Starting phenix.real_space_refine on Mon Dec 30 22:22:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mqs_23951/12_2024/7mqs_23951.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqs_23951/12_2024/7mqs_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mqs_23951/12_2024/7mqs_23951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqs_23951/12_2024/7mqs_23951.map" model { file = "/net/cci-nas-00/data/ceres_data/7mqs_23951/12_2024/7mqs_23951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqs_23951/12_2024/7mqs_23951.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.13, per 1000 atoms: 0.58 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: 3.08 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.83 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: 4.87 Time building geometry restraints manager: 3.70 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: 1.200 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.690 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.280 ------------------------------------------------------------------------------- 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 14356 Z= 0.982 Angle : 1.726 25.984 19457 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.004 TRP F 897 HIS 0.013 0.002 HIS F 263 PHE 0.053 0.005 PHE E 497 TYR 0.059 0.004 TYR F 708 ARG 0.012 0.001 ARG E 118 *********************** 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 : 1.751 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: 0.7816 (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: 0.2613 time to fit residues: 51.4511 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 : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 40.0000 chunk 154 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 21 HIS ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 HIS E 230 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 627 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14356 Z= 0.345 Angle : 0.831 14.596 19457 Z= 0.425 Chirality : 0.048 0.211 2128 Planarity : 0.006 0.063 2511 Dihedral : 7.356 45.013 1899 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.05 % Favored : 92.53 % Rotamer: Outliers : 0.06 % Allowed : 6.30 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.18), residues: 1701 helix: -3.44 (0.23), residues: 220 sheet: -0.56 (0.30), residues: 309 loop : -2.25 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP E 251 HIS 0.007 0.002 HIS E 199 PHE 0.022 0.002 PHE E 475 TYR 0.021 0.002 TYR B 16 ARG 0.007 0.001 ARG E 118 *********************** 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 95 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 MET cc_start: 0.4874 (ppp) cc_final: 0.4555 (ppp) REVERT: E 428 PHE cc_start: 0.9081 (m-10) cc_final: 0.8756 (m-10) REVERT: E 844 LEU cc_start: 0.9587 (mm) cc_final: 0.9043 (mm) REVERT: E 859 LEU cc_start: 0.9046 (tp) cc_final: 0.8798 (tt) REVERT: F 831 MET cc_start: 0.7231 (mpp) cc_final: 0.6847 (mpp) REVERT: G 4 GLU cc_start: 0.8122 (pm20) cc_final: 0.7669 (pm20) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.2617 time to fit residues: 38.6530 Evaluate side-chains 66 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.0020 chunk 47 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 154 optimal weight: 20.0000 chunk 167 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 124 optimal weight: 0.4980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 ASN E 405 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14356 Z= 0.150 Angle : 0.659 11.873 19457 Z= 0.335 Chirality : 0.047 0.196 2128 Planarity : 0.004 0.056 2511 Dihedral : 6.552 43.907 1899 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.17 % Favored : 93.42 % Rotamer: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.19), residues: 1701 helix: -2.69 (0.28), residues: 222 sheet: -0.13 (0.31), residues: 299 loop : -2.15 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 414 HIS 0.004 0.001 HIS E 199 PHE 0.029 0.001 PHE E 88 TYR 0.012 0.001 TYR F 91 ARG 0.004 0.000 ARG E 780 *********************** 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 100 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 83 ARG cc_start: 0.8057 (ttt90) cc_final: 0.7428 (tpp-160) REVERT: E 413 ASP cc_start: 0.7727 (t0) cc_final: 0.7306 (p0) REVERT: E 844 LEU cc_start: 0.9127 (mm) cc_final: 0.8544 (mm) REVERT: E 859 LEU cc_start: 0.9037 (tp) cc_final: 0.8787 (tt) REVERT: G 4 GLU cc_start: 0.7887 (pm20) cc_final: 0.7444 (pm20) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.2558 time to fit residues: 40.6032 Evaluate side-chains 70 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.0010 chunk 116 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 164 optimal weight: 0.0870 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 overall best weight: 0.7568 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14356 Z= 0.148 Angle : 0.631 12.141 19457 Z= 0.319 Chirality : 0.046 0.213 2128 Planarity : 0.004 0.048 2511 Dihedral : 6.058 42.616 1899 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.47 % Favored : 93.12 % Rotamer: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.19), residues: 1701 helix: -2.20 (0.30), residues: 226 sheet: 0.00 (0.30), residues: 302 loop : -1.97 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 414 HIS 0.008 0.001 HIS E 199 PHE 0.028 0.001 PHE E 88 TYR 0.015 0.001 TYR F 3 ARG 0.003 0.000 ARG E 409 *********************** 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 99 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 382 PHE cc_start: 0.9084 (m-10) cc_final: 0.8517 (m-80) REVERT: E 413 ASP cc_start: 0.7852 (t0) cc_final: 0.7409 (p0) REVERT: E 859 LEU cc_start: 0.9020 (tp) cc_final: 0.8771 (tt) REVERT: F 98 MET cc_start: 0.8380 (tpt) cc_final: 0.8163 (tpp) REVERT: F 535 ASP cc_start: 0.9032 (p0) cc_final: 0.8810 (p0) REVERT: G 4 GLU cc_start: 0.7863 (pm20) cc_final: 0.7405 (pm20) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.2307 time to fit residues: 36.2025 Evaluate side-chains 73 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.7980 chunk 93 optimal weight: 0.0050 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 140 optimal weight: 0.0270 chunk 113 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 147 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 overall best weight: 0.7454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 407 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14356 Z= 0.148 Angle : 0.617 11.920 19457 Z= 0.311 Chirality : 0.046 0.250 2128 Planarity : 0.003 0.046 2511 Dihedral : 5.778 41.831 1899 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.82 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.19), residues: 1701 helix: -1.86 (0.31), residues: 236 sheet: -0.02 (0.30), residues: 311 loop : -1.90 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 251 HIS 0.006 0.001 HIS E 199 PHE 0.027 0.001 PHE E 88 TYR 0.013 0.001 TYR F 430 ARG 0.006 0.000 ARG E 887 *********************** 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 100 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: E 413 ASP cc_start: 0.7753 (t0) cc_final: 0.7258 (p0) REVERT: E 428 PHE cc_start: 0.9064 (m-10) cc_final: 0.8775 (m-10) REVERT: E 859 LEU cc_start: 0.9142 (tp) cc_final: 0.8769 (tt) REVERT: F 98 MET cc_start: 0.8336 (tpt) cc_final: 0.8126 (tpp) REVERT: F 535 ASP cc_start: 0.8933 (p0) cc_final: 0.7834 (t70) REVERT: F 642 PHE cc_start: 0.7200 (m-80) cc_final: 0.6810 (m-80) REVERT: D 15 LEU cc_start: 0.8937 (mm) cc_final: 0.8733 (mm) REVERT: G 4 GLU cc_start: 0.7943 (pm20) cc_final: 0.7512 (pm20) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2300 time to fit residues: 37.7372 Evaluate side-chains 73 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 86 optimal weight: 4.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- 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 90 ASN ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 610 GLN ** F 32 HIS ** 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 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14356 Z= 0.311 Angle : 0.750 11.360 19457 Z= 0.377 Chirality : 0.047 0.176 2128 Planarity : 0.005 0.078 2511 Dihedral : 6.123 46.730 1899 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.88 % Favored : 90.77 % Rotamer: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.20), residues: 1701 helix: -1.60 (0.32), residues: 241 sheet: -0.11 (0.30), residues: 305 loop : -1.81 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 414 HIS 0.008 0.001 HIS E 199 PHE 0.027 0.002 PHE F 64 TYR 0.021 0.002 TYR F 512 ARG 0.012 0.001 ARG E 885 *********************** 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 96 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 98 MET cc_start: 0.8499 (mmp) cc_final: 0.7448 (mmp) REVERT: E 382 PHE cc_start: 0.9076 (m-10) cc_final: 0.8766 (m-80) REVERT: E 844 LEU cc_start: 0.9389 (mm) cc_final: 0.9188 (mm) REVERT: E 859 LEU cc_start: 0.9050 (tp) cc_final: 0.8746 (tt) REVERT: F 38 MET cc_start: 0.8864 (mmm) cc_final: 0.8189 (mmm) REVERT: F 642 PHE cc_start: 0.7334 (m-80) cc_final: 0.7051 (m-80) REVERT: G 4 GLU cc_start: 0.7931 (pm20) cc_final: 0.7610 (pm20) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.2082 time to fit residues: 33.2078 Evaluate side-chains 73 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 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 263 HIS ** F 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 HIS ** F 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14356 Z= 0.256 Angle : 0.691 11.255 19457 Z= 0.351 Chirality : 0.046 0.170 2128 Planarity : 0.004 0.061 2511 Dihedral : 6.060 47.432 1899 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.20), residues: 1701 helix: -1.39 (0.33), residues: 235 sheet: -0.10 (0.31), residues: 290 loop : -1.72 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 414 HIS 0.007 0.001 HIS E 199 PHE 0.029 0.002 PHE E 88 TYR 0.017 0.002 TYR F 512 ARG 0.004 0.001 ARG F 873 *********************** 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 97 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 428 PHE cc_start: 0.9039 (m-10) cc_final: 0.8745 (m-10) REVERT: E 859 LEU cc_start: 0.9039 (tp) cc_final: 0.8721 (tt) REVERT: F 38 MET cc_start: 0.8861 (mmm) cc_final: 0.8329 (mmm) REVERT: F 98 MET cc_start: 0.8526 (tpp) cc_final: 0.8248 (tpp) REVERT: G 4 GLU cc_start: 0.8031 (pm20) cc_final: 0.7651 (pm20) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2058 time to fit residues: 33.9478 Evaluate side-chains 74 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 128 optimal weight: 0.3980 chunk 149 optimal weight: 8.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 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 276 GLN ** F 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 627 HIS ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14356 Z= 0.177 Angle : 0.651 12.139 19457 Z= 0.326 Chirality : 0.046 0.285 2128 Planarity : 0.004 0.045 2511 Dihedral : 5.862 45.169 1899 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.82 % Favored : 90.83 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.20), residues: 1701 helix: -1.27 (0.33), residues: 241 sheet: -0.07 (0.30), residues: 309 loop : -1.69 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 414 HIS 0.005 0.001 HIS E 199 PHE 0.030 0.002 PHE E 88 TYR 0.013 0.001 TYR G 14 ARG 0.003 0.000 ARG F 554 *********************** 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 100 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.636 Fit side-chains revert: symmetry clash REVERT: E 382 PHE cc_start: 0.9065 (m-10) cc_final: 0.8835 (m-80) REVERT: E 428 PHE cc_start: 0.8996 (m-10) cc_final: 0.8692 (m-10) REVERT: E 844 LEU cc_start: 0.9372 (mm) cc_final: 0.9134 (mm) REVERT: E 847 VAL cc_start: 0.9590 (t) cc_final: 0.9386 (t) REVERT: E 859 LEU cc_start: 0.9082 (tp) cc_final: 0.8669 (tt) REVERT: F 38 MET cc_start: 0.8725 (mmm) cc_final: 0.8247 (mmm) REVERT: F 535 ASP cc_start: 0.8119 (p0) cc_final: 0.7616 (t70) REVERT: D 15 LEU cc_start: 0.8960 (mm) cc_final: 0.8743 (mm) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2047 time to fit residues: 33.9591 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 : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 152 optimal weight: 20.0000 chunk 91 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 137 optimal weight: 30.0000 chunk 144 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 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 34 GLN ** E 263 HIS ** 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 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14356 Z= 0.175 Angle : 0.655 12.432 19457 Z= 0.328 Chirality : 0.046 0.266 2128 Planarity : 0.004 0.046 2511 Dihedral : 5.749 44.546 1899 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.35 % Favored : 91.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1701 helix: -1.28 (0.33), residues: 246 sheet: 0.09 (0.30), residues: 302 loop : -1.69 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 414 HIS 0.005 0.001 HIS E 247 PHE 0.029 0.001 PHE E 88 TYR 0.013 0.001 TYR G 14 ARG 0.003 0.000 ARG E 19 *********************** 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 95 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.875 Fit side-chains revert: symmetry clash REVERT: E 428 PHE cc_start: 0.8970 (m-10) cc_final: 0.8666 (m-10) REVERT: E 844 LEU cc_start: 0.9329 (mm) cc_final: 0.9085 (mm) REVERT: E 859 LEU cc_start: 0.9043 (tp) cc_final: 0.8681 (tt) REVERT: F 38 MET cc_start: 0.8745 (mmm) cc_final: 0.8286 (mmm) REVERT: F 535 ASP cc_start: 0.8287 (p0) cc_final: 0.7495 (t70) REVERT: D 15 LEU cc_start: 0.8916 (mm) cc_final: 0.8703 (mm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2067 time to fit residues: 33.2745 Evaluate side-chains 69 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 0.0060 chunk 14 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 0.0980 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 ** E 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 264 HIS ** F 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 HIS C 21 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14356 Z= 0.164 Angle : 0.645 12.613 19457 Z= 0.323 Chirality : 0.046 0.250 2128 Planarity : 0.004 0.039 2511 Dihedral : 5.641 43.593 1899 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.20), residues: 1701 helix: -1.23 (0.33), residues: 246 sheet: 0.24 (0.31), residues: 301 loop : -1.71 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 414 HIS 0.005 0.001 HIS E 247 PHE 0.030 0.001 PHE E 88 TYR 0.015 0.001 TYR F 708 ARG 0.004 0.000 ARG E 19 ********************** 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 97 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.835 Fit side-chains revert: symmetry clash REVERT: E 98 MET cc_start: 0.8248 (mmp) cc_final: 0.7968 (mmp) REVERT: E 428 PHE cc_start: 0.8945 (m-10) cc_final: 0.8650 (m-10) REVERT: E 845 TYR cc_start: 0.8807 (m-80) cc_final: 0.8560 (m-80) REVERT: E 859 LEU cc_start: 0.9050 (tp) cc_final: 0.8690 (tt) REVERT: F 38 MET cc_start: 0.8691 (mmm) cc_final: 0.8348 (mmm) REVERT: F 535 ASP cc_start: 0.8335 (p0) cc_final: 0.7514 (t70) REVERT: D 10 GLU cc_start: 0.9244 (mp0) cc_final: 0.8832 (pm20) REVERT: D 11 LEU cc_start: 0.9045 (mt) cc_final: 0.8469 (mt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2073 time to fit residues: 34.2140 Evaluate side-chains 73 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 635 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 HIS ** 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 = 0.3783 r_free = 0.3783 target = 0.069260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.053410 restraints weight = 104711.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.053312 restraints weight = 69161.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.053632 restraints weight = 57771.945| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14356 Z= 0.196 Angle : 0.658 12.287 19457 Z= 0.329 Chirality : 0.046 0.236 2128 Planarity : 0.004 0.037 2511 Dihedral : 5.674 44.470 1899 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.94 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.20), residues: 1701 helix: -1.17 (0.33), residues: 246 sheet: 0.25 (0.31), residues: 301 loop : -1.68 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 414 HIS 0.007 0.001 HIS E 32 PHE 0.022 0.002 PHE E 88 TYR 0.019 0.001 TYR E 60 ARG 0.011 0.000 ARG E 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.85 seconds wall clock time: 44 minutes 25.77 seconds (2665.77 seconds total)