Starting phenix.real_space_refine on Fri Mar 15 14:44:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usm_26739/03_2024/7usm_26739.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usm_26739/03_2024/7usm_26739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usm_26739/03_2024/7usm_26739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usm_26739/03_2024/7usm_26739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usm_26739/03_2024/7usm_26739.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usm_26739/03_2024/7usm_26739.pdb" } resolution = 2.7 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= 0.012 sd= 1.262 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 Ca 4 9.91 5 S 98 5.16 5 C 7386 2.51 5 N 2092 2.21 5 O 2313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 385": "OD1" <-> "OD2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 243": "OD1" <-> "OD2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 642": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11893 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6559 Classifications: {'peptide': 848} Link IDs: {'PCIS': 4, 'PTRANS': 35, 'TRANS': 808} Chain breaks: 4 Chain: "B" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5176 Classifications: {'peptide': 673} Link IDs: {'PCIS': 4, 'PTRANS': 31, 'TRANS': 637} Chain: "C" 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: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 115 Unusual residues: {' CA': 3, 'NAG': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.21, per 1000 atoms: 0.52 Number of scatterers: 11893 At special positions: 0 Unit cell: (122.322, 121.249, 127.687, 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) Ca 4 19.99 S 98 16.00 O 2313 8.00 N 2092 7.00 C 7386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A 982 " - pdb=" SG CYS A1016 " distance=2.03 Simple disulfide: pdb=" SG CYS A1006 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 21 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 450 " - pdb=" SG CYS B 459 " distance=2.03 Simple disulfide: pdb=" SG CYS B 461 " - pdb=" SG CYS B 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 497 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 514 " - pdb=" SG CYS B 537 " distance=2.04 Simple disulfide: pdb=" SG CYS B 519 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 551 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 574 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 596 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 625 " distance=2.03 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 621 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 673 " 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 C 1 " - " NAG C 2 " NAG-ASN " NAG A1204 " - " ASN A1034 " " NAG A1205 " - " ASN A 70 " " NAG A1206 " - " ASN A 718 " " NAG A1207 " - " ASN A 785 " " NAG A1208 " - " ASN A 864 " " NAG A1209 " - " ASN A 884 " " NAG A1210 " - " ASN A1005 " " NAG A1211 " - " ASN A1028 " " NAG B 802 " - " ASN B 94 " " NAG C 1 " - " ASN A 375 " Time building additional restraints: 4.70 Conformation dependent library (CDL) restraints added in 2.4 seconds 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2790 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 32 sheets defined 14.7% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.642A pdb=" N PHE A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 993 through 1001 removed outlier: 3.933A pdb=" N LEU A 998 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1072 removed outlier: 3.638A pdb=" N ALA A1071 " --> pdb=" O GLY A1068 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A1072 " --> pdb=" O GLN A1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1068 through 1072' Processing helix chain 'B' and resid 10 through 17 removed outlier: 3.546A pdb=" N CYS B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE B 15 " --> pdb=" O CYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.977A pdb=" N THR B 30 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 161 through 167 removed outlier: 3.589A pdb=" N ARG B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 removed outlier: 3.665A pdb=" N PHE B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.760A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.686A pdb=" N LYS B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 301 through 315 removed outlier: 4.582A pdb=" N LYS B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU B 311 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.733A pdb=" N LEU B 436 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.819A pdb=" N SER B 569 " --> pdb=" O VAL B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 removed outlier: 4.290A pdb=" N GLY B 601 " --> pdb=" O SER B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 611 removed outlier: 4.494A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 625 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.891A pdb=" N MET A 9 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 25 removed outlier: 3.875A pdb=" N ARG A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 58 " --> pdb=" O GLN A 49 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER A 56 " --> pdb=" O ASP A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 40 removed outlier: 7.160A pdb=" N GLN A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.896A pdb=" N SER A 76 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 92 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS A 104 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N HIS A 94 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR A 102 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 397 removed outlier: 8.370A pdb=" N GLN A 401 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN A 421 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 416 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN A 431 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N MET A 418 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 425 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 448 removed outlier: 5.987A pdb=" N HIS A 465 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLY A 472 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 491 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.607A pdb=" N GLN A 553 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB1, first strand: chain 'A' and resid 674 through 675 removed outlier: 4.153A pdb=" N GLU A 631 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 682 through 689 Processing sheet with id=AB3, first strand: chain 'A' and resid 765 through 769 removed outlier: 3.751A pdb=" N SER A 769 " --> pdb=" O THR A 787 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 787 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 866 " --> pdb=" O ARG A 813 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 797 through 798 removed outlier: 3.538A pdb=" N SER A 797 " --> pdb=" O PHE A 855 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 830 through 832 removed outlier: 4.435A pdb=" N LEU A 881 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 901 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 907 through 908 removed outlier: 6.346A pdb=" N TYR A 907 " --> pdb=" O THR A1064 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 911 through 914 removed outlier: 3.724A pdb=" N GLY A1033 " --> pdb=" O MET A 935 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 937 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A1029 " --> pdb=" O TYR A 939 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 922 through 923 removed outlier: 13.196A pdb=" N LEU A1049 " --> pdb=" O ARG A 960 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N ARG A 960 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL A1051 " --> pdb=" O PRO A 958 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A1053 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A1020 " --> pdb=" O PRO A 950 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER A 952 " --> pdb=" O ILE A1018 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A1018 " --> pdb=" O SER A 952 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL A 954 " --> pdb=" O CYS A1016 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N CYS A1016 " --> pdb=" O VAL A 954 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU A 956 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE A1014 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN A1012 " --> pdb=" O PRO A 958 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A 981 " --> pdb=" O ASP A1017 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 964 through 965 removed outlier: 3.574A pdb=" N THR A1053 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL A1051 " --> pdb=" O PRO A 958 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N ARG A 960 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 13.196A pdb=" N LEU A1049 " --> pdb=" O ARG A 960 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AC2, first strand: chain 'B' and resid 62 through 66 removed outlier: 3.787A pdb=" N LEU B 62 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS B 80 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 76 through 77 removed outlier: 4.014A pdb=" N THR B 388 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 394 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER B 362 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG B 371 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 182 through 189 removed outlier: 7.066A pdb=" N VAL B 185 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N SER B 148 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LYS B 187 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N PHE B 146 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP B 106 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL B 238 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR B 108 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA B 240 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU B 110 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 442 through 444 Processing sheet with id=AC6, first strand: chain 'B' and resid 454 through 455 Processing sheet with id=AC7, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AC8, first strand: chain 'B' and resid 507 through 508 Processing sheet with id=AC9, first strand: chain 'B' and resid 521 through 522 Processing sheet with id=AD1, first strand: chain 'B' and resid 533 through 536 Processing sheet with id=AD2, first strand: chain 'B' and resid 546 through 547 Processing sheet with id=AD3, first strand: chain 'B' and resid 574 through 575 removed outlier: 3.564A pdb=" N VAL B 578 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 629 through 630 removed outlier: 3.550A pdb=" N TYR B 666 " --> pdb=" O THR B 653 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 642 " --> pdb=" O VAL B 650 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 638 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 629 through 630 removed outlier: 3.550A pdb=" N TYR B 666 " --> pdb=" O THR B 653 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU B 672 " --> pdb=" O TRP B 649 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1002 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: 4.72 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4028 1.34 - 1.46: 2635 1.46 - 1.58: 5332 1.58 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 12114 Sorted by residual: bond pdb=" C1 NAG A1207 " pdb=" O5 NAG A1207 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C1 NAG A1211 " pdb=" O5 NAG A1211 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 NAG A1205 " pdb=" O5 NAG A1205 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C1 NAG A1206 " pdb=" O5 NAG A1206 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 NAG A1209 " pdb=" O5 NAG A1209 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 12109 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.44: 272 105.44 - 112.58: 6129 112.58 - 119.71: 4031 119.71 - 126.84: 5850 126.84 - 133.98: 123 Bond angle restraints: 16405 Sorted by residual: angle pdb=" N LEU B 443 " pdb=" CA LEU B 443 " pdb=" C LEU B 443 " ideal model delta sigma weight residual 108.73 115.67 -6.94 1.63e+00 3.76e-01 1.81e+01 angle pdb=" N GLY B 214 " pdb=" CA GLY B 214 " pdb=" C GLY B 214 " ideal model delta sigma weight residual 114.40 118.00 -3.60 1.11e+00 8.12e-01 1.05e+01 angle pdb=" N GLU B 444 " pdb=" CA GLU B 444 " pdb=" CB GLU B 444 " ideal model delta sigma weight residual 111.13 116.75 -5.62 1.79e+00 3.12e-01 9.87e+00 angle pdb=" C PHE B 442 " pdb=" CA PHE B 442 " pdb=" CB PHE B 442 " ideal model delta sigma weight residual 109.38 115.35 -5.97 2.03e+00 2.43e-01 8.65e+00 angle pdb=" N LYS B 5 " pdb=" CA LYS B 5 " pdb=" C LYS B 5 " ideal model delta sigma weight residual 108.41 112.63 -4.22 1.63e+00 3.76e-01 6.69e+00 ... (remaining 16400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6960 17.95 - 35.91: 468 35.91 - 53.86: 75 53.86 - 71.81: 27 71.81 - 89.77: 12 Dihedral angle restraints: 7542 sinusoidal: 3196 harmonic: 4346 Sorted by residual: dihedral pdb=" CB CYS B 593 " pdb=" SG CYS B 593 " pdb=" SG CYS B 596 " pdb=" CB CYS B 596 " ideal model delta sinusoidal sigma weight residual -86.00 -167.73 81.73 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS B 527 " pdb=" SG CYS B 527 " pdb=" SG CYS B 540 " pdb=" CB CYS B 540 " ideal model delta sinusoidal sigma weight residual 93.00 160.09 -67.09 1 1.00e+01 1.00e-02 5.86e+01 dihedral pdb=" CB CYS B 497 " pdb=" SG CYS B 497 " pdb=" SG CYS B 512 " pdb=" CB CYS B 512 " ideal model delta sinusoidal sigma weight residual 93.00 151.69 -58.69 1 1.00e+01 1.00e-02 4.61e+01 ... (remaining 7539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1322 0.042 - 0.084: 370 0.084 - 0.126: 147 0.126 - 0.168: 12 0.168 - 0.210: 3 Chirality restraints: 1854 Sorted by residual: chirality pdb=" CB VAL B 233 " pdb=" CA VAL B 233 " pdb=" CG1 VAL B 233 " pdb=" CG2 VAL B 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CG LEU A 689 " pdb=" CB LEU A 689 " pdb=" CD1 LEU A 689 " pdb=" CD2 LEU A 689 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA GLU B 444 " pdb=" N GLU B 444 " pdb=" C GLU B 444 " pdb=" CB GLU B 444 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 1851 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 373 " -0.062 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO B 374 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 374 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 374 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 529 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO B 530 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 530 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 530 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 385 " -0.051 5.00e-02 4.00e+02 7.71e-02 9.51e+00 pdb=" N PRO B 386 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 386 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 386 " -0.042 5.00e-02 4.00e+02 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 197 2.67 - 3.23: 11157 3.23 - 3.78: 17180 3.78 - 4.34: 24208 4.34 - 4.90: 40055 Nonbonded interactions: 92797 Sorted by model distance: nonbonded pdb=" OG1 THR B 258 " pdb=" O GLU B 276 " model vdw 2.109 2.440 nonbonded pdb=" OD1 ASP B 243 " pdb=" N GLY B 244 " model vdw 2.116 2.520 nonbonded pdb=" OG SER A 21 " pdb=" O GLY A 74 " model vdw 2.138 2.440 nonbonded pdb=" OH TYR B 603 " pdb=" OD1 ASP B 661 " model vdw 2.188 2.440 nonbonded pdb=" OG1 THR A 470 " pdb=" OE1 GLN A 497 " model vdw 2.217 2.440 ... (remaining 92792 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 8.470 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.270 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 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 : 0.003 0.044 12114 Z= 0.197 Angle : 0.631 8.572 16405 Z= 0.327 Chirality : 0.045 0.210 1854 Planarity : 0.006 0.093 2162 Dihedral : 12.829 89.769 4668 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.89 (0.21), residues: 1509 helix: -1.69 (0.39), residues: 157 sheet: 0.48 (0.24), residues: 466 loop : -0.97 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 230 HIS 0.004 0.001 HIS A 852 PHE 0.026 0.002 PHE B 149 TYR 0.021 0.002 TYR A 440 ARG 0.018 0.001 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.184 Fit side-chains REVERT: A 470 THR cc_start: 0.8014 (p) cc_final: 0.7806 (p) REVERT: A 681 SER cc_start: 0.7420 (p) cc_final: 0.7204 (t) REVERT: B 115 TYR cc_start: 0.6654 (t80) cc_final: 0.6433 (t80) REVERT: B 309 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6880 (mm-30) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 1.2331 time to fit residues: 309.1021 Evaluate side-chains 192 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 chunk 137 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN A 852 HIS A 895 ASN A 916 HIS ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12114 Z= 0.270 Angle : 0.649 8.447 16405 Z= 0.340 Chirality : 0.046 0.185 1854 Planarity : 0.005 0.066 2162 Dihedral : 6.588 59.631 1875 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.98 % Allowed : 9.05 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.62 (0.21), residues: 1509 helix: -1.08 (0.41), residues: 151 sheet: 0.51 (0.23), residues: 485 loop : -0.82 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1039 HIS 0.008 0.001 HIS A 540 PHE 0.023 0.002 PHE B 442 TYR 0.015 0.002 TYR B 279 ARG 0.009 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7443 (ptt180) cc_final: 0.7160 (pmm-80) REVERT: A 470 THR cc_start: 0.8052 (p) cc_final: 0.7832 (p) REVERT: A 614 GLU cc_start: 0.6730 (pm20) cc_final: 0.6515 (pm20) REVERT: A 636 ARG cc_start: 0.6134 (mtt-85) cc_final: 0.5920 (mtt-85) REVERT: B 64 GLU cc_start: 0.5029 (mp0) cc_final: 0.4551 (mp0) REVERT: B 295 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7365 (mt0) outliers start: 26 outliers final: 13 residues processed: 236 average time/residue: 1.2533 time to fit residues: 320.4090 Evaluate side-chains 222 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 630 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 110 optimal weight: 0.0980 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 575 GLN A 701 GLN A 895 ASN A 916 HIS ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 12114 Z= 0.319 Angle : 0.660 9.622 16405 Z= 0.348 Chirality : 0.046 0.247 1854 Planarity : 0.005 0.061 2162 Dihedral : 6.586 59.575 1875 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.12 % Allowed : 12.40 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.66 (0.21), residues: 1509 helix: -0.96 (0.42), residues: 150 sheet: 0.47 (0.23), residues: 489 loop : -0.86 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1039 HIS 0.008 0.001 HIS A 540 PHE 0.024 0.003 PHE A1072 TYR 0.015 0.002 TYR B 279 ARG 0.008 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 214 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7463 (ptt180) cc_final: 0.7225 (pmm-80) REVERT: A 470 THR cc_start: 0.8113 (p) cc_final: 0.7894 (p) REVERT: B 64 GLU cc_start: 0.5025 (mp0) cc_final: 0.4554 (mp0) REVERT: B 295 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7371 (mt0) REVERT: B 306 LYS cc_start: 0.7297 (mppt) cc_final: 0.7091 (mppt) REVERT: B 359 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7382 (p) outliers start: 41 outliers final: 21 residues processed: 233 average time/residue: 1.2677 time to fit residues: 319.6533 Evaluate side-chains 229 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 638 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 145 optimal weight: 0.0040 chunk 72 optimal weight: 0.0270 chunk 130 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 overall best weight: 0.4850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 575 GLN A 701 GLN A 895 ASN A 916 HIS ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12114 Z= 0.234 Angle : 0.621 11.704 16405 Z= 0.324 Chirality : 0.045 0.226 1854 Planarity : 0.005 0.054 2162 Dihedral : 6.387 59.667 1875 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.04 % Allowed : 14.68 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.62 (0.21), residues: 1509 helix: -0.88 (0.42), residues: 150 sheet: 0.47 (0.23), residues: 477 loop : -0.82 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1039 HIS 0.005 0.001 HIS A 540 PHE 0.025 0.002 PHE B 149 TYR 0.013 0.001 TYR B 279 ARG 0.006 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 212 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7413 (ptt180) cc_final: 0.7194 (pmm-80) REVERT: A 470 THR cc_start: 0.8136 (p) cc_final: 0.7920 (p) REVERT: A 608 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7239 (mpp) REVERT: A 1035 LEU cc_start: 0.5870 (tp) cc_final: 0.5670 (tp) REVERT: B 64 GLU cc_start: 0.4956 (mp0) cc_final: 0.4500 (mp0) REVERT: B 295 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7310 (mt0) REVERT: B 303 ARG cc_start: 0.7596 (ptm-80) cc_final: 0.7315 (mtm180) REVERT: B 359 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7385 (m) outliers start: 40 outliers final: 12 residues processed: 235 average time/residue: 1.1629 time to fit residues: 297.4664 Evaluate side-chains 215 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 630 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.0770 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 60 optimal weight: 0.0770 chunk 124 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN A 701 GLN A 895 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12114 Z= 0.206 Angle : 0.613 10.524 16405 Z= 0.320 Chirality : 0.044 0.214 1854 Planarity : 0.005 0.050 2162 Dihedral : 6.237 59.850 1875 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.50 % Allowed : 15.13 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.54 (0.21), residues: 1509 helix: -0.82 (0.42), residues: 151 sheet: 0.58 (0.23), residues: 470 loop : -0.79 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1039 HIS 0.004 0.001 HIS A 852 PHE 0.027 0.002 PHE B 149 TYR 0.011 0.001 TYR B 279 ARG 0.009 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 197 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.5931 (OUTLIER) cc_final: 0.4270 (mtt) REVERT: A 470 THR cc_start: 0.8156 (p) cc_final: 0.7939 (p) REVERT: A 555 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8200 (mm) REVERT: B 25 GLN cc_start: 0.5673 (mp-120) cc_final: 0.5011 (mp10) REVERT: B 64 GLU cc_start: 0.4900 (mp0) cc_final: 0.4425 (mp0) REVERT: B 359 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7376 (m) REVERT: B 390 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6908 (mt0) outliers start: 46 outliers final: 19 residues processed: 227 average time/residue: 1.1236 time to fit residues: 278.1200 Evaluate side-chains 207 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 650 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 28 optimal weight: 0.0370 chunk 85 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 0.0570 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN A 701 GLN A 851 ASN A 895 ASN B 390 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12114 Z= 0.233 Angle : 0.626 10.409 16405 Z= 0.327 Chirality : 0.045 0.216 1854 Planarity : 0.004 0.048 2162 Dihedral : 6.290 58.669 1875 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.95 % Allowed : 15.74 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1509 helix: -0.78 (0.43), residues: 145 sheet: 0.56 (0.23), residues: 481 loop : -0.82 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1039 HIS 0.007 0.001 HIS A 852 PHE 0.036 0.002 PHE B 149 TYR 0.012 0.001 TYR B 279 ARG 0.012 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 192 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1072 PHE cc_start: 0.5851 (m-10) cc_final: 0.5464 (m-10) REVERT: B 390 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6955 (mt0) REVERT: B 549 SER cc_start: 0.8296 (m) cc_final: 0.7994 (t) outliers start: 52 outliers final: 26 residues processed: 228 average time/residue: 1.1317 time to fit residues: 281.9819 Evaluate side-chains 212 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 650 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 575 GLN A 701 GLN A 895 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12114 Z= 0.292 Angle : 0.660 10.864 16405 Z= 0.344 Chirality : 0.046 0.226 1854 Planarity : 0.005 0.049 2162 Dihedral : 6.407 59.305 1875 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.42 % Allowed : 17.03 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.71 (0.21), residues: 1509 helix: -0.85 (0.42), residues: 151 sheet: 0.34 (0.23), residues: 483 loop : -0.86 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 967 HIS 0.008 0.001 HIS A 852 PHE 0.044 0.003 PHE B 149 TYR 0.014 0.001 TYR B 279 ARG 0.012 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 GLN cc_start: 0.5733 (mp-120) cc_final: 0.5039 (mp10) REVERT: B 64 GLU cc_start: 0.4818 (mp0) cc_final: 0.4370 (mp0) REVERT: B 390 GLN cc_start: 0.7178 (mt0) cc_final: 0.6896 (mt0) REVERT: B 549 SER cc_start: 0.8362 (m) cc_final: 0.8061 (t) outliers start: 45 outliers final: 31 residues processed: 224 average time/residue: 1.1496 time to fit residues: 280.8998 Evaluate side-chains 222 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 650 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 28 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 114 optimal weight: 0.3980 chunk 132 optimal weight: 4.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 575 GLN A 701 GLN A 851 ASN A 895 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12114 Z= 0.227 Angle : 0.636 11.576 16405 Z= 0.331 Chirality : 0.045 0.217 1854 Planarity : 0.004 0.054 2162 Dihedral : 6.311 58.358 1875 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.12 % Allowed : 18.17 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 (0.21), residues: 1509 helix: -0.74 (0.43), residues: 145 sheet: 0.44 (0.24), residues: 478 loop : -0.87 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 967 HIS 0.008 0.001 HIS A 852 PHE 0.046 0.002 PHE B 149 TYR 0.011 0.001 TYR B 279 ARG 0.012 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 201 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 716 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6517 (ttm110) REVERT: A 874 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8159 (p) REVERT: B 25 GLN cc_start: 0.5749 (mp-120) cc_final: 0.5050 (mp10) REVERT: B 390 GLN cc_start: 0.7108 (mt0) cc_final: 0.6859 (mt0) REVERT: B 549 SER cc_start: 0.8340 (m) cc_final: 0.8045 (t) outliers start: 41 outliers final: 30 residues processed: 223 average time/residue: 1.1717 time to fit residues: 285.5409 Evaluate side-chains 227 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 874 SER Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 650 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 143 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 575 GLN A 701 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12114 Z= 0.260 Angle : 0.662 11.229 16405 Z= 0.344 Chirality : 0.046 0.220 1854 Planarity : 0.005 0.059 2162 Dihedral : 6.362 58.649 1875 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.19 % Allowed : 18.63 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.71 (0.21), residues: 1509 helix: -0.80 (0.42), residues: 151 sheet: 0.39 (0.24), residues: 482 loop : -0.91 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 967 HIS 0.007 0.001 HIS A 852 PHE 0.038 0.002 PHE B 149 TYR 0.013 0.001 TYR B 279 ARG 0.014 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 200 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 716 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6534 (ttm110) REVERT: A 874 SER cc_start: 0.8412 (p) cc_final: 0.8165 (p) REVERT: B 25 GLN cc_start: 0.5777 (mp-120) cc_final: 0.5158 (mp-120) REVERT: B 549 SER cc_start: 0.8359 (m) cc_final: 0.8067 (t) outliers start: 42 outliers final: 31 residues processed: 222 average time/residue: 1.1660 time to fit residues: 283.0190 Evaluate side-chains 222 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 650 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 99 optimal weight: 0.0050 chunk 150 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 95 optimal weight: 0.8980 chunk 127 optimal weight: 0.0570 overall best weight: 0.2912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 575 GLN A 701 GLN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12114 Z= 0.191 Angle : 0.634 12.261 16405 Z= 0.327 Chirality : 0.045 0.207 1854 Planarity : 0.004 0.059 2162 Dihedral : 6.151 56.644 1875 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.36 % Allowed : 19.77 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.61 (0.22), residues: 1509 helix: -0.70 (0.43), residues: 145 sheet: 0.47 (0.24), residues: 478 loop : -0.84 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 967 HIS 0.007 0.001 HIS A 852 PHE 0.040 0.002 PHE B 149 TYR 0.009 0.001 TYR B 279 ARG 0.014 0.000 ARG A 893 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.7469 (tmt) cc_final: 0.7001 (tmt) REVERT: A 709 PRO cc_start: 0.8585 (Cg_endo) cc_final: 0.8382 (Cg_exo) REVERT: A 716 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6403 (ttm110) REVERT: A 874 SER cc_start: 0.8459 (p) cc_final: 0.8214 (p) REVERT: B 25 GLN cc_start: 0.5791 (mp-120) cc_final: 0.5101 (mp10) REVERT: B 549 SER cc_start: 0.8231 (m) cc_final: 0.7975 (t) outliers start: 31 outliers final: 24 residues processed: 216 average time/residue: 1.1711 time to fit residues: 275.3201 Evaluate side-chains 221 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 650 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 575 GLN ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN B 518 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.177858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.156805 restraints weight = 15892.132| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.22 r_work: 0.4030 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12114 Z= 0.291 Angle : 0.692 13.455 16405 Z= 0.357 Chirality : 0.046 0.220 1854 Planarity : 0.005 0.062 2162 Dihedral : 6.350 58.571 1875 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.05 % Allowed : 20.53 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.73 (0.21), residues: 1509 helix: -0.73 (0.43), residues: 145 sheet: 0.33 (0.24), residues: 483 loop : -0.91 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 967 HIS 0.007 0.001 HIS A 852 PHE 0.041 0.003 PHE B 149 TYR 0.015 0.001 TYR B 279 ARG 0.015 0.000 ARG A 893 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5571.31 seconds wall clock time: 98 minutes 37.53 seconds (5917.53 seconds total)