Starting phenix.real_space_refine on Thu Jul 31 12:04:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nsb_12563/07_2025/7nsb_12563.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nsb_12563/07_2025/7nsb_12563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nsb_12563/07_2025/7nsb_12563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nsb_12563/07_2025/7nsb_12563.map" model { file = "/net/cci-nas-00/data/ceres_data/7nsb_12563/07_2025/7nsb_12563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nsb_12563/07_2025/7nsb_12563.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 55 5.16 5 C 8725 2.51 5 N 2277 2.21 5 O 2417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13474 Number of models: 1 Model: "" Number of chains: 4 Chain: "a" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4376 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 19, 'TRANS': 548} Chain breaks: 9 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 10, 'ASP:plan': 16, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 165 Chain: "g" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3173 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 16, 'TRANS': 412} Chain breaks: 5 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 180 Chain: "7" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4075 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 18, 'TRANS': 512} Chain breaks: 11 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 17, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 168 Chain: "h" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1850 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 5 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 15, 'ASN:plan1': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 122 Time building chain proxies: 7.55, per 1000 atoms: 0.56 Number of scatterers: 13474 At special positions: 0 Unit cell: (126.4, 169.06, 102.7, 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 55 16.00 O 2417 8.00 N 2277 7.00 C 8725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.92 Conformation dependent library (CDL) restraints added in 1.6 seconds 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3398 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 16 sheets defined 35.4% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'a' and resid 7 through 17 removed outlier: 4.710A pdb=" N GLU a 11 " --> pdb=" O ASP a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 24 removed outlier: 4.060A pdb=" N GLN a 23 " --> pdb=" O SER a 19 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN a 24 " --> pdb=" O TYR a 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 19 through 24' Processing helix chain 'a' and resid 26 through 36 removed outlier: 3.942A pdb=" N LEU a 30 " --> pdb=" O VAL a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 45 Processing helix chain 'a' and resid 70 through 81 removed outlier: 4.051A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 105 removed outlier: 3.626A pdb=" N TYR a 103 " --> pdb=" O GLN a 99 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE a 104 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 115 Processing helix chain 'a' and resid 318 through 321 No H-bonds generated for 'chain 'a' and resid 318 through 321' Processing helix chain 'a' and resid 497 through 503 Processing helix chain 'a' and resid 597 through 613 removed outlier: 4.255A pdb=" N LYS a 603 " --> pdb=" O GLY a 599 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP a 604 " --> pdb=" O TYR a 600 " (cutoff:3.500A) Processing helix chain 'a' and resid 709 through 724 Processing helix chain 'a' and resid 728 through 741 Processing helix chain 'a' and resid 751 through 766 removed outlier: 3.893A pdb=" N VAL a 755 " --> pdb=" O GLU a 751 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE a 756 " --> pdb=" O SER a 752 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU a 766 " --> pdb=" O GLN a 762 " (cutoff:3.500A) Processing helix chain 'a' and resid 768 through 782 removed outlier: 3.575A pdb=" N ILE a 772 " --> pdb=" O ARG a 768 " (cutoff:3.500A) Processing helix chain 'a' and resid 785 through 794 Processing helix chain 'a' and resid 799 through 802 No H-bonds generated for 'chain 'a' and resid 799 through 802' Processing helix chain 'a' and resid 804 through 822 removed outlier: 4.043A pdb=" N GLU a 809 " --> pdb=" O GLU a 805 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA a 813 " --> pdb=" O GLU a 809 " (cutoff:3.500A) Processing helix chain 'a' and resid 829 through 845 removed outlier: 3.982A pdb=" N ILE a 834 " --> pdb=" O ILE a 830 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU a 835 " --> pdb=" O GLU a 831 " (cutoff:3.500A) Processing helix chain 'a' and resid 852 through 869 removed outlier: 3.722A pdb=" N SER a 859 " --> pdb=" O ARG a 855 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY a 860 " --> pdb=" O ASP a 856 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN a 861 " --> pdb=" O ARG a 857 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU a 862 " --> pdb=" O PHE a 858 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU a 868 " --> pdb=" O ASN a 864 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU a 869 " --> pdb=" O VAL a 865 " (cutoff:3.500A) Processing helix chain 'a' and resid 880 through 885 Processing helix chain 'a' and resid 888 through 907 removed outlier: 4.048A pdb=" N PHE a 896 " --> pdb=" O GLN a 892 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN a 897 " --> pdb=" O GLU a 893 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN a 901 " --> pdb=" O GLN a 897 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU a 907 " --> pdb=" O ILE a 903 " (cutoff:3.500A) Processing helix chain 'a' and resid 915 through 932 removed outlier: 3.739A pdb=" N TYR a 932 " --> pdb=" O THR a 928 " (cutoff:3.500A) Processing helix chain 'a' and resid 951 through 956 Processing helix chain 'g' and resid 31 through 43 removed outlier: 3.530A pdb=" N LEU g 35 " --> pdb=" O GLN g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 53 Processing helix chain 'g' and resid 263 through 278 removed outlier: 4.333A pdb=" N LYS g 269 " --> pdb=" O LEU g 265 " (cutoff:3.500A) Processing helix chain 'g' and resid 576 through 581 Processing helix chain '7' and resid 29 through 43 Processing helix chain '7' and resid 46 through 54 removed outlier: 3.909A pdb=" N LEU 7 53 " --> pdb=" O ALA 7 49 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU 7 54 " --> pdb=" O ASN 7 50 " (cutoff:3.500A) Processing helix chain '7' and resid 65 through 75 Processing helix chain '7' and resid 83 through 87 Processing helix chain '7' and resid 99 through 106 removed outlier: 5.507A pdb=" N GLN 7 103 " --> pdb=" O SER 7 99 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG 7 104 " --> pdb=" O GLU 7 100 " (cutoff:3.500A) Processing helix chain '7' and resid 118 through 136 removed outlier: 3.867A pdb=" N GLN 7 130 " --> pdb=" O GLN 7 126 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU 7 131 " --> pdb=" O TYR 7 127 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET 7 132 " --> pdb=" O LEU 7 128 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER 7 133 " --> pdb=" O GLN 7 129 " (cutoff:3.500A) Processing helix chain '7' and resid 143 through 167 removed outlier: 4.178A pdb=" N ASN 7 150 " --> pdb=" O ALA 7 146 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE 7 166 " --> pdb=" O ILE 7 162 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE 7 167 " --> pdb=" O PHE 7 163 " (cutoff:3.500A) Processing helix chain '7' and resid 182 through 205 removed outlier: 3.814A pdb=" N LEU 7 186 " --> pdb=" O ALA 7 182 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS 7 190 " --> pdb=" O LEU 7 186 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE 7 195 " --> pdb=" O ILE 7 191 " (cutoff:3.500A) Processing helix chain '7' and resid 216 through 229 removed outlier: 3.815A pdb=" N LEU 7 229 " --> pdb=" O LEU 7 225 " (cutoff:3.500A) Processing helix chain '7' and resid 233 through 237 Processing helix chain '7' and resid 243 through 252 Processing helix chain '7' and resid 263 through 278 removed outlier: 3.800A pdb=" N GLN 7 278 " --> pdb=" O TYR 7 274 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 44 Processing helix chain 'h' and resid 89 through 100 removed outlier: 3.723A pdb=" N LEU h 94 " --> pdb=" O PRO h 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 103 through 112 Processing helix chain 'h' and resid 120 through 128 Processing helix chain 'h' and resid 131 through 143 Processing helix chain 'h' and resid 146 through 151 Processing helix chain 'h' and resid 193 through 208 Processing helix chain 'h' and resid 223 through 236 Processing helix chain 'h' and resid 243 through 249 Processing helix chain 'h' and resid 273 through 278 removed outlier: 4.355A pdb=" N TYR h 278 " --> pdb=" O LEU h 274 " (cutoff:3.500A) Processing helix chain 'h' and resid 280 through 299 removed outlier: 4.230A pdb=" N ILE h 286 " --> pdb=" O LEU h 282 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA h 287 " --> pdb=" O ARG h 283 " (cutoff:3.500A) Processing helix chain 'h' and resid 301 through 308 Processing helix chain 'h' and resid 418 through 423 Processing helix chain 'h' and resid 428 through 444 removed outlier: 3.706A pdb=" N HIS h 444 " --> pdb=" O GLU h 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 337 through 340 removed outlier: 5.325A pdb=" N HIS a 346 " --> pdb=" O SER a 340 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N THR a 345 " --> pdb=" O THR a 585 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N THR a 585 " --> pdb=" O THR a 345 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN a 581 " --> pdb=" O PRO a 349 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER a 582 " --> pdb=" O LEU a 409 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR a 400 " --> pdb=" O PHE a 545 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR a 404 " --> pdb=" O CYS a 541 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP a 537 " --> pdb=" O VAL a 408 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLY a 548 " --> pdb=" O ASP a 565 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE a 550 " --> pdb=" O PHE a 563 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 386 through 390 removed outlier: 3.725A pdb=" N ILE a 424 " --> pdb=" O TYR a 512 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY a 511 " --> pdb=" O THR a 520 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS a 513 " --> pdb=" O LEU a 518 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU a 518 " --> pdb=" O CYS a 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'g' and resid 328 through 333 removed outlier: 4.000A pdb=" N PHE g 329 " --> pdb=" O ALA g 342 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER g 333 " --> pdb=" O TYR g 338 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR g 338 " --> pdb=" O SER g 333 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE g 352 " --> pdb=" O CYS g 367 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ASP g 356 " --> pdb=" O ILE g 363 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE g 363 " --> pdb=" O ASP g 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'g' and resid 376 through 380 removed outlier: 5.352A pdb=" N TYR g 385 " --> pdb=" O SER g 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'g' and resid 460 through 465 removed outlier: 5.616A pdb=" N TRP g 473 " --> pdb=" O PHE g 465 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU g 482 " --> pdb=" O SER g 478 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ALA g 483 " --> pdb=" O LEU g 497 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE g 495 " --> pdb=" O VAL g 485 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N SER g 487 " --> pdb=" O SER g 493 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER g 493 " --> pdb=" O SER g 487 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'g' and resid 546 through 551 removed outlier: 5.143A pdb=" N ASP g 547 " --> pdb=" O MET g 560 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N TYR g 556 " --> pdb=" O SER g 551 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL g 565 " --> pdb=" O THR g 561 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA g 596 " --> pdb=" O VAL g 568 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP g 570 " --> pdb=" O ARG g 594 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG g 594 " --> pdb=" O ASP g 570 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'g' and resid 606 through 609 removed outlier: 4.102A pdb=" N CYS g 606 " --> pdb=" O SER g 633 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU g 634 " --> pdb=" O GLU g 638 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU g 638 " --> pdb=" O LEU g 634 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN g 651 " --> pdb=" O MET g 641 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP g 643 " --> pdb=" O LEU g 649 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU g 649 " --> pdb=" O ASP g 643 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 663 through 668 removed outlier: 6.469A pdb=" N ARG g 664 " --> pdb=" O GLY g 677 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY g 677 " --> pdb=" O ARG g 664 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER g 678 " --> pdb=" O LYS g 682 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LYS g 682 " --> pdb=" O SER g 678 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ASP g 687 " --> pdb=" O LEU g 693 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU g 693 " --> pdb=" O ASP g 687 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'g' and resid 715 through 721 removed outlier: 5.838A pdb=" N MET g 727 " --> pdb=" O ASN g 721 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLU g 726 " --> pdb=" O ILE g 742 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS g 738 " --> pdb=" O SER g 730 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY g 732 " --> pdb=" O LYS g 736 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS g 736 " --> pdb=" O GLY g 732 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE g 737 " --> pdb=" O THR g 319 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR g 319 " --> pdb=" O ILE g 737 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE g 739 " --> pdb=" O TRP g 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '7' and resid 329 through 333 removed outlier: 3.801A pdb=" N PHE 7 329 " --> pdb=" O ALA 7 342 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR 7 331 " --> pdb=" O ALA 7 340 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR 7 338 " --> pdb=" O SER 7 333 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR 7 353 " --> pdb=" O SER 7 341 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE 7 352 " --> pdb=" O CYS 7 367 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASP 7 356 " --> pdb=" O ILE 7 363 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE 7 363 " --> pdb=" O ASP 7 356 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '7' and resid 376 through 380 removed outlier: 3.809A pdb=" N TYR 7 376 " --> pdb=" O CYS 7 389 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR 7 385 " --> pdb=" O SER 7 380 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR 7 396 " --> pdb=" O ALA 7 388 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '7' and resid 460 through 465 removed outlier: 4.427A pdb=" N CYS 7 461 " --> pdb=" O GLY 7 477 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP 7 473 " --> pdb=" O PHE 7 465 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL 7 476 " --> pdb=" O ILE 7 484 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE 7 484 " --> pdb=" O VAL 7 476 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER 7 478 " --> pdb=" O GLU 7 482 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU 7 482 " --> pdb=" O SER 7 478 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA 7 483 " --> pdb=" O LEU 7 497 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE 7 495 " --> pdb=" O VAL 7 485 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER 7 487 " --> pdb=" O SER 7 493 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N SER 7 493 " --> pdb=" O SER 7 487 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '7' and resid 546 through 551 removed outlier: 5.236A pdb=" N ASP 7 547 " --> pdb=" O MET 7 560 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TYR 7 556 " --> pdb=" O SER 7 551 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL 7 565 " --> pdb=" O THR 7 561 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA 7 596 " --> pdb=" O VAL 7 568 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP 7 570 " --> pdb=" O ARG 7 594 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG 7 594 " --> pdb=" O ASP 7 570 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '7' and resid 606 through 609 removed outlier: 4.827A pdb=" N CYS 7 606 " --> pdb=" O SER 7 633 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER 7 608 " --> pdb=" O LEU 7 631 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU 7 631 " --> pdb=" O SER 7 608 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL 7 630 " --> pdb=" O TRP 7 642 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU 7 634 " --> pdb=" O GLU 7 638 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU 7 638 " --> pdb=" O LEU 7 634 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN 7 651 " --> pdb=" O MET 7 641 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP 7 643 " --> pdb=" O LEU 7 649 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU 7 649 " --> pdb=" O ASP 7 643 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '7' and resid 663 through 668 removed outlier: 5.946A pdb=" N ARG 7 664 " --> pdb=" O GLY 7 677 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER 7 678 " --> pdb=" O LYS 7 682 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYS 7 682 " --> pdb=" O SER 7 678 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP 7 687 " --> pdb=" O LEU 7 693 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU 7 693 " --> pdb=" O ASP 7 687 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '7' and resid 715 through 721 removed outlier: 4.201A pdb=" N ASN 7 721 " --> pdb=" O MET 7 727 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET 7 727 " --> pdb=" O ASN 7 721 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLU 7 726 " --> pdb=" O ILE 7 742 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE 7 742 " --> pdb=" O GLU 7 726 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY 7 732 " --> pdb=" O LYS 7 736 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS 7 736 " --> pdb=" O GLY 7 732 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE 7 737 " --> pdb=" O THR 7 319 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR 7 319 " --> pdb=" O ILE 7 737 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE 7 739 " --> pdb=" O TRP 7 317 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1650 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: 4.13 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4276 1.34 - 1.46: 2112 1.46 - 1.57: 7289 1.57 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 13760 Sorted by residual: bond pdb=" CB PRO h 314 " pdb=" CG PRO h 314 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.69e+00 bond pdb=" CG1 ILE 7 742 " pdb=" CD1 ILE 7 742 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" C PRO g 295 " pdb=" N PRO g 296 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.25e+00 bond pdb=" CG1 ILE g 683 " pdb=" CD1 ILE g 683 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 9.10e-01 bond pdb=" CB LEU a 895 " pdb=" CG LEU a 895 " ideal model delta sigma weight residual 1.530 1.511 0.019 2.00e-02 2.50e+03 8.89e-01 ... (remaining 13755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 18180 1.75 - 3.50: 464 3.50 - 5.25: 66 5.25 - 6.99: 20 6.99 - 8.74: 5 Bond angle restraints: 18735 Sorted by residual: angle pdb=" C VAL a 108 " pdb=" N ASN a 109 " pdb=" CA ASN a 109 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C ASP a 847 " pdb=" N THR a 848 " pdb=" CA THR a 848 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C PRO g 587 " pdb=" N LYS g 588 " pdb=" CA LYS g 588 " ideal model delta sigma weight residual 121.54 128.10 -6.56 1.91e+00 2.74e-01 1.18e+01 angle pdb=" N ASP a 516 " pdb=" CA ASP a 516 " pdb=" C ASP a 516 " ideal model delta sigma weight residual 114.56 110.68 3.88 1.27e+00 6.20e-01 9.32e+00 angle pdb=" N LYS g 725 " pdb=" CA LYS g 725 " pdb=" CB LYS g 725 " ideal model delta sigma weight residual 113.65 109.71 3.94 1.47e+00 4.63e-01 7.17e+00 ... (remaining 18730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 7271 17.05 - 34.10: 682 34.10 - 51.15: 115 51.15 - 68.20: 13 68.20 - 85.25: 10 Dihedral angle restraints: 8091 sinusoidal: 2872 harmonic: 5219 Sorted by residual: dihedral pdb=" CA GLU 7 726 " pdb=" C GLU 7 726 " pdb=" N MET 7 727 " pdb=" CA MET 7 727 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASN 7 721 " pdb=" C ASN 7 721 " pdb=" N PRO 7 722 " pdb=" CA PRO 7 722 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LEU 7 634 " pdb=" C LEU 7 634 " pdb=" N GLN 7 635 " pdb=" CA GLN 7 635 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 8088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1298 0.034 - 0.068: 611 0.068 - 0.102: 195 0.102 - 0.135: 81 0.135 - 0.169: 13 Chirality restraints: 2198 Sorted by residual: chirality pdb=" CA VAL 7 395 " pdb=" N VAL 7 395 " pdb=" C VAL 7 395 " pdb=" CB VAL 7 395 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA ASN a 109 " pdb=" N ASN a 109 " pdb=" C ASN a 109 " pdb=" CB ASN a 109 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CA ILE g 683 " pdb=" N ILE g 683 " pdb=" C ILE g 683 " pdb=" CB ILE g 683 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 2195 not shown) Planarity restraints: 2359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG 7 189 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C ARG 7 189 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG 7 189 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS 7 190 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO g 295 " -0.049 5.00e-02 4.00e+02 7.37e-02 8.69e+00 pdb=" N PRO g 296 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO g 296 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO g 296 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS a 531 " -0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO a 532 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO a 532 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO a 532 " -0.034 5.00e-02 4.00e+02 ... (remaining 2356 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1840 2.75 - 3.29: 13141 3.29 - 3.83: 20419 3.83 - 4.36: 22934 4.36 - 4.90: 40683 Nonbonded interactions: 99017 Sorted by model distance: nonbonded pdb=" OE1 GLN g 270 " pdb=" NE2 GLN 7 275 " model vdw 2.214 3.120 nonbonded pdb=" OE1 GLU 7 153 " pdb=" OH TYR 7 252 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR a 28 " pdb=" O TYR h 46 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR g 669 " pdb=" O ASN g 745 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR a 426 " pdb=" O CYS a 541 " model vdw 2.265 3.040 ... (remaining 99012 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.380 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: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.050 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.004 0.065 13760 Z= 0.176 Angle : 0.701 8.742 18735 Z= 0.379 Chirality : 0.045 0.169 2198 Planarity : 0.005 0.074 2359 Dihedral : 13.751 85.246 4693 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.21), residues: 1707 helix: 0.88 (0.23), residues: 593 sheet: -1.46 (0.30), residues: 294 loop : -3.16 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP g 686 HIS 0.011 0.001 HIS 7 486 PHE 0.012 0.001 PHE 7 379 TYR 0.014 0.001 TYR a 574 ARG 0.004 0.000 ARG 7 149 Details of bonding type rmsd hydrogen bonds : bond 0.05231 ( 554) hydrogen bonds : angle 5.34383 ( 1650) covalent geometry : bond 0.00406 (13760) covalent geometry : angle 0.70124 (18735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.529 Fit side-chains REVERT: a 31 TRP cc_start: 0.7440 (t-100) cc_final: 0.6985 (t-100) REVERT: a 683 GLU cc_start: 0.8592 (pm20) cc_final: 0.8267 (pm20) REVERT: 7 200 ASP cc_start: 0.9078 (t70) cc_final: 0.8757 (t0) REVERT: 7 226 SER cc_start: 0.9002 (p) cc_final: 0.8585 (p) REVERT: 7 355 TYR cc_start: 0.8951 (m-10) cc_final: 0.8495 (m-10) REVERT: 7 636 ASP cc_start: 0.7234 (m-30) cc_final: 0.6903 (t70) REVERT: 7 675 MET cc_start: 0.8523 (ptp) cc_final: 0.8191 (ptp) REVERT: 7 726 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7200 (tm-30) REVERT: h 245 MET cc_start: 0.8440 (mmm) cc_final: 0.8185 (mmt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2422 time to fit residues: 69.5451 Evaluate side-chains 147 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 567 ASN ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 546 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.099609 restraints weight = 25150.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102176 restraints weight = 14368.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103935 restraints weight = 9980.982| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13760 Z= 0.162 Angle : 0.640 9.211 18735 Z= 0.331 Chirality : 0.044 0.163 2198 Planarity : 0.005 0.059 2359 Dihedral : 5.209 24.434 1880 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 0.66 % Allowed : 9.97 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.21), residues: 1707 helix: 1.07 (0.23), residues: 597 sheet: -1.26 (0.31), residues: 294 loop : -3.05 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP g 686 HIS 0.004 0.001 HIS 7 308 PHE 0.010 0.001 PHE 7 379 TYR 0.021 0.001 TYR h 229 ARG 0.003 0.000 ARG a 944 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 554) hydrogen bonds : angle 5.15816 ( 1650) covalent geometry : bond 0.00387 (13760) covalent geometry : angle 0.63993 (18735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 2.042 Fit side-chains REVERT: a 31 TRP cc_start: 0.7461 (t-100) cc_final: 0.7048 (t-100) REVERT: a 422 ILE cc_start: 0.9219 (mp) cc_final: 0.8825 (mt) REVERT: g 343 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7684 (t) REVERT: g 547 ASP cc_start: 0.8711 (t0) cc_final: 0.8411 (t0) REVERT: 7 200 ASP cc_start: 0.9089 (t70) cc_final: 0.8805 (t0) REVERT: 7 355 TYR cc_start: 0.8928 (m-10) cc_final: 0.8602 (m-10) REVERT: 7 636 ASP cc_start: 0.7264 (m-30) cc_final: 0.6955 (t70) REVERT: 7 647 ASN cc_start: 0.9208 (t0) cc_final: 0.8874 (t0) REVERT: h 245 MET cc_start: 0.8247 (mmm) cc_final: 0.7887 (mmt) outliers start: 9 outliers final: 7 residues processed: 165 average time/residue: 0.3197 time to fit residues: 84.5748 Evaluate side-chains 154 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 82 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 671 ASN ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 194 ASN ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 656 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099523 restraints weight = 25383.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102085 restraints weight = 14427.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103838 restraints weight = 10027.001| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13760 Z= 0.170 Angle : 0.634 9.086 18735 Z= 0.327 Chirality : 0.044 0.161 2198 Planarity : 0.004 0.058 2359 Dihedral : 5.117 22.006 1880 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 2.07 % Allowed : 13.07 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.21), residues: 1707 helix: 1.09 (0.23), residues: 600 sheet: -1.18 (0.30), residues: 308 loop : -3.01 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 686 HIS 0.004 0.001 HIS 7 308 PHE 0.019 0.001 PHE 7 314 TYR 0.017 0.001 TYR h 229 ARG 0.002 0.000 ARG h 117 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 554) hydrogen bonds : angle 5.10785 ( 1650) covalent geometry : bond 0.00405 (13760) covalent geometry : angle 0.63425 (18735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.642 Fit side-chains REVERT: a 31 TRP cc_start: 0.7479 (t-100) cc_final: 0.7081 (t-100) REVERT: a 422 ILE cc_start: 0.9284 (mp) cc_final: 0.8902 (mt) REVERT: a 585 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8601 (m) REVERT: g 32 LEU cc_start: 0.7929 (tt) cc_final: 0.7460 (tt) REVERT: g 343 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7701 (t) REVERT: g 721 ASN cc_start: 0.8816 (t0) cc_final: 0.8492 (t0) REVERT: 7 200 ASP cc_start: 0.9128 (t70) cc_final: 0.8833 (t0) REVERT: 7 355 TYR cc_start: 0.8928 (m-10) cc_final: 0.8528 (m-10) REVERT: 7 636 ASP cc_start: 0.7425 (m-30) cc_final: 0.7001 (t70) REVERT: 7 647 ASN cc_start: 0.9207 (t0) cc_final: 0.8827 (t0) REVERT: 7 727 MET cc_start: 0.8030 (ptm) cc_final: 0.7508 (ptm) REVERT: h 46 TYR cc_start: 0.6591 (t80) cc_final: 0.6170 (t80) REVERT: h 245 MET cc_start: 0.8277 (mmm) cc_final: 0.7834 (mmp) outliers start: 28 outliers final: 17 residues processed: 180 average time/residue: 0.2276 time to fit residues: 63.6913 Evaluate side-chains 168 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 585 THR Chi-restraints excluded: chain a residue 817 VAL Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 567 ASP Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 106 LEU Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain 7 residue 656 GLN Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 153 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 ASN ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 651 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.098110 restraints weight = 25355.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.100677 restraints weight = 14442.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102393 restraints weight = 9998.285| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13760 Z= 0.206 Angle : 0.657 8.853 18735 Z= 0.340 Chirality : 0.045 0.165 2198 Planarity : 0.005 0.057 2359 Dihedral : 5.221 24.480 1880 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 2.58 % Allowed : 13.88 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.21), residues: 1707 helix: 1.10 (0.23), residues: 594 sheet: -1.28 (0.30), residues: 305 loop : -2.97 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 686 HIS 0.006 0.001 HIS 7 308 PHE 0.019 0.001 PHE g 571 TYR 0.015 0.001 TYR h 229 ARG 0.002 0.000 ARG 7 664 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 554) hydrogen bonds : angle 5.17994 ( 1650) covalent geometry : bond 0.00496 (13760) covalent geometry : angle 0.65716 (18735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 1.439 Fit side-chains REVERT: a 31 TRP cc_start: 0.7539 (t-100) cc_final: 0.7117 (t-100) REVERT: a 422 ILE cc_start: 0.9198 (mp) cc_final: 0.8815 (mt) REVERT: a 585 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8608 (m) REVERT: g 343 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7966 (t) REVERT: g 639 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8462 (mt) REVERT: g 721 ASN cc_start: 0.8928 (t0) cc_final: 0.8677 (t0) REVERT: 7 200 ASP cc_start: 0.9162 (t70) cc_final: 0.8869 (t0) REVERT: 7 355 TYR cc_start: 0.8979 (m-10) cc_final: 0.8578 (m-10) REVERT: 7 636 ASP cc_start: 0.7505 (m-30) cc_final: 0.6958 (t70) REVERT: 7 647 ASN cc_start: 0.9209 (t0) cc_final: 0.8811 (t0) REVERT: h 46 TYR cc_start: 0.6754 (t80) cc_final: 0.6476 (t80) REVERT: h 245 MET cc_start: 0.8303 (mmm) cc_final: 0.7801 (mmp) outliers start: 35 outliers final: 26 residues processed: 185 average time/residue: 0.2261 time to fit residues: 64.5782 Evaluate side-chains 183 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 585 THR Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain a residue 817 VAL Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 559 LEU Chi-restraints excluded: chain g residue 639 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 106 LEU Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 374 VAL Chi-restraints excluded: chain 7 residue 486 HIS Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain 7 residue 715 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 107 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.098422 restraints weight = 25476.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101016 restraints weight = 14439.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102604 restraints weight = 9961.737| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13760 Z= 0.175 Angle : 0.633 11.577 18735 Z= 0.327 Chirality : 0.044 0.208 2198 Planarity : 0.004 0.057 2359 Dihedral : 5.116 24.045 1880 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 3.32 % Allowed : 15.21 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.21), residues: 1707 helix: 1.25 (0.23), residues: 587 sheet: -1.16 (0.30), residues: 308 loop : -2.90 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 686 HIS 0.004 0.001 HIS 7 308 PHE 0.019 0.001 PHE g 571 TYR 0.015 0.001 TYR h 229 ARG 0.003 0.000 ARG h 134 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 554) hydrogen bonds : angle 5.08994 ( 1650) covalent geometry : bond 0.00417 (13760) covalent geometry : angle 0.63328 (18735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 1.726 Fit side-chains REVERT: a 31 TRP cc_start: 0.7618 (t-100) cc_final: 0.7217 (t-100) REVERT: a 422 ILE cc_start: 0.9234 (mp) cc_final: 0.8823 (mt) REVERT: a 426 TYR cc_start: 0.8825 (m-80) cc_final: 0.8537 (m-80) REVERT: a 585 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8664 (m) REVERT: g 343 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7846 (t) REVERT: g 721 ASN cc_start: 0.8881 (t0) cc_final: 0.8656 (t0) REVERT: 7 200 ASP cc_start: 0.9139 (t70) cc_final: 0.8865 (t0) REVERT: 7 355 TYR cc_start: 0.8974 (m-10) cc_final: 0.8512 (m-10) REVERT: 7 636 ASP cc_start: 0.7380 (m-30) cc_final: 0.6792 (t70) REVERT: 7 647 ASN cc_start: 0.9194 (t0) cc_final: 0.8782 (t0) REVERT: 7 727 MET cc_start: 0.7998 (ptm) cc_final: 0.7434 (ptm) REVERT: h 46 TYR cc_start: 0.6871 (t80) cc_final: 0.6605 (t80) REVERT: h 245 MET cc_start: 0.8296 (mmm) cc_final: 0.7779 (mmp) outliers start: 45 outliers final: 33 residues processed: 197 average time/residue: 0.2222 time to fit residues: 68.6792 Evaluate side-chains 197 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 108 VAL Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 585 THR Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain a residue 817 VAL Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 486 HIS Chi-restraints excluded: chain g residue 559 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 106 LEU Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 156 ILE Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 204 VAL Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 486 HIS Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 118 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 157 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 656 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.098774 restraints weight = 25681.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101447 restraints weight = 14639.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.103201 restraints weight = 10037.617| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13760 Z= 0.160 Angle : 0.619 8.525 18735 Z= 0.320 Chirality : 0.044 0.185 2198 Planarity : 0.004 0.056 2359 Dihedral : 5.009 23.183 1880 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.13 % Favored : 87.87 % Rotamer: Outliers : 3.55 % Allowed : 15.66 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1707 helix: 1.26 (0.23), residues: 595 sheet: -1.15 (0.30), residues: 308 loop : -2.89 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP g 686 HIS 0.004 0.001 HIS 7 308 PHE 0.020 0.001 PHE g 571 TYR 0.014 0.001 TYR h 229 ARG 0.003 0.000 ARG h 134 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 554) hydrogen bonds : angle 5.02353 ( 1650) covalent geometry : bond 0.00380 (13760) covalent geometry : angle 0.61885 (18735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 1.423 Fit side-chains REVERT: a 31 TRP cc_start: 0.7602 (t-100) cc_final: 0.7214 (t-100) REVERT: a 422 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8810 (mt) REVERT: a 426 TYR cc_start: 0.8828 (m-80) cc_final: 0.8538 (m-80) REVERT: a 585 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8648 (m) REVERT: g 343 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7866 (t) REVERT: g 721 ASN cc_start: 0.8898 (t0) cc_final: 0.8651 (t0) REVERT: 7 200 ASP cc_start: 0.9158 (t70) cc_final: 0.8853 (t0) REVERT: 7 355 TYR cc_start: 0.8969 (m-10) cc_final: 0.8514 (m-10) REVERT: 7 636 ASP cc_start: 0.7394 (m-30) cc_final: 0.6747 (t70) REVERT: 7 647 ASN cc_start: 0.9190 (t0) cc_final: 0.8760 (t0) REVERT: 7 685 ILE cc_start: 0.8728 (mt) cc_final: 0.8454 (mt) REVERT: h 46 TYR cc_start: 0.6771 (t80) cc_final: 0.6528 (t80) REVERT: h 245 MET cc_start: 0.8291 (mmm) cc_final: 0.7769 (mmp) outliers start: 48 outliers final: 35 residues processed: 199 average time/residue: 0.2072 time to fit residues: 64.3023 Evaluate side-chains 205 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 422 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 585 THR Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain a residue 817 VAL Chi-restraints excluded: chain a residue 818 MET Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 486 HIS Chi-restraints excluded: chain g residue 559 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 107 ILE Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 156 ILE Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 374 VAL Chi-restraints excluded: chain 7 residue 486 HIS Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain 7 residue 656 GLN Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 124 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 92 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 656 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099988 restraints weight = 25348.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102612 restraints weight = 14493.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104413 restraints weight = 10011.327| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13760 Z= 0.142 Angle : 0.609 8.513 18735 Z= 0.317 Chirality : 0.043 0.191 2198 Planarity : 0.004 0.056 2359 Dihedral : 4.919 25.661 1880 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 3.18 % Allowed : 17.21 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.21), residues: 1707 helix: 1.29 (0.23), residues: 601 sheet: -0.95 (0.31), residues: 292 loop : -2.87 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 308 PHE 0.021 0.001 PHE g 571 TYR 0.013 0.001 TYR h 229 ARG 0.004 0.000 ARG h 134 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 554) hydrogen bonds : angle 4.95214 ( 1650) covalent geometry : bond 0.00333 (13760) covalent geometry : angle 0.60867 (18735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 1.478 Fit side-chains REVERT: a 31 TRP cc_start: 0.7584 (t-100) cc_final: 0.7195 (t-100) REVERT: a 422 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8853 (mt) REVERT: a 426 TYR cc_start: 0.8840 (m-80) cc_final: 0.8549 (m-80) REVERT: a 585 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8637 (m) REVERT: g 343 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7537 (t) REVERT: g 721 ASN cc_start: 0.8882 (t0) cc_final: 0.8616 (t0) REVERT: 7 121 MET cc_start: 0.9101 (mmt) cc_final: 0.8783 (mmt) REVERT: 7 200 ASP cc_start: 0.9152 (t70) cc_final: 0.8844 (t0) REVERT: 7 314 PHE cc_start: 0.8583 (m-80) cc_final: 0.8233 (m-80) REVERT: 7 355 TYR cc_start: 0.8957 (m-10) cc_final: 0.8545 (m-10) REVERT: 7 647 ASN cc_start: 0.9179 (t0) cc_final: 0.8729 (t0) REVERT: h 245 MET cc_start: 0.8273 (mmm) cc_final: 0.7764 (mmp) outliers start: 43 outliers final: 33 residues processed: 199 average time/residue: 0.2127 time to fit residues: 66.1258 Evaluate side-chains 200 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 317 ILE Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 422 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 585 THR Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain a residue 817 VAL Chi-restraints excluded: chain a residue 818 MET Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 486 HIS Chi-restraints excluded: chain g residue 559 LEU Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 156 ILE Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 204 VAL Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 354 VAL Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 374 VAL Chi-restraints excluded: chain 7 residue 486 HIS Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain 7 residue 656 GLN Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 168 HIS 7 206 ASN ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099778 restraints weight = 25433.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102369 restraints weight = 14477.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104069 restraints weight = 10053.991| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13760 Z= 0.150 Angle : 0.613 8.503 18735 Z= 0.319 Chirality : 0.043 0.174 2198 Planarity : 0.004 0.055 2359 Dihedral : 4.880 25.108 1880 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 3.32 % Allowed : 17.58 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.21), residues: 1707 helix: 1.31 (0.23), residues: 601 sheet: -0.85 (0.31), residues: 292 loop : -2.85 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 308 PHE 0.021 0.001 PHE g 571 TYR 0.017 0.001 TYR h 46 ARG 0.003 0.000 ARG h 134 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 554) hydrogen bonds : angle 4.94199 ( 1650) covalent geometry : bond 0.00353 (13760) covalent geometry : angle 0.61321 (18735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 1.583 Fit side-chains REVERT: a 31 TRP cc_start: 0.7599 (t-100) cc_final: 0.7210 (t-100) REVERT: a 422 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8855 (mt) REVERT: a 426 TYR cc_start: 0.8842 (m-80) cc_final: 0.8549 (m-80) REVERT: a 585 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8574 (m) REVERT: g 343 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7591 (t) REVERT: g 721 ASN cc_start: 0.8978 (t0) cc_final: 0.8721 (t0) REVERT: 7 121 MET cc_start: 0.9098 (mmt) cc_final: 0.8782 (mmt) REVERT: 7 200 ASP cc_start: 0.9153 (t70) cc_final: 0.8841 (t0) REVERT: 7 314 PHE cc_start: 0.8587 (m-80) cc_final: 0.8268 (m-80) REVERT: 7 355 TYR cc_start: 0.8954 (m-10) cc_final: 0.8542 (m-10) REVERT: 7 647 ASN cc_start: 0.9171 (t0) cc_final: 0.8721 (t0) REVERT: h 245 MET cc_start: 0.8281 (mmm) cc_final: 0.7762 (mmp) outliers start: 45 outliers final: 37 residues processed: 196 average time/residue: 0.2039 time to fit residues: 63.0607 Evaluate side-chains 205 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 317 ILE Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 422 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 585 THR Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain a residue 817 VAL Chi-restraints excluded: chain a residue 848 THR Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 486 HIS Chi-restraints excluded: chain g residue 559 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 156 ILE Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 204 VAL Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 354 VAL Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 366 THR Chi-restraints excluded: chain 7 residue 374 VAL Chi-restraints excluded: chain 7 residue 486 HIS Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 146 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 153 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.100151 restraints weight = 25204.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.102676 restraints weight = 14540.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104385 restraints weight = 10151.295| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13760 Z= 0.149 Angle : 0.612 8.621 18735 Z= 0.318 Chirality : 0.043 0.163 2198 Planarity : 0.004 0.055 2359 Dihedral : 4.856 26.415 1880 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 3.40 % Allowed : 17.65 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1707 helix: 1.34 (0.23), residues: 600 sheet: -0.78 (0.31), residues: 290 loop : -2.83 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 308 PHE 0.020 0.001 PHE g 571 TYR 0.013 0.001 TYR a 28 ARG 0.004 0.000 ARG h 134 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 554) hydrogen bonds : angle 4.91851 ( 1650) covalent geometry : bond 0.00351 (13760) covalent geometry : angle 0.61154 (18735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 1.656 Fit side-chains REVERT: a 31 TRP cc_start: 0.7598 (t-100) cc_final: 0.7221 (t-100) REVERT: a 422 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8861 (mt) REVERT: a 426 TYR cc_start: 0.8842 (m-80) cc_final: 0.8552 (m-80) REVERT: a 585 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8564 (m) REVERT: g 343 THR cc_start: 0.7850 (OUTLIER) cc_final: 0.7544 (t) REVERT: g 721 ASN cc_start: 0.8975 (t0) cc_final: 0.8746 (t0) REVERT: 7 200 ASP cc_start: 0.9142 (t70) cc_final: 0.8839 (t0) REVERT: 7 355 TYR cc_start: 0.8962 (m-10) cc_final: 0.8558 (m-10) REVERT: 7 647 ASN cc_start: 0.9182 (t0) cc_final: 0.8739 (t0) REVERT: h 245 MET cc_start: 0.8282 (mmm) cc_final: 0.7761 (mmp) outliers start: 46 outliers final: 37 residues processed: 196 average time/residue: 0.2096 time to fit residues: 65.3567 Evaluate side-chains 202 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 317 ILE Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 422 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain a residue 585 THR Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain a residue 817 VAL Chi-restraints excluded: chain a residue 882 ILE Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 353 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 486 HIS Chi-restraints excluded: chain g residue 559 LEU Chi-restraints excluded: chain g residue 591 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 140 CYS Chi-restraints excluded: chain 7 residue 156 ILE Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 204 VAL Chi-restraints excluded: chain 7 residue 272 ILE Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 354 VAL Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 366 THR Chi-restraints excluded: chain 7 residue 374 VAL Chi-restraints excluded: chain 7 residue 486 HIS Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.0370 chunk 36 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 156 optimal weight: 0.2980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 206 ASN ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.120993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.102083 restraints weight = 25135.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104671 restraints weight = 14236.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106365 restraints weight = 9938.796| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13760 Z= 0.116 Angle : 0.583 8.674 18735 Z= 0.302 Chirality : 0.042 0.170 2198 Planarity : 0.004 0.054 2359 Dihedral : 4.610 28.497 1880 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 2.44 % Allowed : 18.69 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1707 helix: 1.45 (0.23), residues: 603 sheet: -0.68 (0.31), residues: 289 loop : -2.75 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 628 PHE 0.021 0.001 PHE g 571 TYR 0.017 0.001 TYR a 28 ARG 0.003 0.000 ARG h 134 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 554) hydrogen bonds : angle 4.79651 ( 1650) covalent geometry : bond 0.00265 (13760) covalent geometry : angle 0.58250 (18735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 1.591 Fit side-chains REVERT: a 31 TRP cc_start: 0.7520 (t-100) cc_final: 0.7179 (t-100) REVERT: a 422 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8850 (mt) REVERT: a 426 TYR cc_start: 0.8831 (m-80) cc_final: 0.8486 (m-80) REVERT: a 585 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8565 (m) REVERT: g 343 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7440 (t) REVERT: g 721 ASN cc_start: 0.8923 (t0) cc_final: 0.8665 (t0) REVERT: 7 121 MET cc_start: 0.9102 (mmt) cc_final: 0.8795 (mmt) REVERT: 7 200 ASP cc_start: 0.9120 (t70) cc_final: 0.8853 (t0) REVERT: 7 355 TYR cc_start: 0.8921 (m-10) cc_final: 0.8478 (m-10) REVERT: 7 607 ILE cc_start: 0.8153 (mm) cc_final: 0.7858 (mm) REVERT: h 205 MET cc_start: 0.8095 (mmm) cc_final: 0.7571 (tpt) REVERT: h 245 MET cc_start: 0.8254 (mmm) cc_final: 0.7760 (mmp) outliers start: 33 outliers final: 29 residues processed: 191 average time/residue: 0.2051 time to fit residues: 63.0862 Evaluate side-chains 194 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 337 LEU Chi-restraints excluded: chain a residue 339 LEU Chi-restraints excluded: chain a residue 406 ILE Chi-restraints excluded: chain a residue 422 ILE Chi-restraints excluded: chain a residue 541 CYS Chi-restraints excluded: chain a residue 585 THR Chi-restraints excluded: chain a residue 780 ILE Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 301 LEU Chi-restraints excluded: chain g residue 343 THR Chi-restraints excluded: chain g residue 353 THR Chi-restraints excluded: chain g residue 370 LEU Chi-restraints excluded: chain g residue 459 VAL Chi-restraints excluded: chain g residue 486 HIS Chi-restraints excluded: chain g residue 591 LEU Chi-restraints excluded: chain g residue 727 MET Chi-restraints excluded: chain 7 residue 156 ILE Chi-restraints excluded: chain 7 residue 195 PHE Chi-restraints excluded: chain 7 residue 204 VAL Chi-restraints excluded: chain 7 residue 284 ILE Chi-restraints excluded: chain 7 residue 331 THR Chi-restraints excluded: chain 7 residue 354 VAL Chi-restraints excluded: chain 7 residue 357 VAL Chi-restraints excluded: chain 7 residue 366 THR Chi-restraints excluded: chain 7 residue 374 VAL Chi-restraints excluded: chain 7 residue 486 HIS Chi-restraints excluded: chain 7 residue 568 VAL Chi-restraints excluded: chain 7 residue 630 VAL Chi-restraints excluded: chain 7 residue 648 ILE Chi-restraints excluded: chain h residue 35 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain h residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 169 optimal weight: 0.9980 chunk 108 optimal weight: 0.3980 chunk 123 optimal weight: 0.7980 chunk 1 optimal weight: 0.0000 chunk 167 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101937 restraints weight = 25225.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104582 restraints weight = 14476.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106340 restraints weight = 10021.153| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13760 Z= 0.122 Angle : 0.592 9.716 18735 Z= 0.305 Chirality : 0.042 0.157 2198 Planarity : 0.004 0.053 2359 Dihedral : 4.575 28.380 1880 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 2.44 % Allowed : 18.98 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1707 helix: 1.47 (0.23), residues: 603 sheet: -0.70 (0.31), residues: 291 loop : -2.69 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP g 686 HIS 0.003 0.001 HIS 7 628 PHE 0.022 0.001 PHE g 571 TYR 0.022 0.001 TYR a 404 ARG 0.003 0.000 ARG h 134 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 554) hydrogen bonds : angle 4.78814 ( 1650) covalent geometry : bond 0.00282 (13760) covalent geometry : angle 0.59151 (18735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3975.55 seconds wall clock time: 70 minutes 53.06 seconds (4253.06 seconds total)