Starting phenix.real_space_refine on Sat Dec 9 18:31:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usm_26739/12_2023/7usm_26739.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usm_26739/12_2023/7usm_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_26739/12_2023/7usm_26739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usm_26739/12_2023/7usm_26739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usm_26739/12_2023/7usm_26739.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usm_26739/12_2023/7usm_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-1.21rc1-5172/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: 6.35, per 1000 atoms: 0.53 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: 4.54 Conformation dependent library (CDL) restraints added in 2.3 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: 1.49 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: 5.09 Time building geometry restraints manager: 4.94 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 8.430 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 34.740 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.380 ------------------------------------------------------------------------------- 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 : 1.293 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 1.2604 time to fit residues: 316.8355 Evaluate side-chains 191 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9081 ------------------------------------------------------------------------------- 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: 0.6545 moved from start: 0.1360 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= 0.268 Angle : 0.648 8.794 16405 Z= 0.341 Chirality : 0.046 0.178 1854 Planarity : 0.005 0.066 2162 Dihedral : 6.599 59.315 1875 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.83 % Allowed : 9.13 % Favored : 89.05 % 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 (0.21), residues: 1509 helix: -1.05 (0.41), residues: 151 sheet: 0.53 (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 246 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 222 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 235 average time/residue: 1.3065 time to fit residues: 332.7203 Evaluate side-chains 212 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 201 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 5 residues processed: 6 average time/residue: 0.1304 time to fit residues: 3.3181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 110 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 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: 0.6550 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 12114 Z= 0.267 Angle : 0.639 9.098 16405 Z= 0.337 Chirality : 0.046 0.226 1854 Planarity : 0.005 0.060 2162 Dihedral : 6.496 59.423 1875 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.27 % Allowed : 12.02 % Favored : 84.71 % 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: -0.60 (0.21), residues: 1509 helix: -0.90 (0.42), residues: 150 sheet: 0.51 (0.23), residues: 489 loop : -0.83 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1039 HIS 0.007 0.001 HIS A 540 PHE 0.023 0.002 PHE A1072 TYR 0.014 0.001 TYR B 279 ARG 0.010 0.001 ARG A 636 *********************** 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 256 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 213 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 18 residues processed: 234 average time/residue: 1.2916 time to fit residues: 327.8328 Evaluate side-chains 227 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 209 time to evaluate : 1.424 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 8 residues processed: 12 average time/residue: 0.4112 time to fit residues: 8.5064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 0.0030 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 145 optimal weight: 0.0050 chunk 72 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.3404 ------------------------------------------------------------------------------- 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 402 GLN B 518 ASN ** 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: 0.6522 moved from start: 0.2010 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= 0.195 Angle : 0.598 12.998 16405 Z= 0.313 Chirality : 0.044 0.225 1854 Planarity : 0.005 0.054 2162 Dihedral : 6.235 59.732 1875 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.42 % Allowed : 13.99 % Favored : 82.59 % 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: -0.59 (0.21), residues: 1509 helix: -0.98 (0.41), residues: 157 sheet: 0.54 (0.23), residues: 474 loop : -0.79 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1039 HIS 0.004 0.001 HIS A 852 PHE 0.027 0.002 PHE B 149 TYR 0.010 0.001 TYR B 279 ARG 0.010 0.000 ARG A 636 *********************** 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 247 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 202 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 12 residues processed: 229 average time/residue: 1.1532 time to fit residues: 289.0692 Evaluate side-chains 209 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.1171 time to fit residues: 2.7258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.0010 chunk 82 optimal weight: 0.0370 chunk 2 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 100 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 overall best weight: 0.2362 ------------------------------------------------------------------------------- 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 ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN B 518 ASN ** 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: 0.6494 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12114 Z= 0.175 Angle : 0.587 10.155 16405 Z= 0.307 Chirality : 0.044 0.210 1854 Planarity : 0.004 0.050 2162 Dihedral : 6.067 59.276 1875 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.89 % Allowed : 15.44 % Favored : 81.67 % 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: -0.51 (0.21), residues: 1509 helix: -0.97 (0.41), residues: 157 sheet: 0.67 (0.23), residues: 471 loop : -0.78 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1039 HIS 0.005 0.001 HIS A 852 PHE 0.025 0.002 PHE B 149 TYR 0.009 0.001 TYR B 279 ARG 0.010 0.000 ARG A 636 *********************** 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 238 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 200 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 228 average time/residue: 1.1446 time to fit residues: 285.9441 Evaluate side-chains 201 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 1.298 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.6387 time to fit residues: 4.0260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 28 optimal weight: 0.0670 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 B 518 ASN ** 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: 0.6577 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12114 Z= 0.352 Angle : 0.689 12.680 16405 Z= 0.361 Chirality : 0.047 0.237 1854 Planarity : 0.005 0.048 2162 Dihedral : 6.538 59.705 1875 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.19 % Allowed : 16.12 % Favored : 80.68 % 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: -0.62 (0.21), residues: 1509 helix: -0.81 (0.42), residues: 145 sheet: 0.47 (0.23), residues: 491 loop : -0.85 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1039 HIS 0.009 0.002 HIS A 852 PHE 0.040 0.003 PHE B 149 TYR 0.015 0.002 TYR B 279 ARG 0.011 0.001 ARG A 636 *********************** 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 241 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 24 residues processed: 225 average time/residue: 1.1335 time to fit residues: 279.1955 Evaluate side-chains 214 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 1.186 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 9 average time/residue: 0.1461 time to fit residues: 4.0070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.4980 chunk 16 optimal weight: 0.0970 chunk 83 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 chunk 82 optimal weight: 0.4980 chunk 122 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 B 518 ASN ** 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: 0.6533 moved from start: 0.2452 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= 0.217 Angle : 0.633 12.660 16405 Z= 0.330 Chirality : 0.045 0.211 1854 Planarity : 0.004 0.051 2162 Dihedral : 6.301 59.199 1875 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.89 % Allowed : 17.72 % Favored : 79.39 % 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: -0.58 (0.21), residues: 1509 helix: -0.80 (0.43), residues: 145 sheet: 0.60 (0.23), residues: 472 loop : -0.87 (0.21), residues: 892 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 0.043 0.002 PHE B 149 TYR 0.011 0.001 TYR B 279 ARG 0.013 0.000 ARG A 636 *********************** 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 238 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 200 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 22 residues processed: 226 average time/residue: 1.1733 time to fit residues: 289.9867 Evaluate side-chains 223 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 201 time to evaluate : 1.331 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 18 residues processed: 7 average time/residue: 0.1651 time to fit residues: 3.7673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 99 optimal weight: 0.0670 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 132 optimal weight: 0.0980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 292 ASN B 390 GLN B 518 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.2542 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= 0.247 Angle : 0.654 12.604 16405 Z= 0.339 Chirality : 0.045 0.215 1854 Planarity : 0.005 0.055 2162 Dihedral : 6.315 59.198 1875 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.66 % Allowed : 18.63 % Favored : 78.71 % 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: -0.62 (0.22), residues: 1509 helix: -0.82 (0.42), residues: 151 sheet: 0.52 (0.24), residues: 476 loop : -0.86 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 967 HIS 0.008 0.001 HIS A 852 PHE 0.044 0.002 PHE B 149 TYR 0.012 0.001 TYR B 279 ARG 0.013 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 233 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 198 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 223 average time/residue: 1.1669 time to fit residues: 285.4928 Evaluate side-chains 211 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 1.385 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 5 average time/residue: 0.2129 time to fit residues: 3.4026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 0.5980 chunk 127 optimal weight: 0.3980 chunk 135 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 106 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 143 optimal weight: 0.0020 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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 B 390 GLN B 518 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.2633 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= 0.219 Angle : 0.646 12.500 16405 Z= 0.333 Chirality : 0.045 0.206 1854 Planarity : 0.005 0.057 2162 Dihedral : 6.223 58.522 1875 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.83 % Allowed : 19.77 % Favored : 78.40 % 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: -0.57 (0.22), residues: 1509 helix: -0.73 (0.43), residues: 145 sheet: 0.58 (0.24), residues: 474 loop : -0.86 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 967 HIS 0.007 0.001 HIS A 852 PHE 0.037 0.002 PHE B 149 TYR 0.010 0.001 TYR B 279 ARG 0.014 0.001 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 217 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 193 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 21 residues processed: 213 average time/residue: 1.2282 time to fit residues: 289.6607 Evaluate side-chains 212 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 1.326 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 20 residues processed: 3 average time/residue: 0.2741 time to fit residues: 3.1577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 150 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 701 GLN A 851 ASN B 292 ASN B 390 GLN B 518 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12114 Z= 0.287 Angle : 0.690 12.316 16405 Z= 0.356 Chirality : 0.046 0.206 1854 Planarity : 0.005 0.062 2162 Dihedral : 6.388 59.134 1875 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.98 % Allowed : 19.85 % 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: -0.69 (0.21), residues: 1509 helix: -0.82 (0.42), residues: 151 sheet: 0.47 (0.24), residues: 477 loop : -0.92 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 501 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 0.015 0.001 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 221 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 216 average time/residue: 1.1940 time to fit residues: 282.1486 Evaluate side-chains 216 residues out of total 1315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 1.358 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 4 average time/residue: 0.2102 time to fit residues: 3.3268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 119 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 0.0270 chunk 22 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 701 GLN B 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.178259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.156931 restraints weight = 15897.444| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.25 r_work: 0.4034 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12114 Z= 0.259 Angle : 0.673 12.192 16405 Z= 0.349 Chirality : 0.046 0.201 1854 Planarity : 0.005 0.061 2162 Dihedral : 6.351 59.110 1875 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.90 % Allowed : 20.30 % Favored : 77.79 % 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: -0.71 (0.43), residues: 145 sheet: 0.47 (0.24), residues: 482 loop : -0.90 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 501 HIS 0.007 0.001 HIS A 852 PHE 0.044 0.002 PHE B 149 TYR 0.012 0.001 TYR B 279 ARG 0.015 0.001 ARG A 893 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5508.58 seconds wall clock time: 98 minutes 16.21 seconds (5896.21 seconds total)