Starting phenix.real_space_refine on Mon Jul 22 04:05:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4e_41880/07_2024/8u4e_41880_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4e_41880/07_2024/8u4e_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4e_41880/07_2024/8u4e_41880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4e_41880/07_2024/8u4e_41880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4e_41880/07_2024/8u4e_41880_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4e_41880/07_2024/8u4e_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 Residue "A PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 8.34, per 1000 atoms: 0.60 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 - 3.50 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 Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 2.4 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: 1.91 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: 4.91 Time building geometry restraints manager: 6.44 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: 98.36 - 105.91: 331 105.91 - 113.47: 7720 113.47 - 121.03: 6787 121.03 - 128.59: 4380 128.59 - 136.14: 113 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 2.520 nonbonded pdb=" NH2 ARG A 479 " pdb=" O PHE C 19 " model vdw 2.156 2.520 nonbonded pdb=" O SER B 890 " pdb=" OH TYR B 894 " model vdw 2.157 2.440 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.161 2.440 nonbonded pdb=" O LYS A 310 " pdb=" OG1 THR A 334 " model vdw 2.171 2.440 ... (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 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: 0.010 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 41.260 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.340 ------------------------------------------------------------------------------- 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 14276 Z= 0.187 Angle : 0.646 11.143 19331 Z= 0.336 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.594 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: 0.2984 time to fit residues: 24.7546 Evaluate side-chains 42 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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: 6.9990 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** 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 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 ASN B 230 ASN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 HIS ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14276 Z= 0.316 Angle : 0.634 10.878 19331 Z= 0.326 Chirality : 0.045 0.208 2103 Planarity : 0.004 0.043 2493 Dihedral : 4.816 18.760 1890 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.10 % Favored : 88.66 % Rotamer: Outliers : 0.13 % Allowed : 6.00 % Favored : 93.87 % 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: -1.71 (0.21), residues: 1685 helix: -1.23 (0.34), residues: 220 sheet: -0.77 (0.28), residues: 362 loop : -1.27 (0.20), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 412 HIS 0.008 0.001 HIS B 841 PHE 0.014 0.001 PHE A 705 TYR 0.016 0.001 TYR B 708 ARG 0.004 0.000 ARG B 451 *********************** 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 50 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.9142 (tmm) cc_final: 0.8917 (tmm) REVERT: A 294 MET cc_start: 0.9558 (tmm) cc_final: 0.9316 (tmm) REVERT: B 11 MET cc_start: 0.9175 (pmm) cc_final: 0.8843 (pmm) REVERT: B 98 MET cc_start: 0.9205 (mmp) cc_final: 0.8926 (mmp) REVERT: E 48 PHE cc_start: 0.8628 (m-80) cc_final: 0.8254 (m-80) outliers start: 2 outliers final: 0 residues processed: 50 average time/residue: 0.2165 time to fit residues: 18.5505 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 chunk 155 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** 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 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14276 Z= 0.215 Angle : 0.594 11.094 19331 Z= 0.303 Chirality : 0.045 0.230 2103 Planarity : 0.004 0.044 2493 Dihedral : 4.721 19.400 1890 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.91 % Favored : 89.85 % Rotamer: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % 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: -1.65 (0.21), residues: 1685 helix: -1.18 (0.35), residues: 222 sheet: -0.63 (0.29), residues: 357 loop : -1.27 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 412 HIS 0.007 0.001 HIS B 841 PHE 0.014 0.001 PHE A 705 TYR 0.019 0.001 TYR A 864 ARG 0.006 0.000 ARG B 806 *********************** 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 53 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.9174 (tmm) cc_final: 0.8933 (tmm) REVERT: A 294 MET cc_start: 0.9539 (tmm) cc_final: 0.9303 (tmm) REVERT: B 11 MET cc_start: 0.9159 (pmm) cc_final: 0.8938 (pmm) REVERT: E 48 PHE cc_start: 0.8629 (m-80) cc_final: 0.8255 (m-80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2564 time to fit residues: 22.5586 Evaluate side-chains 42 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 30.0000 chunk 74 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** 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 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14276 Z= 0.249 Angle : 0.600 10.889 19331 Z= 0.306 Chirality : 0.045 0.200 2103 Planarity : 0.004 0.051 2493 Dihedral : 4.708 19.329 1890 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.39 % Favored : 89.38 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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: -1.66 (0.21), residues: 1685 helix: -1.17 (0.34), residues: 228 sheet: -0.62 (0.28), residues: 357 loop : -1.28 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 412 HIS 0.008 0.001 HIS B 264 PHE 0.014 0.001 PHE A 705 TYR 0.015 0.001 TYR B 708 ARG 0.012 0.000 ARG B 806 *********************** 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 48 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.5829 (mmp) cc_final: 0.4889 (mmt) REVERT: A 294 MET cc_start: 0.9483 (tmm) cc_final: 0.9274 (tmm) REVERT: B 11 MET cc_start: 0.9180 (pmm) cc_final: 0.8963 (pmm) REVERT: E 48 PHE cc_start: 0.8618 (m-80) cc_final: 0.8241 (m-80) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2181 time to fit residues: 18.0151 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 30.0000 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** 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 470 ASN ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 GLN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14276 Z= 0.302 Angle : 0.627 11.353 19331 Z= 0.318 Chirality : 0.045 0.255 2103 Planarity : 0.004 0.043 2493 Dihedral : 4.772 19.537 1890 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.92 % Favored : 88.84 % Rotamer: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.55 % 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: -1.70 (0.21), residues: 1685 helix: -1.27 (0.34), residues: 228 sheet: -0.67 (0.28), residues: 358 loop : -1.29 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 412 HIS 0.006 0.001 HIS B 841 PHE 0.015 0.001 PHE A 705 TYR 0.028 0.001 TYR C 59 ARG 0.008 0.000 ARG B 806 *********************** 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 51 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.5877 (mmp) cc_final: 0.5005 (mmt) REVERT: A 294 MET cc_start: 0.9501 (tmm) cc_final: 0.9287 (tmm) REVERT: B 11 MET cc_start: 0.9197 (pmm) cc_final: 0.8967 (pmm) REVERT: E 48 PHE cc_start: 0.8660 (m-80) cc_final: 0.8291 (m-80) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.2315 time to fit residues: 19.8841 Evaluate side-chains 43 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 54 optimal weight: 0.1980 chunk 86 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 410 GLN ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14276 Z= 0.168 Angle : 0.582 10.986 19331 Z= 0.293 Chirality : 0.045 0.219 2103 Planarity : 0.003 0.045 2493 Dihedral : 4.588 20.134 1890 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.55 % Favored : 90.27 % Rotamer: Outliers : 0.13 % Allowed : 2.36 % Favored : 97.51 % 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: -1.71 (0.21), residues: 1685 helix: -1.20 (0.33), residues: 228 sheet: -0.64 (0.28), residues: 365 loop : -1.32 (0.20), residues: 1092 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 0.029 0.001 PHE E 19 TYR 0.015 0.001 TYR B 708 ARG 0.011 0.000 ARG B 451 *********************** 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 58 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.5745 (mmp) cc_final: 0.4908 (mmt) REVERT: A 294 MET cc_start: 0.9445 (tmm) cc_final: 0.9227 (tmm) REVERT: A 423 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: E 48 PHE cc_start: 0.8585 (m-80) cc_final: 0.8225 (m-80) outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.2259 time to fit residues: 22.0583 Evaluate side-chains 44 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 0.2980 chunk 164 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14276 Z= 0.219 Angle : 0.590 11.124 19331 Z= 0.298 Chirality : 0.045 0.214 2103 Planarity : 0.004 0.047 2493 Dihedral : 4.593 19.906 1890 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.79 % Favored : 90.03 % Rotamer: Outliers : 0.06 % Allowed : 1.91 % Favored : 98.02 % 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: -1.64 (0.21), residues: 1685 helix: -1.06 (0.35), residues: 224 sheet: -0.63 (0.29), residues: 358 loop : -1.28 (0.20), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 412 HIS 0.006 0.001 HIS B 841 PHE 0.014 0.001 PHE A 705 TYR 0.030 0.001 TYR C 59 ARG 0.008 0.000 ARG B 875 *********************** 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 49 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.5808 (mmp) cc_final: 0.4959 (mmt) REVERT: A 294 MET cc_start: 0.9462 (tmm) cc_final: 0.9249 (tmm) REVERT: E 48 PHE cc_start: 0.8525 (m-80) cc_final: 0.8154 (m-80) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.2375 time to fit residues: 19.4582 Evaluate side-chains 42 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 129 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14276 Z= 0.160 Angle : 0.578 10.875 19331 Z= 0.289 Chirality : 0.044 0.242 2103 Planarity : 0.003 0.046 2493 Dihedral : 4.500 19.126 1890 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.26 % Favored : 90.56 % Rotamer: Outliers : 0.06 % Allowed : 0.96 % Favored : 98.98 % 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: -1.65 (0.21), residues: 1685 helix: -1.05 (0.34), residues: 224 sheet: -0.57 (0.29), residues: 361 loop : -1.33 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 412 HIS 0.009 0.001 HIS B 841 PHE 0.028 0.001 PHE E 19 TYR 0.014 0.001 TYR B 708 ARG 0.007 0.000 ARG B 554 *********************** 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 52 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.5776 (mmp) cc_final: 0.4917 (mmt) REVERT: A 294 MET cc_start: 0.9467 (tmm) cc_final: 0.9246 (tmm) REVERT: E 48 PHE cc_start: 0.8503 (m-80) cc_final: 0.8129 (m-80) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.2661 time to fit residues: 22.1959 Evaluate side-chains 43 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 30.0000 chunk 144 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 100 optimal weight: 0.0050 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14276 Z= 0.192 Angle : 0.583 11.137 19331 Z= 0.292 Chirality : 0.044 0.225 2103 Planarity : 0.003 0.046 2493 Dihedral : 4.516 18.681 1890 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.73 % Favored : 90.09 % Rotamer: Outliers : 0.06 % Allowed : 0.89 % Favored : 99.04 % 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: -1.62 (0.21), residues: 1685 helix: -1.05 (0.34), residues: 224 sheet: -0.57 (0.28), residues: 364 loop : -1.29 (0.20), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 412 HIS 0.007 0.001 HIS B 841 PHE 0.022 0.001 PHE E 19 TYR 0.013 0.001 TYR B 708 ARG 0.004 0.000 ARG A 83 *********************** 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 54 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.5866 (mmp) cc_final: 0.4976 (mmt) REVERT: E 48 PHE cc_start: 0.8520 (m-80) cc_final: 0.8147 (m-80) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.2267 time to fit residues: 20.4520 Evaluate side-chains 42 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.0980 chunk 99 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14276 Z= 0.185 Angle : 0.584 10.882 19331 Z= 0.292 Chirality : 0.044 0.220 2103 Planarity : 0.003 0.046 2493 Dihedral : 4.516 20.361 1890 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.26 % Favored : 90.56 % 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: -1.60 (0.21), residues: 1685 helix: -1.02 (0.35), residues: 224 sheet: -0.53 (0.29), residues: 364 loop : -1.29 (0.20), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 412 HIS 0.009 0.001 HIS B 264 PHE 0.022 0.001 PHE E 19 TYR 0.013 0.001 TYR B 708 ARG 0.004 0.000 ARG B 806 ********************** 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 fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.5879 (mmp) cc_final: 0.4988 (mmt) REVERT: A 294 MET cc_start: 0.9463 (tmm) cc_final: 0.9208 (tmm) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.2831 time to fit residues: 23.7696 Evaluate side-chains 41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 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 = 0.3583 r_free = 0.3583 target = 0.050296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.032955 restraints weight = 132106.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.033754 restraints weight = 74569.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.034333 restraints weight = 52736.462| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.147 14276 Z= 0.620 Angle : 0.890 11.297 19331 Z= 0.451 Chirality : 0.050 0.236 2103 Planarity : 0.006 0.087 2493 Dihedral : 5.574 25.245 1890 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 36.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.64 % Favored : 87.18 % Rotamer: Outliers : 0.06 % Allowed : 0.64 % Favored : 99.30 % 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: -2.15 (0.21), residues: 1685 helix: -1.76 (0.31), residues: 227 sheet: -1.10 (0.27), residues: 389 loop : -1.51 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 412 HIS 0.012 0.002 HIS B 199 PHE 0.026 0.003 PHE D 26 TYR 0.025 0.003 TYR B 245 ARG 0.009 0.001 ARG B 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.92 seconds wall clock time: 41 minutes 26.74 seconds (2486.74 seconds total)