Starting phenix.real_space_refine on Sun May 18 10:31:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4e_41880/05_2025/8u4e_41880_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4e_41880/05_2025/8u4e_41880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u4e_41880/05_2025/8u4e_41880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4e_41880/05_2025/8u4e_41880.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4e_41880/05_2025/8u4e_41880_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4e_41880/05_2025/8u4e_41880_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3397 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 8854 2.51 5 N 2407 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13948 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6386 Classifications: {'peptide': 787} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 745} Chain breaks: 9 Chain: "B" Number of atoms: 6516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6516 Classifications: {'peptide': 805} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 761} Chain breaks: 5 Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 323 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain breaks: 1 Chain: "D" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 420 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Chain: "E" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 1 Time building chain proxies: 8.63, per 1000 atoms: 0.62 Number of scatterers: 13948 At special positions: 0 Unit cell: (124.2, 130.68, 183.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 2576 8.00 N 2407 7.00 C 8854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 872 " distance=2.03 Simple disulfide: pdb=" SG CYS A 798 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 872 " distance=2.03 Simple disulfide: pdb=" SG CYS B 798 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 47 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 47 " distance=2.04 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 51 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.8 seconds 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 33 sheets defined 16.4% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 removed outlier: 4.020A pdb=" N ASN A 25 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 26 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.864A pdb=" N ARG A 47 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 323 through 329 removed outlier: 4.330A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.926A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.537A pdb=" N LEU A 500 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 644 Processing helix chain 'A' and resid 692 through 714 removed outlier: 3.615A pdb=" N LEU A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 881 Processing helix chain 'B' and resid 16 through 24 removed outlier: 4.205A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.965A pdb=" N ASP B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 removed outlier: 4.189A pdb=" N ASP B 74 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.258A pdb=" N ASN B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.663A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.815A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.011A pdb=" N PHE B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.880A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 700 through 715 removed outlier: 3.807A pdb=" N GLU B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP B 707 " --> pdb=" O LYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 881 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.904A pdb=" N CYS C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.913A pdb=" N CYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 17 removed outlier: 4.002A pdb=" N ASP D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'E' and resid 11 through 22 removed outlier: 3.949A pdb=" N ASP E 15 " --> pdb=" O GLY E 11 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY E 22 " --> pdb=" O GLN E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 removed outlier: 3.530A pdb=" N THR E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.289A pdb=" N LEU A 33 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N PHE A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 35 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 66 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET A 98 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ARG A 65 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ARG A 118 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A 94 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N GLU A 120 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE A 96 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASN A 122 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET A 98 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 144 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.891A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 212 through 216 removed outlier: 5.668A pdb=" N LEU A 213 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS A 228 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASN A 215 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 314 removed outlier: 4.255A pdb=" N LEU A 314 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N SER A 339 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE A 364 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.251A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE A 400 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N HIS A 429 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 477 removed outlier: 3.653A pdb=" N ARG A 488 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 Processing sheet with id=AB4, first strand: chain 'A' and resid 599 through 604 removed outlier: 6.704A pdb=" N LYS A 614 " --> pdb=" O PRO A 601 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER A 603 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 612 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 771 through 774 Processing sheet with id=AB6, first strand: chain 'A' and resid 840 through 842 Processing sheet with id=AB7, first strand: chain 'A' and resid 868 through 874 removed outlier: 3.565A pdb=" N LEU A 856 " --> pdb=" O THR A 901 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 892 through 894 removed outlier: 3.529A pdb=" N PHE A 915 " --> pdb=" O TYR A 894 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.571A pdb=" N LEU B 36 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.515A pdb=" N ILE B 57 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC3, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC4, first strand: chain 'B' and resid 278 through 279 Processing sheet with id=AC5, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC7, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.514A pdb=" N LEU B 340 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ARG B 371 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 342 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU B 368 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N LEU B 403 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B 370 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC9, first strand: chain 'B' and resid 477 through 479 Processing sheet with id=AD1, first strand: chain 'B' and resid 530 through 534 Processing sheet with id=AD2, first strand: chain 'B' and resid 599 through 604 removed outlier: 6.685A pdb=" N LYS B 614 " --> pdb=" O PRO B 601 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER B 603 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 612 " --> pdb=" O SER B 603 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 771 through 774 removed outlier: 3.533A pdb=" N GLU B 772 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 630 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN B 800 " --> pdb=" O ARG B 806 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 771 through 774 removed outlier: 3.533A pdb=" N GLU B 772 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 630 " --> pdb=" O GLU B 772 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 831 through 834 Processing sheet with id=AD6, first strand: chain 'B' and resid 868 through 874 324 hydrogen bonds defined for protein. 792 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: 5.42 Time building geometry restraints manager: 3.67 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: 4569 1.34 - 1.46: 3378 1.46 - 1.58: 6196 1.58 - 1.70: 0 1.70 - 1.82: 133 Bond restraints: 14276 Sorted by residual: bond pdb=" C GLU B 30 " pdb=" N GLY B 31 " ideal model delta sigma weight residual 1.335 1.326 0.009 7.50e-03 1.78e+04 1.29e+00 bond pdb=" CA GLU D 44 " pdb=" C GLU D 44 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.80e-02 3.09e+03 9.40e-01 bond pdb=" N ASN B 90 " pdb=" CA ASN B 90 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 9.30e-01 bond pdb=" N GLY E 11 " pdb=" CA GLY E 11 " ideal model delta sigma weight residual 1.449 1.463 -0.013 1.45e-02 4.76e+03 8.55e-01 bond pdb=" C VAL D 43 " pdb=" N GLU D 44 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.62e-02 3.81e+03 7.87e-01 ... (remaining 14271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 19015 2.23 - 4.46: 289 4.46 - 6.69: 19 6.69 - 8.91: 5 8.91 - 11.14: 3 Bond angle restraints: 19331 Sorted by residual: angle pdb=" C PHE B 701 " pdb=" CA PHE B 701 " pdb=" CB PHE B 701 " ideal model delta sigma weight residual 115.79 109.64 6.15 1.19e+00 7.06e-01 2.67e+01 angle pdb=" C PHE B 714 " pdb=" N VAL B 715 " pdb=" CA VAL B 715 " ideal model delta sigma weight residual 122.13 129.62 -7.49 1.85e+00 2.92e-01 1.64e+01 angle pdb=" C ILE E 42 " pdb=" N VAL E 43 " pdb=" CA VAL E 43 " ideal model delta sigma weight residual 121.97 127.88 -5.91 1.80e+00 3.09e-01 1.08e+01 angle pdb=" CA GLU B 804 " pdb=" CB GLU B 804 " pdb=" CG GLU B 804 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.82e+00 angle pdb=" N THR C 58 " pdb=" CA THR C 58 " pdb=" C THR C 58 " ideal model delta sigma weight residual 111.14 114.27 -3.13 1.08e+00 8.57e-01 8.41e+00 ... (remaining 19326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7796 17.87 - 35.74: 711 35.74 - 53.60: 119 53.60 - 71.47: 23 71.47 - 89.34: 16 Dihedral angle restraints: 8665 sinusoidal: 3627 harmonic: 5038 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 1.57 -87.57 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 253 " pdb=" CB CYS B 253 " ideal model delta sinusoidal sigma weight residual -86.00 -171.32 85.32 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CB CYS A 304 " pdb=" SG CYS A 304 " pdb=" SG CYS A 308 " pdb=" CB CYS A 308 " ideal model delta sinusoidal sigma weight residual 93.00 176.47 -83.47 1 1.00e+01 1.00e-02 8.51e+01 ... (remaining 8662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1564 0.046 - 0.092: 374 0.092 - 0.137: 153 0.137 - 0.183: 10 0.183 - 0.229: 2 Chirality restraints: 2103 Sorted by residual: chirality pdb=" CB VAL E 43 " pdb=" CA VAL E 43 " pdb=" CG1 VAL E 43 " pdb=" CG2 VAL E 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE A 342 " pdb=" CA ILE A 342 " pdb=" CG1 ILE A 342 " pdb=" CG2 ILE A 342 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CB ILE A 370 " pdb=" CA ILE A 370 " pdb=" CG1 ILE A 370 " pdb=" CG2 ILE A 370 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 2100 not shown) Planarity restraints: 2493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 30 " 0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO D 31 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 31 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 31 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 846 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO B 847 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 847 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 847 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 59 " 0.009 2.00e-02 2.50e+03 1.08e-02 2.34e+00 pdb=" CG TYR C 59 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 59 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C 59 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR C 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 59 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 59 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 59 " 0.000 2.00e-02 2.50e+03 ... (remaining 2490 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 1 2.00 - 2.72: 902 2.72 - 3.45: 21554 3.45 - 4.17: 35193 4.17 - 4.90: 59249 Nonbonded interactions: 116899 Sorted by model distance: nonbonded pdb=" OH TYR A 708 " pdb=" NH2 ARG D 37 " model vdw 1.274 3.120 nonbonded pdb=" NH2 ARG A 479 " pdb=" O PHE C 19 " model vdw 2.156 3.120 nonbonded pdb=" O SER B 890 " pdb=" OH TYR B 894 " model vdw 2.157 3.040 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.161 3.040 nonbonded pdb=" O LYS A 310 " pdb=" OG1 THR A 334 " model vdw 2.171 3.040 ... (remaining 116894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 518 or resid 528 through 539 or resid 546 throug \ h 656 or resid 699 through 917)) selection = (chain 'B' and (resid 3 through 152 or resid 179 through 270 or resid 274 throug \ h 314 or resid 317 through 346 or resid 351 through 573 or resid 577 through 917 \ )) } ncs_group { reference = (chain 'C' and (resid 8 through 25 or resid 43 through 62)) selection = (chain 'E' and (resid 8 through 41 or resid 43 through 62)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.090 Find NCS groups from input model: 0.530 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 0.030 14317 Z= 0.135 Angle : 0.649 11.143 19413 Z= 0.338 Chirality : 0.046 0.229 2103 Planarity : 0.004 0.045 2493 Dihedral : 13.409 89.339 5286 Min Nonbonded Distance : 1.274 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.55 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.21), residues: 1685 helix: -1.37 (0.36), residues: 201 sheet: -0.69 (0.29), residues: 341 loop : -1.24 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 412 HIS 0.008 0.001 HIS B 841 PHE 0.014 0.001 PHE A 705 TYR 0.026 0.001 TYR C 59 ARG 0.004 0.000 ARG A 14 Details of bonding type rmsd hydrogen bonds : bond 0.19289 ( 314) hydrogen bonds : angle 8.41183 ( 792) SS BOND : bond 0.00262 ( 41) SS BOND : angle 1.22256 ( 82) covalent geometry : bond 0.00286 (14276) covalent geometry : angle 0.64563 (19331) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.645 Fit side-chains revert: symmetry clash REVERT: A 294 MET cc_start: 0.9483 (tmm) cc_final: 0.9219 (tmm) REVERT: B 11 MET cc_start: 0.9233 (pmm) cc_final: 0.8901 (pmm) REVERT: E 48 PHE cc_start: 0.8634 (m-80) cc_final: 0.8258 (m-80) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2886 time to fit residues: 24.0379 Evaluate side-chains 42 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 691 GLN A 776 ASN ** A 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 870 HIS C 18 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.051278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.033912 restraints weight = 129258.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.034834 restraints weight = 71738.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.035414 restraints weight = 49822.147| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14317 Z= 0.215 Angle : 0.647 10.777 19413 Z= 0.335 Chirality : 0.046 0.232 2103 Planarity : 0.004 0.048 2493 Dihedral : 4.807 18.256 1890 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.91 % Favored : 89.91 % Rotamer: Outliers : 0.19 % Allowed : 5.36 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.21), residues: 1685 helix: -1.30 (0.33), residues: 225 sheet: -0.80 (0.28), residues: 360 loop : -1.26 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 412 HIS 0.007 0.001 HIS B 841 PHE 0.016 0.001 PHE A 705 TYR 0.015 0.001 TYR B 708 ARG 0.005 0.001 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 314) hydrogen bonds : angle 7.23357 ( 792) SS BOND : bond 0.00306 ( 41) SS BOND : angle 1.02375 ( 82) covalent geometry : bond 0.00472 (14276) covalent geometry : angle 0.64474 (19331) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.9552 (tmm) cc_final: 0.9318 (tmm) REVERT: B 11 MET cc_start: 0.9243 (pmm) cc_final: 0.8895 (pmm) REVERT: B 98 MET cc_start: 0.9244 (mmp) cc_final: 0.9030 (mmp) REVERT: E 48 PHE cc_start: 0.8607 (m-80) cc_final: 0.8215 (m-80) outliers start: 3 outliers final: 0 residues processed: 54 average time/residue: 0.2251 time to fit residues: 20.6165 Evaluate side-chains 42 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN A 877 HIS B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.051301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.033804 restraints weight = 127799.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034789 restraints weight = 69190.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.035401 restraints weight = 47060.099| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14317 Z= 0.180 Angle : 0.623 11.218 19413 Z= 0.321 Chirality : 0.046 0.283 2103 Planarity : 0.004 0.052 2493 Dihedral : 4.781 19.511 1890 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.61 % Favored : 90.21 % Rotamer: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.21), residues: 1685 helix: -1.41 (0.33), residues: 226 sheet: -0.81 (0.28), residues: 362 loop : -1.32 (0.20), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 412 HIS 0.008 0.001 HIS B 841 PHE 0.017 0.001 PHE A 705 TYR 0.017 0.001 TYR B 708 ARG 0.004 0.000 ARG A 863 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 314) hydrogen bonds : angle 6.91978 ( 792) SS BOND : bond 0.00272 ( 41) SS BOND : angle 1.01172 ( 82) covalent geometry : bond 0.00396 (14276) covalent geometry : angle 0.62098 (19331) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 504 MET cc_start: 0.8898 (mmp) cc_final: 0.8581 (mmm) REVERT: B 11 MET cc_start: 0.9211 (pmm) cc_final: 0.8928 (pmm) REVERT: B 98 MET cc_start: 0.9206 (mmp) cc_final: 0.8910 (mmp) REVERT: E 48 PHE cc_start: 0.8618 (m-80) cc_final: 0.8219 (m-80) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.2338 time to fit residues: 21.5451 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 157 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 72 optimal weight: 40.0000 chunk 149 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 GLN A 691 GLN B 199 HIS B 230 ASN B 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.050612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.033014 restraints weight = 128897.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.033911 restraints weight = 71294.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.034478 restraints weight = 49696.334| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 14317 Z= 0.274 Angle : 0.700 10.507 19413 Z= 0.358 Chirality : 0.047 0.312 2103 Planarity : 0.004 0.044 2493 Dihedral : 5.006 21.293 1890 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.10 % Favored : 88.72 % Rotamer: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.21), residues: 1685 helix: -1.58 (0.32), residues: 226 sheet: -1.00 (0.27), residues: 381 loop : -1.38 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 412 HIS 0.008 0.001 HIS B 199 PHE 0.020 0.002 PHE A 705 TYR 0.016 0.002 TYR B 477 ARG 0.004 0.001 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 314) hydrogen bonds : angle 6.98011 ( 792) SS BOND : bond 0.00379 ( 41) SS BOND : angle 1.32295 ( 82) covalent geometry : bond 0.00601 (14276) covalent geometry : angle 0.69658 (19331) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.5972 (mmp) cc_final: 0.5573 (mmm) REVERT: A 294 MET cc_start: 0.9552 (tmm) cc_final: 0.9323 (tmm) REVERT: B 11 MET cc_start: 0.9119 (pmm) cc_final: 0.8829 (pmm) REVERT: E 48 PHE cc_start: 0.8635 (m-80) cc_final: 0.8248 (m-80) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.2158 time to fit residues: 19.1260 Evaluate side-chains 41 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 0.0370 chunk 6 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 50.0000 chunk 105 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 30.0000 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN A 610 GLN A 691 GLN ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.051911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.034486 restraints weight = 126183.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035472 restraints weight = 67282.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.036093 restraints weight = 45977.105| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14317 Z= 0.115 Angle : 0.608 11.145 19413 Z= 0.308 Chirality : 0.046 0.314 2103 Planarity : 0.004 0.053 2493 Dihedral : 4.691 19.501 1890 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.84 % Favored : 90.98 % Rotamer: Outliers : 0.13 % Allowed : 2.74 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.21), residues: 1685 helix: -1.42 (0.33), residues: 227 sheet: -0.83 (0.28), residues: 371 loop : -1.35 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 412 HIS 0.006 0.001 HIS B 841 PHE 0.027 0.001 PHE E 19 TYR 0.016 0.001 TYR B 708 ARG 0.008 0.000 ARG B 806 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 314) hydrogen bonds : angle 6.57686 ( 792) SS BOND : bond 0.00280 ( 41) SS BOND : angle 1.12776 ( 82) covalent geometry : bond 0.00256 (14276) covalent geometry : angle 0.60481 (19331) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.8632 (ppp) cc_final: 0.8423 (ppp) REVERT: A 38 MET cc_start: 0.5676 (mmp) cc_final: 0.4883 (mmt) REVERT: B 98 MET cc_start: 0.9080 (mmp) cc_final: 0.8808 (mmp) REVERT: E 48 PHE cc_start: 0.8611 (m-80) cc_final: 0.8213 (m-80) outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.2257 time to fit residues: 22.1941 Evaluate side-chains 43 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 45 optimal weight: 0.0980 chunk 83 optimal weight: 0.0010 chunk 125 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 overall best weight: 1.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.051457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.034183 restraints weight = 127300.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035104 restraints weight = 69788.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.035690 restraints weight = 48188.452| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14317 Z= 0.151 Angle : 0.604 10.722 19413 Z= 0.309 Chirality : 0.045 0.286 2103 Planarity : 0.004 0.065 2493 Dihedral : 4.649 19.657 1890 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.84 % Favored : 90.98 % Rotamer: Outliers : 0.06 % Allowed : 2.17 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.21), residues: 1685 helix: -1.35 (0.34), residues: 227 sheet: -0.83 (0.28), residues: 369 loop : -1.34 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 412 HIS 0.006 0.001 HIS B 841 PHE 0.017 0.001 PHE A 705 TYR 0.015 0.001 TYR B 708 ARG 0.006 0.000 ARG B 806 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 314) hydrogen bonds : angle 6.45120 ( 792) SS BOND : bond 0.00244 ( 41) SS BOND : angle 1.02091 ( 82) covalent geometry : bond 0.00339 (14276) covalent geometry : angle 0.60185 (19331) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.8630 (ppp) cc_final: 0.8421 (ppp) REVERT: A 38 MET cc_start: 0.5703 (mmp) cc_final: 0.4901 (mmt) REVERT: A 294 MET cc_start: 0.9497 (tmm) cc_final: 0.9277 (tmm) REVERT: B 11 MET cc_start: 0.9165 (pmm) cc_final: 0.8929 (pmm) REVERT: B 98 MET cc_start: 0.9173 (mmp) cc_final: 0.8774 (mmp) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.2282 time to fit residues: 20.5941 Evaluate side-chains 43 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 145 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 162 optimal weight: 0.0980 chunk 163 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.051843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.034492 restraints weight = 127589.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035486 restraints weight = 68376.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.036124 restraints weight = 46494.254| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14317 Z= 0.113 Angle : 0.596 11.083 19413 Z= 0.301 Chirality : 0.046 0.355 2103 Planarity : 0.004 0.054 2493 Dihedral : 4.533 19.490 1890 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.13 % Favored : 91.69 % Rotamer: Outliers : 0.06 % Allowed : 1.72 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.21), residues: 1685 helix: -1.30 (0.34), residues: 227 sheet: -0.72 (0.28), residues: 367 loop : -1.40 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 412 HIS 0.006 0.001 HIS B 841 PHE 0.030 0.001 PHE E 19 TYR 0.030 0.001 TYR C 59 ARG 0.004 0.000 ARG B 806 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 314) hydrogen bonds : angle 6.23321 ( 792) SS BOND : bond 0.00215 ( 41) SS BOND : angle 0.95980 ( 82) covalent geometry : bond 0.00251 (14276) covalent geometry : angle 0.59351 (19331) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.8554 (ppp) cc_final: 0.8287 (ppp) REVERT: A 38 MET cc_start: 0.5560 (mmp) cc_final: 0.4797 (mmt) REVERT: A 294 MET cc_start: 0.9479 (tmm) cc_final: 0.9253 (tmm) REVERT: B 98 MET cc_start: 0.9009 (mmp) cc_final: 0.8415 (mmp) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.2313 time to fit residues: 21.7229 Evaluate side-chains 42 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 148 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 156 optimal weight: 20.0000 chunk 34 optimal weight: 0.5980 chunk 166 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 87 optimal weight: 0.4980 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.051584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.034336 restraints weight = 125605.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035526 restraints weight = 74306.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.036515 restraints weight = 43839.047| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14317 Z= 0.146 Angle : 0.601 10.734 19413 Z= 0.304 Chirality : 0.045 0.328 2103 Planarity : 0.004 0.049 2493 Dihedral : 4.547 19.367 1890 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.84 % Favored : 90.98 % Rotamer: Outliers : 0.06 % Allowed : 0.57 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.21), residues: 1685 helix: -1.31 (0.34), residues: 228 sheet: -0.70 (0.28), residues: 365 loop : -1.34 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 412 HIS 0.005 0.001 HIS B 841 PHE 0.015 0.001 PHE A 705 TYR 0.014 0.001 TYR B 708 ARG 0.004 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 314) hydrogen bonds : angle 6.12368 ( 792) SS BOND : bond 0.00225 ( 41) SS BOND : angle 0.93117 ( 82) covalent geometry : bond 0.00328 (14276) covalent geometry : angle 0.59901 (19331) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.8469 (ppp) cc_final: 0.8216 (ppp) REVERT: A 38 MET cc_start: 0.5694 (mmp) cc_final: 0.4868 (mmt) REVERT: A 294 MET cc_start: 0.9504 (tmm) cc_final: 0.9258 (tmm) REVERT: B 98 MET cc_start: 0.9151 (mmp) cc_final: 0.8899 (mmp) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.2390 time to fit residues: 20.7685 Evaluate side-chains 42 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 158 optimal weight: 0.0770 chunk 107 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.051463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.034033 restraints weight = 126950.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.034974 restraints weight = 68518.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.035570 restraints weight = 47054.743| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14317 Z= 0.153 Angle : 0.608 11.286 19413 Z= 0.306 Chirality : 0.045 0.311 2103 Planarity : 0.004 0.049 2493 Dihedral : 4.574 19.021 1890 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.08 % Favored : 90.74 % Rotamer: Outliers : 0.06 % Allowed : 0.77 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.21), residues: 1685 helix: -1.31 (0.34), residues: 228 sheet: -0.68 (0.28), residues: 358 loop : -1.35 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 412 HIS 0.006 0.001 HIS B 841 PHE 0.026 0.001 PHE E 19 TYR 0.014 0.001 TYR B 708 ARG 0.004 0.000 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 314) hydrogen bonds : angle 6.11728 ( 792) SS BOND : bond 0.00234 ( 41) SS BOND : angle 0.92401 ( 82) covalent geometry : bond 0.00342 (14276) covalent geometry : angle 0.60587 (19331) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.8633 (ppp) cc_final: 0.8393 (ppp) REVERT: A 38 MET cc_start: 0.5778 (mmp) cc_final: 0.4968 (mmt) REVERT: A 294 MET cc_start: 0.9537 (tmm) cc_final: 0.9288 (tmm) REVERT: B 11 MET cc_start: 0.9152 (pmm) cc_final: 0.8950 (pmm) REVERT: B 98 MET cc_start: 0.9150 (mmp) cc_final: 0.8875 (mmp) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.2206 time to fit residues: 19.4551 Evaluate side-chains 42 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 133 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.051134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.034731 restraints weight = 127890.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.035029 restraints weight = 73477.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.035471 restraints weight = 57287.490| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14317 Z= 0.190 Angle : 0.632 10.704 19413 Z= 0.320 Chirality : 0.045 0.317 2103 Planarity : 0.004 0.049 2493 Dihedral : 4.678 19.257 1890 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.91 % Favored : 89.91 % Rotamer: Outliers : 0.06 % Allowed : 0.32 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.21), residues: 1685 helix: -1.34 (0.34), residues: 228 sheet: -0.77 (0.28), residues: 356 loop : -1.36 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 412 HIS 0.009 0.001 HIS B 199 PHE 0.020 0.001 PHE E 19 TYR 0.015 0.001 TYR C 59 ARG 0.005 0.000 ARG B 806 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 314) hydrogen bonds : angle 6.18463 ( 792) SS BOND : bond 0.00267 ( 41) SS BOND : angle 1.02370 ( 82) covalent geometry : bond 0.00423 (14276) covalent geometry : angle 0.62987 (19331) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.8387 (ppp) cc_final: 0.8149 (ppp) REVERT: A 38 MET cc_start: 0.5871 (mmp) cc_final: 0.4986 (mmt) REVERT: A 294 MET cc_start: 0.9541 (tmm) cc_final: 0.9308 (tmm) REVERT: B 11 MET cc_start: 0.9148 (pmm) cc_final: 0.8889 (pmm) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.2229 time to fit residues: 19.5403 Evaluate side-chains 42 residues out of total 1567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 157 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN A 691 GLN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.051047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.034083 restraints weight = 127467.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.034771 restraints weight = 80800.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.035101 restraints weight = 52256.031| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14317 Z= 0.187 Angle : 0.635 11.351 19413 Z= 0.320 Chirality : 0.046 0.306 2103 Planarity : 0.004 0.047 2493 Dihedral : 4.736 19.412 1890 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.61 % Favored : 90.21 % Rotamer: Outliers : 0.13 % Allowed : 0.45 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.21), residues: 1685 helix: -1.36 (0.34), residues: 229 sheet: -0.79 (0.28), residues: 355 loop : -1.37 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 412 HIS 0.010 0.001 HIS B 264 PHE 0.020 0.001 PHE E 19 TYR 0.014 0.001 TYR B 708 ARG 0.005 0.000 ARG B 806 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 314) hydrogen bonds : angle 6.23558 ( 792) SS BOND : bond 0.00262 ( 41) SS BOND : angle 1.03813 ( 82) covalent geometry : bond 0.00415 (14276) covalent geometry : angle 0.63225 (19331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4581.80 seconds wall clock time: 81 minutes 24.57 seconds (4884.57 seconds total)