Starting phenix.real_space_refine on Wed Mar 4 21:40:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lzj_23608/03_2026/7lzj_23608.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lzj_23608/03_2026/7lzj_23608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lzj_23608/03_2026/7lzj_23608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lzj_23608/03_2026/7lzj_23608.map" model { file = "/net/cci-nas-00/data/ceres_data/7lzj_23608/03_2026/7lzj_23608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lzj_23608/03_2026/7lzj_23608.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 66 5.16 5 C 10497 2.51 5 N 2799 2.21 5 O 3228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16590 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5530 Classifications: {'peptide': 716} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 684} Chain: "B" Number of atoms: 5530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5530 Classifications: {'peptide': 716} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 684} Chain: "C" Number of atoms: 5530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5530 Classifications: {'peptide': 716} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 684} Time building chain proxies: 3.35, per 1000 atoms: 0.20 Number of scatterers: 16590 At special positions: 0 Unit cell: (93.975, 94.87, 172.735, 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 66 16.00 O 3228 8.00 N 2799 7.00 C 10497 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: 1.46 Conformation dependent library (CDL) restraints added in 691.2 milliseconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3906 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 26 sheets defined 13.5% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 205 through 211 removed outlier: 3.717A pdb=" N ASN A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.594A pdb=" N GLY A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 561 through 569 removed outlier: 3.822A pdb=" N GLU A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 646 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 662 through 665 Processing helix chain 'A' and resid 773 through 775 No H-bonds generated for 'chain 'A' and resid 773 through 775' Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 862 through 867 Processing helix chain 'A' and resid 887 through 902 removed outlier: 4.233A pdb=" N VAL A 891 " --> pdb=" O GLY A 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 removed outlier: 3.808A pdb=" N ASP B 198 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 199 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 200 " --> pdb=" O PHE B 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 195 through 200' Processing helix chain 'B' and resid 205 through 211 removed outlier: 3.793A pdb=" N ASN B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 280 Processing helix chain 'B' and resid 301 through 315 Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.598A pdb=" N GLY B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 569 removed outlier: 3.784A pdb=" N GLU B 566 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 646 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 662 through 665 Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.558A pdb=" N PHE B 788 " --> pdb=" O PRO B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 827 removed outlier: 3.506A pdb=" N PHE B 827 " --> pdb=" O LEU B 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 823 through 827' Processing helix chain 'B' and resid 862 through 867 Processing helix chain 'B' and resid 887 through 902 removed outlier: 3.895A pdb=" N VAL B 891 " --> pdb=" O GLY B 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 removed outlier: 4.030A pdb=" N ASP C 198 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 199 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 200 " --> pdb=" O PHE C 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 200' Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.626A pdb=" N ASN C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 280 Processing helix chain 'C' and resid 301 through 315 Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.676A pdb=" N GLY C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 569 removed outlier: 3.792A pdb=" N GLU C 566 " --> pdb=" O ILE C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 646 Processing helix chain 'C' and resid 653 through 659 Processing helix chain 'C' and resid 662 through 666 removed outlier: 3.517A pdb=" N VAL C 666 " --> pdb=" O LYS C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 775 No H-bonds generated for 'chain 'C' and resid 773 through 775' Processing helix chain 'C' and resid 784 through 788 Processing helix chain 'C' and resid 823 through 827 removed outlier: 3.512A pdb=" N PHE C 827 " --> pdb=" O LEU C 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 823 through 827' Processing helix chain 'C' and resid 862 through 867 Processing helix chain 'C' and resid 887 through 902 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 3.606A pdb=" N TYR A 264 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 263 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 275 removed outlier: 6.513A pdb=" N PHE A 274 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 405 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS A 407 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU A 405 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N CYS A 433 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N HIS A 407 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ALA A 435 " --> pdb=" O HIS A 407 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N TYR A 409 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHE A 430 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A 537 " --> pdb=" O ASN A 509 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLN A 511 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE A 539 " --> pdb=" O GLN A 511 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 513 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.056A pdb=" N THR A 348 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 405 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS A 407 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU A 405 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N CYS A 433 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N HIS A 407 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ALA A 435 " --> pdb=" O HIS A 407 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N TYR A 409 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE A 466 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS A 433 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASN A 468 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA A 435 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE A 593 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLU A 545 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS A 595 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 597 " --> pdb=" O ILE A 547 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 336 removed outlier: 7.193A pdb=" N ILE A 391 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A 367 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE A 393 " --> pdb=" O ASN A 367 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A 389 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR A 418 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 391 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP A 415 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 444 " --> pdb=" O TRP A 415 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE A 417 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLU A 446 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL A 419 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN A 441 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR A 503 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE A 443 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLN A 505 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 445 " --> pdb=" O GLN A 505 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N CYS A 500 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU A 528 " --> pdb=" O CYS A 500 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ALA A 577 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER A 527 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL A 579 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA A 529 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N SER A 581 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A 531 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR A 601 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N TRP A 627 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 602 " --> pdb=" O TRP A 627 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 480 through 482 Processing sheet with id=AA6, first strand: chain 'A' and resid 612 through 613 Processing sheet with id=AA7, first strand: chain 'A' and resid 795 through 801 removed outlier: 6.801A pdb=" N VAL A 844 " --> pdb=" O LYS A 750 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE A 752 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR A 842 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE A 754 " --> pdb=" O LYS A 840 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS A 840 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR A 756 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE A 838 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 839 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN A 672 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 841 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AA9, first strand: chain 'A' and resid 727 through 732 removed outlier: 4.010A pdb=" N LEU A 727 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE A 768 " --> pdb=" O SER A 780 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER A 780 " --> pdb=" O ILE A 768 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 770 " --> pdb=" O LEU A 778 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 858 through 859 removed outlier: 6.846A pdb=" N SER B 667 " --> pdb=" O TYR B 845 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR B 845 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU B 669 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA B 843 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS B 671 " --> pdb=" O ILE B 841 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE B 838 " --> pdb=" O THR B 757 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR B 757 " --> pdb=" O PHE B 838 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.556A pdb=" N TYR B 264 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 263 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.524A pdb=" N PHE B 274 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 405 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER B 377 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS B 407 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE B 430 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE B 537 " --> pdb=" O ASN B 509 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN B 511 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 539 " --> pdb=" O GLN B 511 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 513 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.022A pdb=" N THR B 348 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 405 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER B 377 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS B 407 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE B 593 " --> pdb=" O ASP B 543 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU B 545 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS B 595 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 597 " --> pdb=" O ILE B 547 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 334 through 336 removed outlier: 6.377A pdb=" N LEU B 334 " --> pdb=" O ASN B 367 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 391 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN B 367 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE B 393 " --> pdb=" O ASN B 367 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS B 389 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TYR B 418 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 391 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP B 415 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE B 444 " --> pdb=" O TRP B 415 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE B 417 " --> pdb=" O PHE B 444 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU B 446 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 419 " --> pdb=" O GLU B 446 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN B 441 " --> pdb=" O GLN B 501 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N TYR B 503 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE B 443 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N GLN B 505 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 445 " --> pdb=" O GLN B 505 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N CYS B 500 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU B 528 " --> pdb=" O CYS B 500 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ALA B 577 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL B 579 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR B 530 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N SER B 581 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR B 532 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR B 601 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TRP B 627 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 602 " --> pdb=" O TRP B 627 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 480 through 482 Processing sheet with id=AB7, first strand: chain 'B' and resid 612 through 613 Processing sheet with id=AB8, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AB9, first strand: chain 'B' and resid 727 through 732 removed outlier: 4.057A pdb=" N LEU B 727 " --> pdb=" O PHE B 813 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 811 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 768 " --> pdb=" O SER B 780 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER B 780 " --> pdb=" O ILE B 768 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 770 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 858 through 859 removed outlier: 6.493A pdb=" N ILE C 841 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN C 672 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU C 839 " --> pdb=" O ASN C 672 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE C 838 " --> pdb=" O THR C 757 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR C 757 " --> pdb=" O PHE C 838 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 220 through 223 removed outlier: 3.545A pdb=" N TYR C 263 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 273 through 275 removed outlier: 6.493A pdb=" N PHE C 274 " --> pdb=" O ASN C 320 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU C 405 " --> pdb=" O ARG C 375 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS C 407 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE C 430 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLU C 406 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER C 432 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL C 408 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE C 466 " --> pdb=" O HIS C 431 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N CYS C 433 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ASN C 468 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA C 435 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE C 593 " --> pdb=" O ASP C 543 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU C 545 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS C 595 " --> pdb=" O GLU C 545 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 324 through 328 removed outlier: 5.102A pdb=" N THR C 348 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU C 405 " --> pdb=" O ARG C 375 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS C 407 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE C 430 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLU C 406 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER C 432 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL C 408 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE C 430 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER C 508 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N ILE C 538 " --> pdb=" O SER C 508 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 510 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR C 540 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR C 512 " --> pdb=" O TYR C 540 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP C 589 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 334 through 336 removed outlier: 7.205A pdb=" N ILE C 391 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN C 367 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE C 393 " --> pdb=" O ASN C 367 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS C 389 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR C 418 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 391 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TRP C 415 " --> pdb=" O GLY C 442 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE C 444 " --> pdb=" O TRP C 415 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE C 417 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLU C 446 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL C 419 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N TYR C 503 " --> pdb=" O GLN C 441 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE C 443 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLN C 505 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE C 445 " --> pdb=" O GLN C 505 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 529 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N SER C 581 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE C 531 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR C 601 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TRP C 627 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C 602 " --> pdb=" O TRP C 627 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 480 through 482 Processing sheet with id=AC7, first strand: chain 'C' and resid 711 through 712 Processing sheet with id=AC8, first strand: chain 'C' and resid 727 through 732 removed outlier: 4.011A pdb=" N LEU C 727 " --> pdb=" O PHE C 813 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 768 " --> pdb=" O SER C 780 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER C 780 " --> pdb=" O ILE C 768 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 770 " --> pdb=" O LEU C 778 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1050 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: 3.44 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3493 1.33 - 1.45: 4330 1.45 - 1.57: 9079 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 17007 Sorted by residual: bond pdb=" C VAL B 688 " pdb=" N PRO B 689 " ideal model delta sigma weight residual 1.332 1.384 -0.052 1.12e-02 7.97e+03 2.14e+01 bond pdb=" N VAL C 867 " pdb=" CA VAL C 867 " ideal model delta sigma weight residual 1.460 1.496 -0.036 8.60e-03 1.35e+04 1.72e+01 bond pdb=" C GLU A 855 " pdb=" N PRO A 856 " ideal model delta sigma weight residual 1.329 1.378 -0.048 1.18e-02 7.18e+03 1.68e+01 bond pdb=" N VAL B 688 " pdb=" CA VAL B 688 " ideal model delta sigma weight residual 1.462 1.497 -0.035 9.10e-03 1.21e+04 1.45e+01 bond pdb=" N GLU A 855 " pdb=" CA GLU A 855 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.35e+01 ... (remaining 17002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 22453 1.95 - 3.90: 577 3.90 - 5.86: 59 5.86 - 7.81: 4 7.81 - 9.76: 1 Bond angle restraints: 23094 Sorted by residual: angle pdb=" CA VAL B 688 " pdb=" C VAL B 688 " pdb=" N PRO B 689 " ideal model delta sigma weight residual 117.00 122.06 -5.06 9.50e-01 1.11e+00 2.84e+01 angle pdb=" N ASP B 589 " pdb=" CA ASP B 589 " pdb=" C ASP B 589 " ideal model delta sigma weight residual 111.90 118.90 -7.00 1.32e+00 5.74e-01 2.81e+01 angle pdb=" CA ASN B 438 " pdb=" C ASN B 438 " pdb=" O ASN B 438 " ideal model delta sigma weight residual 120.43 114.72 5.71 1.09e+00 8.42e-01 2.75e+01 angle pdb=" N TYR B 439 " pdb=" CA TYR B 439 " pdb=" C TYR B 439 " ideal model delta sigma weight residual 111.11 117.36 -6.25 1.20e+00 6.94e-01 2.71e+01 angle pdb=" CA TYR B 439 " pdb=" C TYR B 439 " pdb=" O TYR B 439 " ideal model delta sigma weight residual 120.90 115.83 5.07 1.07e+00 8.73e-01 2.25e+01 ... (remaining 23089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9300 17.86 - 35.72: 538 35.72 - 53.58: 57 53.58 - 71.44: 14 71.44 - 89.30: 6 Dihedral angle restraints: 9915 sinusoidal: 3759 harmonic: 6156 Sorted by residual: dihedral pdb=" C THR A 412 " pdb=" N THR A 412 " pdb=" CA THR A 412 " pdb=" CB THR A 412 " ideal model delta harmonic sigma weight residual -122.00 -134.76 12.76 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C THR B 412 " pdb=" N THR B 412 " pdb=" CA THR B 412 " pdb=" CB THR B 412 " ideal model delta harmonic sigma weight residual -122.00 -134.31 12.31 0 2.50e+00 1.60e-01 2.42e+01 dihedral pdb=" C THR C 412 " pdb=" N THR C 412 " pdb=" CA THR C 412 " pdb=" CB THR C 412 " ideal model delta harmonic sigma weight residual -122.00 -134.23 12.23 0 2.50e+00 1.60e-01 2.39e+01 ... (remaining 9912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2142 0.083 - 0.166: 321 0.166 - 0.249: 23 0.249 - 0.332: 1 0.332 - 0.415: 3 Chirality restraints: 2490 Sorted by residual: chirality pdb=" CA THR A 412 " pdb=" N THR A 412 " pdb=" C THR A 412 " pdb=" CB THR A 412 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA THR B 412 " pdb=" N THR B 412 " pdb=" C THR B 412 " pdb=" CB THR B 412 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA THR C 412 " pdb=" N THR C 412 " pdb=" C THR C 412 " pdb=" CB THR C 412 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 2487 not shown) Planarity restraints: 3039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 438 " -0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C ASN B 438 " 0.089 2.00e-02 2.50e+03 pdb=" O ASN B 438 " -0.033 2.00e-02 2.50e+03 pdb=" N TYR B 439 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 414 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C ARG B 414 " 0.056 2.00e-02 2.50e+03 pdb=" O ARG B 414 " -0.021 2.00e-02 2.50e+03 pdb=" N TRP B 415 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 436 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLN B 436 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN B 436 " -0.020 2.00e-02 2.50e+03 pdb=" N SER B 437 " -0.019 2.00e-02 2.50e+03 ... (remaining 3036 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 23 2.36 - 2.99: 8612 2.99 - 3.63: 23871 3.63 - 4.26: 42822 4.26 - 4.90: 70773 Nonbonded interactions: 146101 Sorted by model distance: nonbonded pdb=" OE1 GLU C 545 " pdb=" CE1 PHE C 594 " model vdw 1.725 3.340 nonbonded pdb=" OE1 GLU C 545 " pdb=" CZ PHE C 594 " model vdw 1.942 3.340 nonbonded pdb=" CB GLU C 545 " pdb=" CE1 PHE C 594 " model vdw 1.963 3.740 nonbonded pdb=" OD1 ASP A 589 " pdb=" NZ LYS B 587 " model vdw 2.094 3.120 nonbonded pdb=" O SER B 590 " pdb=" OG SER B 590 " model vdw 2.122 3.040 ... (remaining 146096 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic 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: 2.180 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.760 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 0.052 17007 Z= 0.310 Angle : 0.660 9.762 23094 Z= 0.452 Chirality : 0.055 0.415 2490 Planarity : 0.004 0.051 3039 Dihedral : 11.180 89.305 6009 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.17 % Allowed : 1.82 % Favored : 98.01 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.15), residues: 2142 helix: -3.67 (0.18), residues: 243 sheet: -1.16 (0.20), residues: 657 loop : -2.33 (0.14), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.013 0.001 TYR A 758 PHE 0.016 0.001 PHE B 413 TRP 0.007 0.001 TRP A 782 HIS 0.003 0.001 HIS B 826 Details of bonding type rmsd covalent geometry : bond 0.00425 (17007) covalent geometry : angle 0.66038 (23094) hydrogen bonds : bond 0.23431 ( 365) hydrogen bonds : angle 8.79280 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 259 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 401 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7780 (ttt180) REVERT: A 612 GLU cc_start: 0.7990 (tt0) cc_final: 0.7601 (tt0) REVERT: A 874 MET cc_start: 0.8580 (mtm) cc_final: 0.8361 (mtp) REVERT: B 401 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7828 (ttt180) outliers start: 3 outliers final: 2 residues processed: 262 average time/residue: 0.6734 time to fit residues: 194.2946 Evaluate side-chains 141 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 741 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 356 ASN A 367 ASN A 431 HIS A 438 ASN A 461 HIS A 468 ASN A 486 ASN A 501 GLN A 525 ASN A 533 GLN A 606 ASN A 671 HIS A 687 ASN A 726 HIS A 902 ASN B 220 HIS B 306 GLN B 431 HIS B 438 ASN B 452 GLN B 461 HIS B 501 GLN B 525 ASN B 533 GLN B 548 ASN B 606 ASN B 671 HIS B 726 HIS B 853 GLN B 902 ASN C 220 HIS C 306 GLN C 431 HIS C 438 ASN C 452 GLN C 461 HIS C 501 GLN C 525 ASN C 606 ASN C 671 HIS C 687 ASN C 718 HIS C 726 HIS C 744 ASN C 893 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.114381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.093818 restraints weight = 18238.048| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.38 r_work: 0.2883 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17007 Z= 0.117 Angle : 0.521 6.428 23094 Z= 0.286 Chirality : 0.046 0.140 2490 Planarity : 0.004 0.062 3039 Dihedral : 4.794 19.500 2324 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.05 % Allowed : 7.52 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.16), residues: 2142 helix: -2.03 (0.25), residues: 270 sheet: -0.94 (0.19), residues: 690 loop : -2.10 (0.15), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 414 TYR 0.010 0.001 TYR B 842 PHE 0.020 0.001 PHE B 382 TRP 0.009 0.001 TRP C 782 HIS 0.003 0.001 HIS A 718 Details of bonding type rmsd covalent geometry : bond 0.00257 (17007) covalent geometry : angle 0.52145 (23094) hydrogen bonds : bond 0.03914 ( 365) hydrogen bonds : angle 5.97894 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.581 Fit side-chains REVERT: A 401 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8215 (ttt180) REVERT: A 487 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6879 (mt-10) REVERT: A 572 ASP cc_start: 0.8416 (t70) cc_final: 0.8004 (t70) REVERT: A 612 GLU cc_start: 0.8843 (tt0) cc_final: 0.8543 (tt0) REVERT: A 705 ASP cc_start: 0.8520 (t0) cc_final: 0.8254 (t0) REVERT: A 874 MET cc_start: 0.8730 (mtm) cc_final: 0.8283 (mtp) REVERT: A 902 ASN cc_start: 0.8421 (m110) cc_final: 0.8165 (m-40) REVERT: B 395 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7570 (tmt170) REVERT: B 401 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.8327 (ttt180) REVERT: B 602 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8832 (mm) REVERT: B 612 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 684 THR cc_start: 0.8549 (t) cc_final: 0.8203 (m) REVERT: B 739 SER cc_start: 0.8863 (m) cc_final: 0.8463 (t) REVERT: C 487 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6975 (mt-10) REVERT: C 572 ASP cc_start: 0.8352 (t0) cc_final: 0.8122 (t0) REVERT: C 597 LYS cc_start: 0.7928 (tmtt) cc_final: 0.7530 (tmtt) REVERT: C 602 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8916 (mm) REVERT: C 853 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7605 (mt0) outliers start: 19 outliers final: 5 residues processed: 157 average time/residue: 0.6323 time to fit residues: 110.0902 Evaluate side-chains 140 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 869 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 73 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 99 optimal weight: 0.0060 chunk 129 optimal weight: 8.9990 chunk 122 optimal weight: 0.0020 chunk 81 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 overall best weight: 2.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 687 ASN C 533 GLN C 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.087805 restraints weight = 18505.549| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.36 r_work: 0.2792 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17007 Z= 0.184 Angle : 0.597 7.332 23094 Z= 0.327 Chirality : 0.049 0.162 2490 Planarity : 0.004 0.054 3039 Dihedral : 5.385 21.878 2322 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.38 % Allowed : 8.29 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.17), residues: 2142 helix: -1.46 (0.28), residues: 270 sheet: -0.79 (0.20), residues: 690 loop : -1.94 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 799 TYR 0.012 0.002 TYR B 540 PHE 0.022 0.002 PHE B 382 TRP 0.014 0.002 TRP C 782 HIS 0.006 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00437 (17007) covalent geometry : angle 0.59663 (23094) hydrogen bonds : bond 0.04506 ( 365) hydrogen bonds : angle 5.93377 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 487 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7135 (mt-10) REVERT: A 572 ASP cc_start: 0.8585 (t70) cc_final: 0.8155 (t70) REVERT: A 612 GLU cc_start: 0.8806 (tt0) cc_final: 0.8445 (tt0) REVERT: A 874 MET cc_start: 0.8690 (mtm) cc_final: 0.8396 (mtp) REVERT: B 304 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.7709 (mmt) REVERT: B 395 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7558 (tmt170) REVERT: B 602 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8919 (mm) REVERT: B 612 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8103 (mt-10) REVERT: B 684 THR cc_start: 0.8584 (t) cc_final: 0.8266 (m) REVERT: C 487 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7126 (mt-10) REVERT: C 572 ASP cc_start: 0.8474 (t0) cc_final: 0.8222 (t0) REVERT: C 597 LYS cc_start: 0.8153 (tmtt) cc_final: 0.7899 (tmtt) REVERT: C 853 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7676 (mt0) outliers start: 25 outliers final: 7 residues processed: 160 average time/residue: 0.6704 time to fit residues: 118.3801 Evaluate side-chains 143 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 201 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 73 optimal weight: 0.0020 chunk 16 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN A 902 ASN B 392 ASN B 786 GLN B 902 ASN C 548 ASN C 818 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.106232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.086410 restraints weight = 18530.580| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.34 r_work: 0.2764 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17007 Z= 0.240 Angle : 0.644 7.909 23094 Z= 0.355 Chirality : 0.051 0.181 2490 Planarity : 0.005 0.049 3039 Dihedral : 5.693 24.238 2322 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.66 % Allowed : 8.51 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.17), residues: 2142 helix: -1.32 (0.30), residues: 270 sheet: -0.73 (0.20), residues: 660 loop : -1.89 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 799 TYR 0.014 0.002 TYR C 264 PHE 0.025 0.002 PHE B 382 TRP 0.011 0.002 TRP A 782 HIS 0.008 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00578 (17007) covalent geometry : angle 0.64447 (23094) hydrogen bonds : bond 0.04527 ( 365) hydrogen bonds : angle 5.96411 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.609 Fit side-chains REVERT: A 487 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7237 (mt-10) REVERT: A 545 GLU cc_start: 0.8612 (pt0) cc_final: 0.8239 (pt0) REVERT: A 587 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8742 (tttt) REVERT: A 602 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8934 (mm) REVERT: A 612 GLU cc_start: 0.8810 (tt0) cc_final: 0.8446 (tt0) REVERT: A 705 ASP cc_start: 0.8752 (t0) cc_final: 0.8550 (t0) REVERT: A 874 MET cc_start: 0.8758 (mtm) cc_final: 0.8491 (mtp) REVERT: A 902 ASN cc_start: 0.8540 (m110) cc_final: 0.8294 (m-40) REVERT: B 304 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.7738 (mmt) REVERT: B 395 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7560 (tmt170) REVERT: B 490 LYS cc_start: 0.8731 (mptt) cc_final: 0.8284 (mmtt) REVERT: B 597 LYS cc_start: 0.8042 (tmtt) cc_final: 0.7803 (tmtt) REVERT: B 602 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8938 (mm) REVERT: B 612 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8140 (mt-10) REVERT: B 684 THR cc_start: 0.8564 (t) cc_final: 0.8277 (m) REVERT: C 487 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7247 (mt-10) REVERT: C 572 ASP cc_start: 0.8556 (t0) cc_final: 0.8311 (t0) REVERT: C 573 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8828 (mm) REVERT: C 597 LYS cc_start: 0.8221 (tmtt) cc_final: 0.7928 (tmtt) REVERT: C 602 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9011 (mm) REVERT: C 782 TRP cc_start: 0.8128 (OUTLIER) cc_final: 0.7679 (m-10) outliers start: 30 outliers final: 9 residues processed: 154 average time/residue: 0.6876 time to fit residues: 116.8879 Evaluate side-chains 146 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 782 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN A 468 ASN B 436 GLN B 786 GLN C 436 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.110589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.090274 restraints weight = 18277.660| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.36 r_work: 0.2826 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17007 Z= 0.098 Angle : 0.498 6.494 23094 Z= 0.273 Chirality : 0.045 0.136 2490 Planarity : 0.004 0.046 3039 Dihedral : 5.152 22.315 2322 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.16 % Allowed : 9.40 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.17), residues: 2142 helix: -0.92 (0.31), residues: 270 sheet: -0.66 (0.20), residues: 678 loop : -1.68 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 799 TYR 0.009 0.001 TYR C 264 PHE 0.016 0.001 PHE B 382 TRP 0.004 0.001 TRP C 230 HIS 0.004 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00214 (17007) covalent geometry : angle 0.49843 (23094) hydrogen bonds : bond 0.03335 ( 365) hydrogen bonds : angle 5.47822 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.564 Fit side-chains REVERT: A 304 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8310 (mtp) REVERT: A 487 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7154 (mt-10) REVERT: A 572 ASP cc_start: 0.8485 (t70) cc_final: 0.8133 (t70) REVERT: A 612 GLU cc_start: 0.8767 (tt0) cc_final: 0.8407 (tt0) REVERT: A 705 ASP cc_start: 0.8630 (t0) cc_final: 0.8415 (t0) REVERT: A 874 MET cc_start: 0.8706 (mtm) cc_final: 0.8187 (mtp) REVERT: A 906 SER cc_start: 0.8191 (t) cc_final: 0.7800 (m) REVERT: B 395 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7636 (tmt170) REVERT: B 490 LYS cc_start: 0.8657 (mptt) cc_final: 0.8215 (mmtt) REVERT: B 602 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8838 (mm) REVERT: B 612 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8080 (mt-10) REVERT: B 684 THR cc_start: 0.8524 (t) cc_final: 0.8234 (m) REVERT: C 487 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7099 (mt-10) REVERT: C 494 SER cc_start: 0.8119 (t) cc_final: 0.7723 (p) REVERT: C 602 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8954 (mm) REVERT: C 782 TRP cc_start: 0.7931 (OUTLIER) cc_final: 0.7502 (m-10) REVERT: C 853 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: C 902 ASN cc_start: 0.8204 (m110) cc_final: 0.7999 (m110) outliers start: 21 outliers final: 6 residues processed: 155 average time/residue: 0.6708 time to fit residues: 114.9920 Evaluate side-chains 144 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 158 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN A 902 ASN B 786 GLN C 292 ASN C 356 ASN C 818 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.087199 restraints weight = 18435.091| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.34 r_work: 0.2785 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17007 Z= 0.201 Angle : 0.600 7.521 23094 Z= 0.329 Chirality : 0.050 0.167 2490 Planarity : 0.004 0.045 3039 Dihedral : 5.496 22.870 2322 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.44 % Allowed : 9.67 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.17), residues: 2142 helix: -0.93 (0.31), residues: 270 sheet: -0.62 (0.20), residues: 678 loop : -1.73 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 799 TYR 0.013 0.002 TYR C 264 PHE 0.023 0.002 PHE B 382 TRP 0.008 0.001 TRP A 695 HIS 0.007 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00482 (17007) covalent geometry : angle 0.59951 (23094) hydrogen bonds : bond 0.04100 ( 365) hydrogen bonds : angle 5.68670 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.644 Fit side-chains REVERT: A 487 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7199 (mt-10) REVERT: A 572 ASP cc_start: 0.8629 (t70) cc_final: 0.8226 (t70) REVERT: A 587 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8669 (tttt) REVERT: A 602 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8913 (mm) REVERT: A 612 GLU cc_start: 0.8780 (tt0) cc_final: 0.8427 (tt0) REVERT: A 874 MET cc_start: 0.8786 (mtm) cc_final: 0.8438 (mtp) REVERT: A 902 ASN cc_start: 0.8484 (m110) cc_final: 0.8243 (m-40) REVERT: B 395 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7568 (tmt170) REVERT: B 490 LYS cc_start: 0.8688 (mptt) cc_final: 0.8265 (mmtt) REVERT: B 602 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8932 (mm) REVERT: B 612 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 684 THR cc_start: 0.8551 (t) cc_final: 0.8279 (m) REVERT: C 487 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7170 (mt-10) REVERT: C 494 SER cc_start: 0.8101 (t) cc_final: 0.7705 (p) REVERT: C 597 LYS cc_start: 0.8291 (ttpt) cc_final: 0.7645 (tmtt) REVERT: C 782 TRP cc_start: 0.8013 (OUTLIER) cc_final: 0.7628 (m-10) REVERT: C 853 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7638 (mt0) outliers start: 26 outliers final: 12 residues processed: 154 average time/residue: 0.6555 time to fit residues: 111.4146 Evaluate side-chains 146 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 786 GLN Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 83 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 786 GLN C 818 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.086876 restraints weight = 18309.362| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.35 r_work: 0.2773 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17007 Z= 0.180 Angle : 0.583 7.463 23094 Z= 0.320 Chirality : 0.049 0.161 2490 Planarity : 0.004 0.043 3039 Dihedral : 5.519 23.086 2322 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.66 % Allowed : 9.95 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.17), residues: 2142 helix: -0.97 (0.31), residues: 270 sheet: -0.59 (0.20), residues: 675 loop : -1.72 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 799 TYR 0.012 0.002 TYR C 264 PHE 0.022 0.002 PHE B 382 TRP 0.007 0.001 TRP A 782 HIS 0.006 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00428 (17007) covalent geometry : angle 0.58261 (23094) hydrogen bonds : bond 0.03959 ( 365) hydrogen bonds : angle 5.64077 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.462 Fit side-chains REVERT: A 487 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7142 (mt-10) REVERT: A 572 ASP cc_start: 0.8646 (t70) cc_final: 0.8234 (t70) REVERT: A 573 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8578 (mm) REVERT: A 578 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8757 (mm) REVERT: A 587 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8651 (tttt) REVERT: A 602 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8909 (mm) REVERT: A 612 GLU cc_start: 0.8801 (tt0) cc_final: 0.8441 (tt0) REVERT: A 874 MET cc_start: 0.8786 (mtm) cc_final: 0.8443 (mtp) REVERT: B 304 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.7981 (mtp) REVERT: B 395 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7558 (tmt170) REVERT: B 490 LYS cc_start: 0.8699 (mptt) cc_final: 0.8261 (mmtt) REVERT: B 602 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8914 (mm) REVERT: B 612 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 684 THR cc_start: 0.8557 (t) cc_final: 0.8280 (m) REVERT: B 782 TRP cc_start: 0.8227 (OUTLIER) cc_final: 0.7659 (m-10) REVERT: C 221 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8668 (t) REVERT: C 487 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7119 (mt-10) REVERT: C 494 SER cc_start: 0.8087 (t) cc_final: 0.7680 (p) REVERT: C 597 LYS cc_start: 0.8331 (ttpt) cc_final: 0.7646 (tmtt) REVERT: C 602 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.9028 (mm) REVERT: C 782 TRP cc_start: 0.7984 (OUTLIER) cc_final: 0.7602 (m-10) REVERT: C 853 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7610 (mt0) outliers start: 30 outliers final: 10 residues processed: 156 average time/residue: 0.6524 time to fit residues: 112.2986 Evaluate side-chains 151 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 782 TRP Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 182 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 178 optimal weight: 0.4980 chunk 173 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 902 ASN C 818 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.088305 restraints weight = 18298.591| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.36 r_work: 0.2798 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17007 Z= 0.130 Angle : 0.536 7.035 23094 Z= 0.294 Chirality : 0.047 0.146 2490 Planarity : 0.004 0.043 3039 Dihedral : 5.319 22.424 2322 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.38 % Allowed : 10.56 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.17), residues: 2142 helix: -0.84 (0.31), residues: 270 sheet: -0.58 (0.20), residues: 678 loop : -1.62 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 799 TYR 0.011 0.001 TYR C 264 PHE 0.020 0.001 PHE B 382 TRP 0.006 0.001 TRP C 782 HIS 0.005 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00302 (17007) covalent geometry : angle 0.53632 (23094) hydrogen bonds : bond 0.03575 ( 365) hydrogen bonds : angle 5.47227 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.687 Fit side-chains REVERT: A 304 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8267 (mtp) REVERT: A 487 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7141 (mt-10) REVERT: A 572 ASP cc_start: 0.8586 (t70) cc_final: 0.8211 (t70) REVERT: A 573 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8551 (mm) REVERT: A 587 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8573 (tttt) REVERT: A 612 GLU cc_start: 0.8797 (tt0) cc_final: 0.8447 (tt0) REVERT: A 782 TRP cc_start: 0.7986 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: A 874 MET cc_start: 0.8802 (mtm) cc_final: 0.8467 (mtp) REVERT: A 902 ASN cc_start: 0.8461 (m110) cc_final: 0.8206 (m-40) REVERT: A 906 SER cc_start: 0.8167 (t) cc_final: 0.7862 (m) REVERT: B 304 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7958 (mtp) REVERT: B 395 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7620 (tmt170) REVERT: B 490 LYS cc_start: 0.8692 (mptt) cc_final: 0.8254 (mmtt) REVERT: B 602 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8864 (mm) REVERT: B 612 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8102 (mt-10) REVERT: B 684 THR cc_start: 0.8529 (t) cc_final: 0.8246 (m) REVERT: B 782 TRP cc_start: 0.8038 (OUTLIER) cc_final: 0.7518 (m-10) REVERT: C 221 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8653 (t) REVERT: C 487 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7109 (mt-10) REVERT: C 494 SER cc_start: 0.8066 (t) cc_final: 0.7735 (p) REVERT: C 597 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7639 (tmtt) REVERT: C 782 TRP cc_start: 0.7940 (OUTLIER) cc_final: 0.7545 (m-10) REVERT: C 853 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7574 (mt0) outliers start: 25 outliers final: 10 residues processed: 152 average time/residue: 0.6633 time to fit residues: 111.2848 Evaluate side-chains 149 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 782 TRP Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 782 TRP Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 170 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 147 optimal weight: 0.2980 chunk 159 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 818 ASN C 902 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.110181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.089850 restraints weight = 18205.048| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.36 r_work: 0.2823 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17007 Z= 0.110 Angle : 0.511 6.633 23094 Z= 0.278 Chirality : 0.046 0.139 2490 Planarity : 0.004 0.044 3039 Dihedral : 5.112 22.907 2322 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.38 % Allowed : 10.89 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.17), residues: 2142 helix: -0.76 (0.32), residues: 273 sheet: -0.51 (0.20), residues: 693 loop : -1.62 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 799 TYR 0.009 0.001 TYR C 264 PHE 0.018 0.001 PHE B 382 TRP 0.006 0.001 TRP C 782 HIS 0.004 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00250 (17007) covalent geometry : angle 0.51051 (23094) hydrogen bonds : bond 0.03297 ( 365) hydrogen bonds : angle 5.31074 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.560 Fit side-chains REVERT: A 304 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8278 (mtp) REVERT: A 487 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7143 (mt-10) REVERT: A 572 ASP cc_start: 0.8570 (t70) cc_final: 0.8210 (t70) REVERT: A 573 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8508 (mm) REVERT: A 587 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8518 (tttt) REVERT: A 602 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8835 (mm) REVERT: A 612 GLU cc_start: 0.8784 (tt0) cc_final: 0.8448 (tt0) REVERT: A 873 GLN cc_start: 0.8235 (tt0) cc_final: 0.7913 (tt0) REVERT: A 874 MET cc_start: 0.8838 (mtm) cc_final: 0.8411 (mtp) REVERT: A 906 SER cc_start: 0.8165 (t) cc_final: 0.7821 (m) REVERT: B 304 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.7905 (mtp) REVERT: B 395 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7714 (tmt170) REVERT: B 490 LYS cc_start: 0.8656 (mptt) cc_final: 0.8221 (mmtt) REVERT: B 602 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8814 (mm) REVERT: B 612 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7715 (mp0) REVERT: B 684 THR cc_start: 0.8473 (t) cc_final: 0.8201 (m) REVERT: B 782 TRP cc_start: 0.7957 (OUTLIER) cc_final: 0.7398 (m-10) REVERT: C 487 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7090 (mt-10) REVERT: C 494 SER cc_start: 0.8152 (t) cc_final: 0.7835 (p) REVERT: C 782 TRP cc_start: 0.7905 (OUTLIER) cc_final: 0.7497 (m-10) REVERT: C 853 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7607 (mt0) outliers start: 25 outliers final: 11 residues processed: 150 average time/residue: 0.6660 time to fit residues: 110.4164 Evaluate side-chains 155 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 782 TRP Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 90 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 81 optimal weight: 0.0170 chunk 60 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.0770 chunk 55 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 902 ASN C 818 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.090827 restraints weight = 18236.718| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.36 r_work: 0.2837 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17007 Z= 0.098 Angle : 0.497 6.385 23094 Z= 0.270 Chirality : 0.045 0.138 2490 Planarity : 0.004 0.043 3039 Dihedral : 4.970 24.284 2322 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.27 % Allowed : 11.00 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.17), residues: 2142 helix: -0.69 (0.32), residues: 273 sheet: -0.50 (0.20), residues: 708 loop : -1.54 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 799 TYR 0.009 0.001 TYR C 264 PHE 0.017 0.001 PHE B 382 TRP 0.006 0.001 TRP C 782 HIS 0.004 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00219 (17007) covalent geometry : angle 0.49726 (23094) hydrogen bonds : bond 0.03121 ( 365) hydrogen bonds : angle 5.19904 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.445 Fit side-chains REVERT: A 487 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7135 (mt-10) REVERT: A 572 ASP cc_start: 0.8549 (t70) cc_final: 0.8193 (t70) REVERT: A 573 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8475 (mm) REVERT: A 587 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8467 (tttt) REVERT: A 602 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8832 (mm) REVERT: A 612 GLU cc_start: 0.8764 (tt0) cc_final: 0.8411 (tt0) REVERT: A 705 ASP cc_start: 0.8592 (t0) cc_final: 0.8389 (t0) REVERT: A 873 GLN cc_start: 0.8229 (tt0) cc_final: 0.7902 (tt0) REVERT: A 874 MET cc_start: 0.8844 (mtm) cc_final: 0.8401 (mtp) REVERT: A 902 ASN cc_start: 0.8475 (m110) cc_final: 0.8222 (m-40) REVERT: A 906 SER cc_start: 0.8137 (t) cc_final: 0.7793 (m) REVERT: B 395 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7687 (tmt170) REVERT: B 490 LYS cc_start: 0.8646 (mptt) cc_final: 0.8214 (mmtt) REVERT: B 612 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7730 (mp0) REVERT: B 684 THR cc_start: 0.8483 (t) cc_final: 0.8207 (m) REVERT: B 782 TRP cc_start: 0.7950 (OUTLIER) cc_final: 0.7352 (m-10) REVERT: C 487 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7071 (mt-10) REVERT: C 494 SER cc_start: 0.8140 (t) cc_final: 0.7864 (p) REVERT: C 782 TRP cc_start: 0.7856 (OUTLIER) cc_final: 0.7424 (m-10) REVERT: C 853 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7588 (mt0) outliers start: 23 outliers final: 11 residues processed: 157 average time/residue: 0.6254 time to fit residues: 109.0095 Evaluate side-chains 152 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 782 TRP Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 145 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 163 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 HIS C 548 ASN C 818 ASN C 902 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.110618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.090235 restraints weight = 18254.551| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.37 r_work: 0.2827 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17007 Z= 0.111 Angle : 0.510 6.522 23094 Z= 0.278 Chirality : 0.046 0.138 2490 Planarity : 0.004 0.043 3039 Dihedral : 5.009 24.056 2322 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.16 % Allowed : 11.33 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.17), residues: 2142 helix: -0.69 (0.32), residues: 273 sheet: -0.48 (0.20), residues: 708 loop : -1.52 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 799 TYR 0.010 0.001 TYR C 264 PHE 0.019 0.001 PHE B 382 TRP 0.006 0.001 TRP C 782 HIS 0.004 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00252 (17007) covalent geometry : angle 0.51033 (23094) hydrogen bonds : bond 0.03250 ( 365) hydrogen bonds : angle 5.23267 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4809.20 seconds wall clock time: 82 minutes 50.84 seconds (4970.84 seconds total)