARG cc_start: 0.7708 (mmt180) cc_final: 0.7037 (mtm-85) REVERT: A 791 ARG cc_start: 0.7453 (ptp-110) cc_final: 0.6594 (ptm-80) REVERT: A 809 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7305 (p90) REVERT: A 1202 THR cc_start: 0.8937 (t) cc_final: 0.8713 (m) REVERT: A 1269 GLN cc_start: 0.7616 (mt0) cc_final: 0.6496 (mm-40) REVERT: A 1642 MET cc_start: 0.6184 (tmm) cc_final: 0.5983 (pmm) REVERT: A 1694 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5553 (mpt) REVERT: A 1739 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7294 (tp30) outliers start: 38 outliers final: 11 residues processed: 185 average time/residue: 1.2802 time to fit residues: 260.1801 Evaluate side-chains 160 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 119 optimal weight: 0.0670 chunk 133 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 30.0000 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A 721 ASN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 ASN A1688 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13203 Z= 0.237 Angle : 0.614 10.708 17978 Z= 0.295 Chirality : 0.042 0.162 2024 Planarity : 0.004 0.051 2147 Dihedral : 14.047 173.555 2966 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.36 % Allowed : 17.11 % Favored : 79.53 % 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: -0.04 (0.22), residues: 1461 helix: 0.31 (0.17), residues: 885 sheet: 0.46 (0.64), residues: 66 loop : -0.49 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 664 HIS 0.008 0.001 HIS A1195 PHE 0.013 0.001 PHE A1581 TYR 0.016 0.001 TYR A 308 ARG 0.008 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 155 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7323 (mt) REVERT: A 386 LYS cc_start: 0.8566 (mmmt) cc_final: 0.7948 (mmtt) REVERT: A 443 ARG cc_start: 0.7576 (mtm180) cc_final: 0.6334 (mtm110) REVERT: A 533 TRP cc_start: 0.7233 (t60) cc_final: 0.5880 (m100) REVERT: A 620 MET cc_start: 0.7853 (mmm) cc_final: 0.7640 (tpp) REVERT: A 640 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8279 (mp) REVERT: A 745 LYS cc_start: 0.7810 (ttmt) cc_final: 0.7535 (mptt) REVERT: A 763 ARG cc_start: 0.7721 (mmt180) cc_final: 0.7056 (mtm-85) REVERT: A 791 ARG cc_start: 0.7424 (ptp-110) cc_final: 0.6626 (ptm-80) REVERT: A 862 ARG cc_start: 0.5470 (OUTLIER) cc_final: 0.4492 (tpm170) REVERT: A 1057 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 1202 THR cc_start: 0.8956 (t) cc_final: 0.8674 (m) REVERT: A 1268 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7134 (tt0) REVERT: A 1269 GLN cc_start: 0.7558 (mt0) cc_final: 0.6505 (mm-40) outliers start: 44 outliers final: 19 residues processed: 179 average time/residue: 1.3503 time to fit residues: 263.6221 Evaluate side-chains 174 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 977 GLN Chi-restraints excluded: chain A residue 1061 ASN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 ASN A1688 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13203 Z= 0.248 Angle : 0.598 10.698 17978 Z= 0.291 Chirality : 0.041 0.169 2024 Planarity : 0.004 0.050 2147 Dihedral : 12.782 166.783 2966 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.97 % Allowed : 16.88 % Favored : 79.14 % 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: 0.14 (0.22), residues: 1461 helix: 0.50 (0.17), residues: 890 sheet: 0.48 (0.64), residues: 66 loop : -0.53 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 664 HIS 0.009 0.001 HIS A1195 PHE 0.013 0.002 PHE A1581 TYR 0.016 0.001 TYR A 308 ARG 0.007 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 157 time to evaluate : 1.419 Fit side-chains REVERT: A 230 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7309 (mt) REVERT: A 386 LYS cc_start: 0.8571 (mmmt) cc_final: 0.7974 (mmtt) REVERT: A 533 TRP cc_start: 0.7222 (t60) cc_final: 0.5903 (m100) REVERT: A 620 MET cc_start: 0.7806 (mmm) cc_final: 0.7577 (tpp) REVERT: A 640 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8271 (mp) REVERT: A 725 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6270 (mtm180) REVERT: A 745 LYS cc_start: 0.7768 (ttmt) cc_final: 0.7482 (mptt) REVERT: A 763 ARG cc_start: 0.7709 (mmt180) cc_final: 0.7053 (mtm-85) REVERT: A 791 ARG cc_start: 0.7341 (ptp-110) cc_final: 0.6559 (ptm-80) REVERT: A 1057 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7190 (tm-30) REVERT: A 1202 THR cc_start: 0.8897 (t) cc_final: 0.8601 (m) REVERT: A 1269 GLN cc_start: 0.7565 (mt0) cc_final: 0.6511 (mm-40) REVERT: A 1737 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7570 (mp) REVERT: A 1836 VAL cc_start: 0.7865 (m) cc_final: 0.7592 (p) outliers start: 52 outliers final: 22 residues processed: 189 average time/residue: 1.2926 time to fit residues: 267.5457 Evaluate side-chains 175 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1737 LEU Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 0.0470 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 98 optimal weight: 0.0010 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13203 Z= 0.236 Angle : 0.573 10.334 17978 Z= 0.281 Chirality : 0.041 0.162 2024 Planarity : 0.004 0.048 2147 Dihedral : 12.238 151.135 2966 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.28 % Allowed : 16.88 % Favored : 78.84 % 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: 0.30 (0.22), residues: 1461 helix: 0.67 (0.17), residues: 887 sheet: 0.49 (0.63), residues: 66 loop : -0.52 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 664 HIS 0.007 0.001 HIS A1195 PHE 0.013 0.002 PHE A 887 TYR 0.016 0.001 TYR A 308 ARG 0.009 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 152 time to evaluate : 1.387 Fit side-chains REVERT: A 230 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7281 (mt) REVERT: A 386 LYS cc_start: 0.8571 (mmmt) cc_final: 0.7974 (mmtt) REVERT: A 443 ARG cc_start: 0.7574 (mtm180) cc_final: 0.6335 (mtm110) REVERT: A 533 TRP cc_start: 0.7226 (t60) cc_final: 0.5901 (m100) REVERT: A 620 MET cc_start: 0.7800 (mmm) cc_final: 0.7565 (tpp) REVERT: A 640 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8257 (mp) REVERT: A 725 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.6268 (mtm180) REVERT: A 745 LYS cc_start: 0.7745 (ttmt) cc_final: 0.7466 (mptt) REVERT: A 763 ARG cc_start: 0.7703 (mmt180) cc_final: 0.7049 (mtm-85) REVERT: A 791 ARG cc_start: 0.7336 (ptp-110) cc_final: 0.6569 (ptm-80) REVERT: A 809 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7205 (p90) REVERT: A 862 ARG cc_start: 0.5584 (OUTLIER) cc_final: 0.4235 (tpm170) REVERT: A 1202 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8637 (m) REVERT: A 1269 GLN cc_start: 0.7591 (mt0) cc_final: 0.6538 (mm-40) REVERT: A 1836 VAL cc_start: 0.7831 (m) cc_final: 0.7566 (p) outliers start: 56 outliers final: 29 residues processed: 187 average time/residue: 1.2788 time to fit residues: 262.9261 Evaluate side-chains 184 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 ASN A1269 GLN A1688 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13203 Z= 0.172 Angle : 0.541 9.613 17978 Z= 0.267 Chirality : 0.040 0.152 2024 Planarity : 0.004 0.048 2147 Dihedral : 11.761 145.214 2966 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.51 % Allowed : 17.80 % Favored : 78.69 % 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: 0.53 (0.22), residues: 1461 helix: 0.91 (0.18), residues: 883 sheet: 0.43 (0.63), residues: 66 loop : -0.50 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 664 HIS 0.009 0.001 HIS A1195 PHE 0.014 0.001 PHE A 887 TYR 0.014 0.001 TYR A 308 ARG 0.009 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 1.433 Fit side-chains REVERT: A 386 LYS cc_start: 0.8574 (mmmt) cc_final: 0.7983 (mmtt) REVERT: A 443 ARG cc_start: 0.7552 (mtm180) cc_final: 0.6326 (mtm110) REVERT: A 533 TRP cc_start: 0.7241 (t60) cc_final: 0.5866 (m100) REVERT: A 620 MET cc_start: 0.7785 (mmm) cc_final: 0.7539 (tpp) REVERT: A 725 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6267 (mtm180) REVERT: A 745 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7437 (mptt) REVERT: A 763 ARG cc_start: 0.7693 (mmt180) cc_final: 0.7039 (mtm-85) REVERT: A 791 ARG cc_start: 0.7366 (ptp-110) cc_final: 0.6577 (ptm-80) REVERT: A 1202 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8662 (m) REVERT: A 1269 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6436 (mm-40) REVERT: A 1836 VAL cc_start: 0.7805 (m) cc_final: 0.7560 (p) outliers start: 46 outliers final: 26 residues processed: 178 average time/residue: 1.2595 time to fit residues: 245.6631 Evaluate side-chains 180 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1694 MET Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 120 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A 824 GLN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 ASN A1269 GLN A1688 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13203 Z= 0.165 Angle : 0.533 9.039 17978 Z= 0.262 Chirality : 0.039 0.151 2024 Planarity : 0.004 0.048 2147 Dihedral : 11.517 141.124 2966 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.13 % Allowed : 18.33 % Favored : 78.53 % 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: 0.65 (0.22), residues: 1461 helix: 1.03 (0.18), residues: 879 sheet: 0.05 (0.62), residues: 71 loop : -0.44 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 664 HIS 0.008 0.001 HIS A1195 PHE 0.012 0.001 PHE A1581 TYR 0.014 0.001 TYR A 308 ARG 0.008 0.000 ARG A 852 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 154 time to evaluate : 1.370 Fit side-chains REVERT: A 386 LYS cc_start: 0.8570 (mmmt) cc_final: 0.7984 (mmtt) REVERT: A 443 ARG cc_start: 0.7530 (mtm180) cc_final: 0.6308 (mtm110) REVERT: A 533 TRP cc_start: 0.7240 (t60) cc_final: 0.5862 (m100) REVERT: A 620 MET cc_start: 0.7782 (mmm) cc_final: 0.7533 (tpp) REVERT: A 640 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 725 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6167 (mtm180) REVERT: A 745 LYS cc_start: 0.7635 (ttmt) cc_final: 0.7388 (mptt) REVERT: A 763 ARG cc_start: 0.7689 (mmt180) cc_final: 0.7033 (mtm-85) REVERT: A 791 ARG cc_start: 0.7347 (ptp-110) cc_final: 0.6533 (ptm-80) REVERT: A 809 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7160 (p90) REVERT: A 862 ARG cc_start: 0.5624 (OUTLIER) cc_final: 0.4374 (tpm170) REVERT: A 1202 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8705 (m) REVERT: A 1268 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: A 1269 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6503 (mm-40) REVERT: A 1836 VAL cc_start: 0.7803 (m) cc_final: 0.7566 (p) outliers start: 41 outliers final: 25 residues processed: 177 average time/residue: 1.3171 time to fit residues: 255.0276 Evaluate side-chains 182 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 862 ARG Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1816 ILE Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 129 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A 824 GLN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 ASN A1269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13203 Z= 0.338 Angle : 0.619 11.066 17978 Z= 0.304 Chirality : 0.043 0.174 2024 Planarity : 0.005 0.047 2147 Dihedral : 11.656 140.584 2966 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.36 % Allowed : 18.11 % Favored : 78.53 % 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: 0.44 (0.22), residues: 1461 helix: 0.83 (0.17), residues: 875 sheet: 0.42 (0.65), residues: 66 loop : -0.51 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 224 HIS 0.006 0.001 HIS A1195 PHE 0.016 0.002 PHE A1363 TYR 0.019 0.002 TYR A 308 ARG 0.008 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 156 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7283 (mt) REVERT: A 386 LYS cc_start: 0.8591 (mmmt) cc_final: 0.7983 (mmtt) REVERT: A 443 ARG cc_start: 0.7577 (mtm180) cc_final: 0.6318 (mtm110) REVERT: A 533 TRP cc_start: 0.7236 (t60) cc_final: 0.5907 (m100) REVERT: A 620 MET cc_start: 0.7825 (mmm) cc_final: 0.7587 (tpp) REVERT: A 640 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8283 (mp) REVERT: A 725 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.6200 (mtm180) REVERT: A 745 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7439 (mptt) REVERT: A 763 ARG cc_start: 0.7742 (mmt180) cc_final: 0.7064 (mtm-85) REVERT: A 791 ARG cc_start: 0.7367 (ptp-110) cc_final: 0.6542 (ptm-80) REVERT: A 809 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7219 (p90) REVERT: A 1202 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8616 (m) REVERT: A 1268 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: A 1269 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6564 (mm110) REVERT: A 1642 MET cc_start: 0.5469 (tmm) cc_final: 0.5065 (pmm) REVERT: A 1836 VAL cc_start: 0.7868 (m) cc_final: 0.7609 (p) outliers start: 44 outliers final: 26 residues processed: 182 average time/residue: 1.3368 time to fit residues: 265.7117 Evaluate side-chains 184 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 1061 ASN Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 140 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A 824 GLN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 ASN A1269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13203 Z= 0.163 Angle : 0.546 9.128 17978 Z= 0.269 Chirality : 0.039 0.157 2024 Planarity : 0.004 0.047 2147 Dihedral : 11.336 135.201 2966 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.90 % Allowed : 18.72 % Favored : 78.38 % 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: 0.63 (0.22), residues: 1461 helix: 1.01 (0.18), residues: 884 sheet: 0.07 (0.62), residues: 71 loop : -0.46 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 884 HIS 0.008 0.001 HIS A1195 PHE 0.013 0.001 PHE A1581 TYR 0.015 0.001 TYR A1503 ARG 0.007 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8564 (mmmt) cc_final: 0.7963 (mmtt) REVERT: A 443 ARG cc_start: 0.7541 (mtm180) cc_final: 0.6298 (mtm110) REVERT: A 533 TRP cc_start: 0.7240 (t60) cc_final: 0.5865 (m100) REVERT: A 620 MET cc_start: 0.7790 (mmm) cc_final: 0.7541 (tpp) REVERT: A 640 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8253 (mp) REVERT: A 725 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.6257 (mtm180) REVERT: A 745 LYS cc_start: 0.7625 (ttmt) cc_final: 0.7363 (mptt) REVERT: A 791 ARG cc_start: 0.7345 (ptp-110) cc_final: 0.6526 (ptm-80) REVERT: A 809 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7340 (p90) REVERT: A 1202 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8675 (m) REVERT: A 1268 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7058 (tt0) REVERT: A 1269 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6507 (mm-40) REVERT: A 1380 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6432 (tt0) REVERT: A 1642 MET cc_start: 0.5336 (tmm) cc_final: 0.4795 (pmm) REVERT: A 1836 VAL cc_start: 0.7822 (m) cc_final: 0.7584 (p) outliers start: 38 outliers final: 25 residues processed: 170 average time/residue: 1.3270 time to fit residues: 246.8389 Evaluate side-chains 179 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1380 GLU Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1816 ILE Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 147 optimal weight: 0.2980 chunk 135 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A 824 GLN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 ASN A1269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13203 Z= 0.270 Angle : 0.592 10.291 17978 Z= 0.291 Chirality : 0.042 0.159 2024 Planarity : 0.004 0.047 2147 Dihedral : 11.384 134.079 2965 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.98 % Allowed : 18.72 % Favored : 78.30 % 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: 0.52 (0.22), residues: 1461 helix: 0.89 (0.17), residues: 892 sheet: 0.08 (0.63), residues: 71 loop : -0.45 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 884 HIS 0.008 0.001 HIS A1195 PHE 0.025 0.002 PHE A1657 TYR 0.017 0.001 TYR A 308 ARG 0.009 0.000 ARG A 852 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8577 (mmmt) cc_final: 0.7971 (mmtt) REVERT: A 443 ARG cc_start: 0.7543 (mtm180) cc_final: 0.6310 (mtm110) REVERT: A 533 TRP cc_start: 0.7237 (t60) cc_final: 0.5885 (m100) REVERT: A 620 MET cc_start: 0.7817 (mmm) cc_final: 0.7561 (tpp) REVERT: A 640 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8265 (mp) REVERT: A 725 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6270 (mtm180) REVERT: A 745 LYS cc_start: 0.7646 (ttmt) cc_final: 0.7368 (mptt) REVERT: A 763 ARG cc_start: 0.7642 (mmt180) cc_final: 0.6903 (mtm-85) REVERT: A 791 ARG cc_start: 0.7362 (ptp-110) cc_final: 0.6538 (ptm-80) REVERT: A 809 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7335 (p90) REVERT: A 1202 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8643 (m) REVERT: A 1268 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7100 (tt0) REVERT: A 1269 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6494 (mm110) REVERT: A 1642 MET cc_start: 0.5362 (tmm) cc_final: 0.4863 (pmm) REVERT: A 1739 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7400 (tp30) REVERT: A 1836 VAL cc_start: 0.7852 (m) cc_final: 0.7608 (p) outliers start: 39 outliers final: 24 residues processed: 168 average time/residue: 1.3360 time to fit residues: 244.8026 Evaluate side-chains 178 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 527 HIS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1269 GLN Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1612 VAL Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1690 MET Chi-restraints excluded: chain A residue 1751 LEU Chi-restraints excluded: chain A residue 1816 ILE Chi-restraints excluded: chain A residue 1847 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 17 optimal weight: 0.0470 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A 824 GLN ** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 ASN A1269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.157800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107086 restraints weight = 14125.130| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.57 r_work: 0.3111 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13203 Z= 0.149 Angle : 0.550 10.046 17978 Z= 0.269 Chirality : 0.039 0.158 2024 Planarity : 0.004 0.047 2147 Dihedral : 11.130 129.961 2965 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.37 % Allowed : 19.17 % Favored : 78.46 % 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: 0.79 (0.22), residues: 1461 helix: 1.18 (0.18), residues: 879 sheet: 0.11 (0.63), residues: 71 loop : -0.48 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 445 HIS 0.010 0.001 HIS A1195 PHE 0.020 0.001 PHE A1657 TYR 0.014 0.001 TYR A1503 ARG 0.008 0.000 ARG A 376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5007.50 seconds wall clock time: 90 minutes 59.40 seconds (5459.40 seconds total)