Starting phenix.real_space_refine on Wed Mar 4 14:05:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mqs_23951/03_2026/7mqs_23951.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqs_23951/03_2026/7mqs_23951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mqs_23951/03_2026/7mqs_23951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqs_23951/03_2026/7mqs_23951.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mqs_23951/03_2026/7mqs_23951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqs_23951/03_2026/7mqs_23951.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 8894 2.51 5 N 2403 2.21 5 O 2617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14028 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 6521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6521 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 762} Chain breaks: 6 Chain: "F" Number of atoms: 6563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6563 Classifications: {'peptide': 811} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 767} Chain breaks: 5 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "G" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "H" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Time building chain proxies: 3.18, per 1000 atoms: 0.23 Number of scatterers: 14028 At special positions: 0 Unit cell: (158.34, 101.01, 173.355, 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 114 16.00 O 2617 8.00 N 2403 7.00 C 8894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.03 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.02 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.04 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.04 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 647 " - pdb=" SG CYS E 860 " distance=2.03 Simple disulfide: pdb=" SG CYS E 786 " - pdb=" SG CYS E 795 " distance=2.03 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.03 Simple disulfide: pdb=" SG CYS F 192 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.04 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.02 Simple disulfide: pdb=" SG CYS F 647 " - pdb=" SG CYS F 860 " distance=2.04 Simple disulfide: pdb=" SG CYS F 786 " - pdb=" SG CYS F 795 " distance=2.03 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.02 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.02 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=2.05 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 19 " distance=2.04 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 11 " distance=2.03 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS H 7 " distance=2.02 Simple disulfide: pdb=" SG CYS G 20 " - pdb=" SG CYS H 19 " distance=2.04 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: 1.15 Conformation dependent library (CDL) restraints added in 509.0 milliseconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3288 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 33 sheets defined 13.5% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 255 through 266 Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 351 through 359 Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 496 through 500 removed outlier: 3.823A pdb=" N LEU E 500 " --> pdb=" O PHE E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 714 removed outlier: 3.670A pdb=" N GLU E 697 " --> pdb=" O LEU E 693 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER E 699 " --> pdb=" O GLU E 695 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER E 700 " --> pdb=" O LEU E 696 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG E 702 " --> pdb=" O GLU E 698 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 703 " --> pdb=" O SER E 699 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR E 708 " --> pdb=" O THR E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'F' and resid 16 through 24 removed outlier: 4.363A pdb=" N ARG F 19 " --> pdb=" O ASN F 16 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 20 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS F 21 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU F 22 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 23 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU F 24 " --> pdb=" O HIS F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 16 through 24' Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.798A pdb=" N PHE F 46 " --> pdb=" O PRO F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 255 through 265 removed outlier: 3.676A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 262 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS F 263 " --> pdb=" O CYS F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 350 through 358 removed outlier: 3.871A pdb=" N GLU F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 444 removed outlier: 3.739A pdb=" N ILE F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 707 removed outlier: 3.571A pdb=" N PHE F 701 " --> pdb=" O GLU F 697 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG F 702 " --> pdb=" O GLU F 698 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS F 703 " --> pdb=" O SER F 699 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 704 " --> pdb=" O SER F 700 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE F 705 " --> pdb=" O PHE F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 813 removed outlier: 3.874A pdb=" N ASP F 812 " --> pdb=" O ALA F 809 " (cutoff:3.500A) Processing helix chain 'F' and resid 862 through 870 removed outlier: 3.678A pdb=" N GLU F 869 " --> pdb=" O HIS F 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.947A pdb=" N LEU C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 23 " --> pdb=" O TYR C 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 18 Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 13 through 19 Processing helix chain 'H' and resid 9 through 19 removed outlier: 3.654A pdb=" N CYS H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 7 through 13 removed outlier: 5.595A pdb=" N HIS E 32 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP E 12 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN E 34 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 29 " --> pdb=" O MET E 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 7 through 13 removed outlier: 5.595A pdb=" N HIS E 32 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP E 12 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN E 34 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LEU E 62 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU E 33 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N PHE E 64 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE E 35 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU E 61 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N PHE E 96 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU E 63 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU E 93 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLU E 120 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE E 95 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 212 through 216 removed outlier: 3.819A pdb=" N ALA E 227 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ASN E 215 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N CYS E 225 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 232 Processing sheet with id=AA5, first strand: chain 'E' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'E' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'E' and resid 292 through 295 removed outlier: 3.519A pdb=" N ASN E 295 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU E 300 " --> pdb=" O ASN E 295 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 311 through 321 removed outlier: 10.321A pdb=" N VAL E 335 " --> pdb=" O HIS E 313 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N LEU E 315 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 9.836A pdb=" N ASN E 337 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY E 317 " --> pdb=" O ASN E 337 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE E 341 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N LYS E 369 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU E 340 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG E 371 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE E 342 " --> pdb=" O ARG E 371 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE E 427 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR E 401 " --> pdb=" O PHE E 427 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N HIS E 429 " --> pdb=" O TYR E 401 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU E 403 " --> pdb=" O HIS E 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 363 through 364 removed outlier: 4.012A pdb=" N ILE E 364 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 475 through 479 removed outlier: 3.744A pdb=" N ILE E 485 " --> pdb=" O MET E 553 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 532 through 534 removed outlier: 3.562A pdb=" N VAL E 532 " --> pdb=" O LEU E 505 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 505 " --> pdb=" O VAL E 532 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE E 503 " --> pdb=" O ILE E 534 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY E 502 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE E 565 " --> pdb=" O PHE E 506 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 588 " --> pdb=" O TYR E 562 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 564 " --> pdb=" O ILE E 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 611 through 614 Processing sheet with id=AB4, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.606A pdb=" N GLU E 760 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN E 788 " --> pdb=" O ARG E 794 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.606A pdb=" N GLU E 760 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 801 " --> pdb=" O ILE E 781 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 818 through 822 removed outlier: 3.524A pdb=" N HIS E 829 " --> pdb=" O GLU E 821 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 856 through 861 Processing sheet with id=AB8, first strand: chain 'E' and resid 856 through 861 removed outlier: 3.688A pdb=" N VAL E 884 " --> pdb=" O THR E 901 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 901 " --> pdb=" O VAL E 884 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 12 through 15 removed outlier: 4.439A pdb=" N ASN F 15 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET F 38 " --> pdb=" O ASN F 15 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL F 66 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU F 61 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE F 96 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU F 63 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU F 93 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLU F 120 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE F 95 " --> pdb=" O GLU F 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 28 through 29 removed outlier: 3.916A pdb=" N ILE F 57 " --> pdb=" O VAL F 81 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 171 through 173 removed outlier: 3.741A pdb=" N VAL F 179 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 212 through 216 removed outlier: 3.952A pdb=" N ALA F 227 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASN F 215 " --> pdb=" O CYS F 225 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N CYS F 225 " --> pdb=" O ASN F 215 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 231 through 233 Processing sheet with id=AC5, first strand: chain 'F' and resid 246 through 248 Processing sheet with id=AC6, first strand: chain 'F' and resid 278 through 279 Processing sheet with id=AC7, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AC8, first strand: chain 'F' and resid 311 through 321 removed outlier: 3.979A pdb=" N LEU F 314 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER F 339 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLU F 316 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N ILE F 341 " --> pdb=" O GLU F 316 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N GLU F 318 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N LEU F 403 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE F 370 " --> pdb=" O LEU F 403 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 311 through 321 removed outlier: 3.979A pdb=" N LEU F 314 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER F 339 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLU F 316 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N ILE F 341 " --> pdb=" O GLU F 316 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N GLU F 318 " --> pdb=" O ILE F 341 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 475 through 480 removed outlier: 3.881A pdb=" N ILE F 485 " --> pdb=" O MET F 553 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET F 553 " --> pdb=" O ILE F 485 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 530 through 534 removed outlier: 3.567A pdb=" N THR F 530 " --> pdb=" O TYR F 507 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR F 507 " --> pdb=" O THR F 530 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL F 532 " --> pdb=" O LEU F 505 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 505 " --> pdb=" O VAL F 532 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 567 " --> pdb=" O MET F 504 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 602 through 604 Processing sheet with id=AD4, first strand: chain 'F' and resid 759 through 762 removed outlier: 3.580A pdb=" N ALA F 799 " --> pdb=" O LEU F 783 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 819 through 822 Processing sheet with id=AD6, first strand: chain 'F' and resid 857 through 861 removed outlier: 4.229A pdb=" N LEU F 857 " --> pdb=" O TYR F 849 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR F 849 " --> pdb=" O LEU F 857 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU F 859 " --> pdb=" O VAL F 847 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 846 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: 2.39 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3196 1.33 - 1.46: 4217 1.46 - 1.59: 6804 1.59 - 1.72: 3 1.72 - 1.85: 136 Bond restraints: 14356 Sorted by residual: bond pdb=" C THR F 302 " pdb=" N PRO F 303 " ideal model delta sigma weight residual 1.332 1.403 -0.072 1.32e-02 5.74e+03 2.95e+01 bond pdb=" C THR E 790 " pdb=" N PRO E 791 " ideal model delta sigma weight residual 1.334 1.457 -0.124 2.34e-02 1.83e+03 2.79e+01 bond pdb=" C THR F 790 " pdb=" N PRO F 791 " ideal model delta sigma weight residual 1.334 1.434 -0.100 2.34e-02 1.83e+03 1.84e+01 bond pdb=" CB ASN F 349 " pdb=" CG ASN F 349 " ideal model delta sigma weight residual 1.516 1.613 -0.097 2.50e-02 1.60e+03 1.50e+01 bond pdb=" C LEU G 16 " pdb=" N GLU G 17 " ideal model delta sigma weight residual 1.333 1.386 -0.053 1.49e-02 4.50e+03 1.25e+01 ... (remaining 14351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.20: 19032 5.20 - 10.39: 365 10.39 - 15.59: 48 15.59 - 20.79: 8 20.79 - 25.98: 4 Bond angle restraints: 19457 Sorted by residual: angle pdb=" CA LEU E 37 " pdb=" CB LEU E 37 " pdb=" CG LEU E 37 " ideal model delta sigma weight residual 116.30 142.28 -25.98 3.50e+00 8.16e-02 5.51e+01 angle pdb=" C GLU F 469 " pdb=" N ASN F 470 " pdb=" CA ASN F 470 " ideal model delta sigma weight residual 121.54 135.41 -13.87 1.91e+00 2.74e-01 5.27e+01 angle pdb=" C PRO F 791 " pdb=" N GLU F 792 " pdb=" CA GLU F 792 " ideal model delta sigma weight residual 121.54 135.36 -13.82 1.91e+00 2.74e-01 5.24e+01 angle pdb=" CA ARG E 870 " pdb=" CB ARG E 870 " pdb=" CG ARG E 870 " ideal model delta sigma weight residual 114.10 128.39 -14.29 2.00e+00 2.50e-01 5.10e+01 angle pdb=" C THR F 578 " pdb=" N TYR F 579 " pdb=" CA TYR F 579 " ideal model delta sigma weight residual 121.54 135.15 -13.61 1.91e+00 2.74e-01 5.07e+01 ... (remaining 19452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 7570 17.32 - 34.64: 964 34.64 - 51.97: 160 51.97 - 69.29: 36 69.29 - 86.61: 12 Dihedral angle restraints: 8742 sinusoidal: 3654 harmonic: 5088 Sorted by residual: dihedral pdb=" CA THR F 578 " pdb=" C THR F 578 " pdb=" N TYR F 579 " pdb=" CA TYR F 579 " ideal model delta harmonic sigma weight residual 180.00 120.81 59.19 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CB CYS G 6 " pdb=" SG CYS G 6 " pdb=" SG CYS G 11 " pdb=" CB CYS G 11 " ideal model delta sinusoidal sigma weight residual 93.00 175.99 -82.99 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CA ASN E 111 " pdb=" C ASN E 111 " pdb=" N ILE E 112 " pdb=" CA ILE E 112 " ideal model delta harmonic sigma weight residual 180.00 137.85 42.15 0 5.00e+00 4.00e-02 7.11e+01 ... (remaining 8739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 2018 0.181 - 0.362: 81 0.362 - 0.543: 20 0.543 - 0.725: 8 0.725 - 0.906: 1 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CB ILE F 342 " pdb=" CA ILE F 342 " pdb=" CG1 ILE F 342 " pdb=" CG2 ILE F 342 " both_signs ideal model delta sigma weight residual False 2.64 1.74 0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CB ILE F 57 " pdb=" CA ILE F 57 " pdb=" CG1 ILE F 57 " pdb=" CG2 ILE F 57 " both_signs ideal model delta sigma weight residual False 2.64 1.95 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CB VAL E 712 " pdb=" CA VAL E 712 " pdb=" CG1 VAL E 712 " pdb=" CG2 VAL E 712 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.21e+01 ... (remaining 2125 not shown) Planarity restraints: 2511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 2 " 0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ILE A 2 " -0.078 2.00e-02 2.50e+03 pdb=" O ILE A 2 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL A 3 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 94 " -0.021 2.00e-02 2.50e+03 4.27e-02 1.83e+01 pdb=" C VAL F 94 " 0.074 2.00e-02 2.50e+03 pdb=" O VAL F 94 " -0.028 2.00e-02 2.50e+03 pdb=" N ILE F 95 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 708 " -0.004 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR F 708 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR F 708 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR F 708 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR F 708 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR F 708 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 708 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR F 708 " 0.001 2.00e-02 2.50e+03 ... (remaining 2508 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 5125 2.91 - 3.41: 10746 3.41 - 3.91: 25001 3.91 - 4.40: 24779 4.40 - 4.90: 42077 Nonbonded interactions: 107728 Sorted by model distance: nonbonded pdb=" O MET E 442 " pdb=" OG SER E 446 " model vdw 2.416 3.040 nonbonded pdb=" O VAL E 715 " pdb=" OG SER G 22 " model vdw 2.418 3.040 nonbonded pdb=" OE2 GLU E 698 " pdb=" OH TYR F 144 " model vdw 2.418 3.040 nonbonded pdb=" OG SER E 573 " pdb=" OE1 GLU E 575 " model vdw 2.419 3.040 nonbonded pdb=" OG SER F 481 " pdb=" O LYS F 484 " model vdw 2.420 3.040 ... (remaining 107723 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' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = (chain 'H' and resid 5 through 20) } ncs_group { reference = (chain 'E' and (resid 5 through 656 or resid 696 through 710 or resid 754 throug \ h 910)) selection = (chain 'F' and (resid 5 through 172 or resid 177 through 267 or resid 274 throug \ h 515 or resid 531 through 910)) } 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=0.50 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.720 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.015 0.124 14400 Z= 0.640 Angle : 1.727 25.984 19545 Z= 0.883 Chirality : 0.102 0.906 2128 Planarity : 0.011 0.098 2511 Dihedral : 15.001 86.609 5322 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.59 % Allowed : 9.64 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.17), residues: 1701 helix: -4.98 (0.10), residues: 236 sheet: -0.80 (0.30), residues: 282 loop : -2.77 (0.15), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 118 TYR 0.059 0.004 TYR F 708 PHE 0.053 0.005 PHE E 497 TRP 0.023 0.004 TRP F 897 HIS 0.013 0.002 HIS F 263 Details of bonding type rmsd covalent geometry : bond 0.01500 (14356) covalent geometry : angle 1.72558 (19457) SS BOND : bond 0.00601 ( 44) SS BOND : angle 1.97959 ( 88) hydrogen bonds : bond 0.25175 ( 283) hydrogen bonds : angle 11.34906 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 110 MET cc_start: 0.7856 (mpp) cc_final: 0.5668 (tpp) REVERT: E 382 PHE cc_start: 0.9112 (m-80) cc_final: 0.8269 (m-80) REVERT: E 849 TYR cc_start: 0.9183 (p90) cc_final: 0.8867 (p90) REVERT: E 859 LEU cc_start: 0.9189 (tp) cc_final: 0.8760 (pp) REVERT: F 38 MET cc_start: 0.7623 (mmp) cc_final: 0.7197 (mmp) REVERT: F 90 ASN cc_start: 0.7815 (p0) cc_final: 0.7579 (p0) REVERT: F 292 TYR cc_start: 0.8507 (m-80) cc_final: 0.8197 (m-80) REVERT: F 830 LEU cc_start: 0.8427 (tp) cc_final: 0.8095 (mm) REVERT: F 831 MET cc_start: 0.7627 (mpp) cc_final: 0.6950 (mpp) REVERT: D 15 LEU cc_start: 0.8957 (mm) cc_final: 0.8747 (mm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1022 time to fit residues: 20.6066 Evaluate side-chains 85 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 21 HIS E 209 HIS E 230 ASN ** E 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN E 627 HIS ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.071786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.055788 restraints weight = 105368.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.056079 restraints weight = 65243.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.056747 restraints weight = 51271.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.056849 restraints weight = 47344.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.057149 restraints weight = 41606.365| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14400 Z= 0.138 Angle : 0.713 14.953 19545 Z= 0.366 Chirality : 0.047 0.246 2128 Planarity : 0.005 0.069 2511 Dihedral : 7.075 41.555 1899 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.94 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.18), residues: 1701 helix: -3.73 (0.22), residues: 226 sheet: -0.43 (0.29), residues: 320 loop : -2.30 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 479 TYR 0.014 0.001 TYR F 91 PHE 0.014 0.002 PHE E 497 TRP 0.034 0.002 TRP E 251 HIS 0.004 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00293 (14356) covalent geometry : angle 0.71109 (19457) SS BOND : bond 0.00284 ( 44) SS BOND : angle 1.11155 ( 88) hydrogen bonds : bond 0.04938 ( 283) hydrogen bonds : angle 7.77751 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 83 ARG cc_start: 0.7930 (ttt90) cc_final: 0.7552 (tpp-160) REVERT: E 428 PHE cc_start: 0.9041 (m-10) cc_final: 0.8714 (m-10) REVERT: E 859 LEU cc_start: 0.8967 (tp) cc_final: 0.8701 (tt) REVERT: F 831 MET cc_start: 0.7518 (mpp) cc_final: 0.7144 (mpp) REVERT: G 4 GLU cc_start: 0.7738 (pm20) cc_final: 0.7341 (pm20) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1051 time to fit residues: 16.6283 Evaluate side-chains 77 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 97 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 143 optimal weight: 30.0000 chunk 162 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 ASN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 GLN F 90 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 GLN F 328 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 GLN F 417 HIS ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN C 21 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.068827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.053531 restraints weight = 108342.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.052984 restraints weight = 65733.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.053551 restraints weight = 58107.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.053706 restraints weight = 49585.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.053852 restraints weight = 46094.270| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14400 Z= 0.213 Angle : 0.755 11.904 19545 Z= 0.383 Chirality : 0.047 0.175 2128 Planarity : 0.005 0.048 2511 Dihedral : 6.604 44.200 1899 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.88 % Favored : 91.77 % Rotamer: Outliers : 0.32 % Allowed : 5.61 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.19), residues: 1701 helix: -2.50 (0.29), residues: 225 sheet: 0.04 (0.32), residues: 287 loop : -2.13 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 14 TYR 0.019 0.002 TYR F 512 PHE 0.031 0.002 PHE F 64 TRP 0.022 0.002 TRP E 414 HIS 0.007 0.001 HIS E 417 Details of bonding type rmsd covalent geometry : bond 0.00445 (14356) covalent geometry : angle 0.75390 (19457) SS BOND : bond 0.00363 ( 44) SS BOND : angle 0.92782 ( 88) hydrogen bonds : bond 0.04723 ( 283) hydrogen bonds : angle 7.07041 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 83 ARG cc_start: 0.7614 (ttt90) cc_final: 0.6962 (tpp-160) REVERT: E 330 LEU cc_start: 0.7695 (tp) cc_final: 0.7487 (tp) REVERT: E 386 ARG cc_start: 0.6704 (mmt180) cc_final: 0.6372 (tpt170) REVERT: E 844 LEU cc_start: 0.9366 (mm) cc_final: 0.8720 (mm) REVERT: E 859 LEU cc_start: 0.8963 (tp) cc_final: 0.8685 (tt) REVERT: F 322 ASP cc_start: 0.8522 (t0) cc_final: 0.8030 (t0) REVERT: F 642 PHE cc_start: 0.7259 (m-80) cc_final: 0.7004 (m-80) REVERT: F 806 MET cc_start: 0.6524 (ptp) cc_final: 0.6275 (ptp) REVERT: G 4 GLU cc_start: 0.7967 (pm20) cc_final: 0.7523 (pm20) outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.1058 time to fit residues: 16.6532 Evaluate side-chains 76 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 74 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 429 HIS F 440 HIS C 21 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.069730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.053706 restraints weight = 107563.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.053806 restraints weight = 71518.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.054352 restraints weight = 54038.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.054454 restraints weight = 53156.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.054674 restraints weight = 45302.859| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14400 Z= 0.139 Angle : 0.661 11.236 19545 Z= 0.336 Chirality : 0.046 0.213 2128 Planarity : 0.004 0.041 2511 Dihedral : 6.235 39.759 1899 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.70 % Favored : 92.95 % Rotamer: Outliers : 0.13 % Allowed : 3.47 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.19), residues: 1701 helix: -2.00 (0.31), residues: 227 sheet: -0.01 (0.31), residues: 295 loop : -1.98 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 887 TYR 0.020 0.001 TYR G 14 PHE 0.026 0.002 PHE E 88 TRP 0.022 0.002 TRP E 414 HIS 0.009 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00303 (14356) covalent geometry : angle 0.65974 (19457) SS BOND : bond 0.00318 ( 44) SS BOND : angle 0.97219 ( 88) hydrogen bonds : bond 0.03974 ( 283) hydrogen bonds : angle 6.64354 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 MET cc_start: 0.5715 (ppp) cc_final: 0.5377 (ppp) REVERT: E 859 LEU cc_start: 0.8893 (tp) cc_final: 0.8638 (tt) REVERT: F 98 MET cc_start: 0.8501 (tpp) cc_final: 0.8294 (tpp) REVERT: F 322 ASP cc_start: 0.8573 (t0) cc_final: 0.8188 (t0) REVERT: F 535 ASP cc_start: 0.9076 (p0) cc_final: 0.8848 (p0) REVERT: F 642 PHE cc_start: 0.7263 (m-80) cc_final: 0.7009 (m-80) REVERT: G 4 GLU cc_start: 0.7921 (pm20) cc_final: 0.7457 (pm20) outliers start: 2 outliers final: 1 residues processed: 101 average time/residue: 0.0976 time to fit residues: 15.5795 Evaluate side-chains 77 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 140 optimal weight: 0.0270 chunk 127 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 124 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 407 ASN F 90 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 276 GLN C 21 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.070466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.053053 restraints weight = 106086.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.054592 restraints weight = 71287.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.055467 restraints weight = 46297.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.055613 restraints weight = 40463.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.055720 restraints weight = 37538.240| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14400 Z= 0.106 Angle : 0.636 11.916 19545 Z= 0.320 Chirality : 0.046 0.247 2128 Planarity : 0.003 0.042 2511 Dihedral : 5.874 38.943 1899 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.88 % Favored : 91.77 % Rotamer: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.20), residues: 1701 helix: -1.66 (0.33), residues: 228 sheet: -0.17 (0.30), residues: 321 loop : -1.84 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 65 TYR 0.015 0.001 TYR A 14 PHE 0.026 0.001 PHE E 88 TRP 0.022 0.001 TRP E 251 HIS 0.007 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00233 (14356) covalent geometry : angle 0.63431 (19457) SS BOND : bond 0.00212 ( 44) SS BOND : angle 0.86862 ( 88) hydrogen bonds : bond 0.03729 ( 283) hydrogen bonds : angle 6.32127 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 MET cc_start: 0.5114 (ppp) cc_final: 0.4754 (ppp) REVERT: E 382 PHE cc_start: 0.9060 (m-10) cc_final: 0.8519 (m-80) REVERT: E 413 ASP cc_start: 0.7810 (t0) cc_final: 0.7410 (p0) REVERT: E 428 PHE cc_start: 0.8970 (m-80) cc_final: 0.8746 (m-10) REVERT: E 859 LEU cc_start: 0.9019 (tp) cc_final: 0.8632 (tt) REVERT: F 98 MET cc_start: 0.8651 (tpp) cc_final: 0.8400 (tpp) REVERT: F 322 ASP cc_start: 0.8649 (t0) cc_final: 0.8248 (t0) REVERT: F 535 ASP cc_start: 0.9114 (p0) cc_final: 0.8576 (t70) REVERT: F 642 PHE cc_start: 0.7181 (m-80) cc_final: 0.6793 (m-80) REVERT: G 4 GLU cc_start: 0.7819 (pm20) cc_final: 0.7516 (pm20) outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 0.0966 time to fit residues: 15.9732 Evaluate side-chains 81 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS ** E 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 561 GLN E 635 GLN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 HIS ** F 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.065549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.049805 restraints weight = 112078.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.050117 restraints weight = 70101.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.050134 restraints weight = 63105.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.050175 restraints weight = 61164.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.050792 restraints weight = 54361.899| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 14400 Z= 0.352 Angle : 0.929 12.545 19545 Z= 0.466 Chirality : 0.050 0.196 2128 Planarity : 0.006 0.072 2511 Dihedral : 6.829 43.608 1899 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.76 % Favored : 88.95 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.20), residues: 1701 helix: -1.83 (0.30), residues: 231 sheet: -0.35 (0.30), residues: 297 loop : -1.94 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 554 TYR 0.034 0.003 TYR F 512 PHE 0.036 0.003 PHE F 89 TRP 0.026 0.003 TRP E 414 HIS 0.011 0.002 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00743 (14356) covalent geometry : angle 0.92672 (19457) SS BOND : bond 0.00497 ( 44) SS BOND : angle 1.27500 ( 88) hydrogen bonds : bond 0.05343 ( 283) hydrogen bonds : angle 7.19791 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 93 LEU cc_start: 0.9299 (mm) cc_final: 0.9071 (tp) REVERT: E 844 LEU cc_start: 0.9295 (mm) cc_final: 0.8872 (mm) REVERT: E 859 LEU cc_start: 0.8994 (tp) cc_final: 0.8674 (tt) REVERT: F 38 MET cc_start: 0.8797 (mmm) cc_final: 0.8240 (mmm) REVERT: F 98 MET cc_start: 0.8772 (tpp) cc_final: 0.8474 (tpp) REVERT: F 642 PHE cc_start: 0.7286 (m-80) cc_final: 0.6995 (m-80) REVERT: G 4 GLU cc_start: 0.8122 (pm20) cc_final: 0.7898 (pm20) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0861 time to fit residues: 12.8199 Evaluate side-chains 70 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 131 optimal weight: 0.0050 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 154 optimal weight: 9.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN ** E 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 561 GLN E 610 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.067876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.052465 restraints weight = 109392.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.052397 restraints weight = 68012.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.052883 restraints weight = 56182.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.053100 restraints weight = 50267.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.053228 restraints weight = 45502.132| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14400 Z= 0.157 Angle : 0.691 11.934 19545 Z= 0.350 Chirality : 0.047 0.206 2128 Planarity : 0.004 0.071 2511 Dihedral : 6.271 41.856 1899 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.11 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.20), residues: 1701 helix: -1.60 (0.32), residues: 240 sheet: -0.23 (0.30), residues: 307 loop : -1.86 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 873 TYR 0.016 0.002 TYR G 14 PHE 0.028 0.002 PHE E 88 TRP 0.025 0.002 TRP F 414 HIS 0.007 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00345 (14356) covalent geometry : angle 0.68976 (19457) SS BOND : bond 0.00311 ( 44) SS BOND : angle 1.00050 ( 88) hydrogen bonds : bond 0.04097 ( 283) hydrogen bonds : angle 6.59165 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 11 MET cc_start: 0.5467 (ppp) cc_final: 0.5088 (ppp) REVERT: E 859 LEU cc_start: 0.8898 (tp) cc_final: 0.8561 (tt) REVERT: G 4 GLU cc_start: 0.8195 (pm20) cc_final: 0.7828 (pm20) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0839 time to fit residues: 13.2569 Evaluate side-chains 70 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 166 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 0.0270 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN F 15 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 GLN ** F 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 HIS C 21 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.068273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.052886 restraints weight = 108889.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.052802 restraints weight = 65298.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.053254 restraints weight = 55211.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.053528 restraints weight = 48351.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.053754 restraints weight = 43848.939| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14400 Z= 0.136 Angle : 0.687 12.745 19545 Z= 0.343 Chirality : 0.047 0.290 2128 Planarity : 0.004 0.055 2511 Dihedral : 6.027 41.658 1899 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.82 % Favored : 89.89 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.20), residues: 1701 helix: -1.38 (0.33), residues: 240 sheet: -0.08 (0.30), residues: 307 loop : -1.79 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 885 TYR 0.020 0.001 TYR G 14 PHE 0.028 0.002 PHE E 88 TRP 0.025 0.002 TRP F 414 HIS 0.006 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00300 (14356) covalent geometry : angle 0.68579 (19457) SS BOND : bond 0.00315 ( 44) SS BOND : angle 0.88200 ( 88) hydrogen bonds : bond 0.03871 ( 283) hydrogen bonds : angle 6.35229 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 LEU cc_start: 0.8996 (mt) cc_final: 0.8678 (mt) REVERT: E 859 LEU cc_start: 0.8968 (tp) cc_final: 0.8571 (tt) REVERT: G 4 GLU cc_start: 0.8168 (pm20) cc_final: 0.7790 (pm20) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0816 time to fit residues: 13.2490 Evaluate side-chains 71 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 18 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 HIS E 34 GLN E 199 HIS ** E 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.066511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.050731 restraints weight = 109840.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.051264 restraints weight = 67777.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.051455 restraints weight = 56144.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.051495 restraints weight = 52038.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.051651 restraints weight = 48145.641| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14400 Z= 0.229 Angle : 0.766 12.416 19545 Z= 0.382 Chirality : 0.048 0.252 2128 Planarity : 0.004 0.059 2511 Dihedral : 6.313 43.751 1899 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.64 % Favored : 89.07 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.20), residues: 1701 helix: -1.43 (0.32), residues: 244 sheet: -0.08 (0.30), residues: 290 loop : -1.85 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 86 TYR 0.022 0.002 TYR F 579 PHE 0.023 0.002 PHE E 89 TRP 0.024 0.002 TRP F 414 HIS 0.011 0.001 HIS E 32 Details of bonding type rmsd covalent geometry : bond 0.00496 (14356) covalent geometry : angle 0.76519 (19457) SS BOND : bond 0.00392 ( 44) SS BOND : angle 0.96339 ( 88) hydrogen bonds : bond 0.04373 ( 283) hydrogen bonds : angle 6.62341 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 109 LEU cc_start: 0.8906 (mt) cc_final: 0.8688 (mt) REVERT: E 859 LEU cc_start: 0.8939 (tp) cc_final: 0.8612 (tt) REVERT: F 98 MET cc_start: 0.9004 (tpt) cc_final: 0.8786 (tpp) REVERT: G 4 GLU cc_start: 0.8212 (pm20) cc_final: 0.7744 (tm-30) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0811 time to fit residues: 12.0483 Evaluate side-chains 71 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 165 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 132 optimal weight: 0.0470 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 263 HIS E 276 GLN E 407 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS F 343 ASN ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.068716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.052838 restraints weight = 106668.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.052620 restraints weight = 70933.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.053291 restraints weight = 54450.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.053398 restraints weight = 51621.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.053654 restraints weight = 43681.827| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14400 Z= 0.112 Angle : 0.678 13.442 19545 Z= 0.335 Chirality : 0.047 0.271 2128 Planarity : 0.004 0.046 2511 Dihedral : 5.904 40.187 1899 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.58 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.20), residues: 1701 helix: -1.37 (0.33), residues: 244 sheet: 0.07 (0.31), residues: 294 loop : -1.75 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 885 TYR 0.017 0.001 TYR G 14 PHE 0.019 0.001 PHE E 89 TRP 0.028 0.002 TRP F 414 HIS 0.005 0.001 HIS E 247 Details of bonding type rmsd covalent geometry : bond 0.00254 (14356) covalent geometry : angle 0.67639 (19457) SS BOND : bond 0.00264 ( 44) SS BOND : angle 0.89258 ( 88) hydrogen bonds : bond 0.03738 ( 283) hydrogen bonds : angle 6.28540 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 MET cc_start: 0.5645 (ppp) cc_final: 0.5435 (ppp) REVERT: E 93 LEU cc_start: 0.9471 (mm) cc_final: 0.9166 (tp) REVERT: E 109 LEU cc_start: 0.8836 (mt) cc_final: 0.8524 (mt) REVERT: E 859 LEU cc_start: 0.8946 (tp) cc_final: 0.8586 (tt) REVERT: F 38 MET cc_start: 0.8520 (mmm) cc_final: 0.8318 (mmp) REVERT: F 98 MET cc_start: 0.8829 (tpt) cc_final: 0.8205 (tpp) REVERT: F 535 ASP cc_start: 0.8965 (p0) cc_final: 0.8757 (p0) REVERT: G 4 GLU cc_start: 0.8072 (pm20) cc_final: 0.7700 (pm20) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0936 time to fit residues: 15.1810 Evaluate side-chains 77 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 0.0670 chunk 113 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 chunk 92 optimal weight: 0.2980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 407 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN F 627 HIS ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 858 HIS C 21 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.069721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.054078 restraints weight = 107442.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.053945 restraints weight = 68766.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.054511 restraints weight = 53916.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.054709 restraints weight = 50086.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.054853 restraints weight = 42636.620| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14400 Z= 0.103 Angle : 0.655 13.348 19545 Z= 0.323 Chirality : 0.047 0.268 2128 Planarity : 0.004 0.043 2511 Dihedral : 5.643 39.243 1899 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.41 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.20), residues: 1701 helix: -1.35 (0.32), residues: 243 sheet: 0.25 (0.32), residues: 287 loop : -1.69 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 850 TYR 0.026 0.001 TYR F 708 PHE 0.023 0.002 PHE E 428 TRP 0.022 0.002 TRP F 414 HIS 0.005 0.001 HIS E 247 Details of bonding type rmsd covalent geometry : bond 0.00230 (14356) covalent geometry : angle 0.65379 (19457) SS BOND : bond 0.00227 ( 44) SS BOND : angle 0.82248 ( 88) hydrogen bonds : bond 0.03507 ( 283) hydrogen bonds : angle 6.13367 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2138.07 seconds wall clock time: 37 minutes 44.38 seconds (2264.38 seconds total)