Starting phenix.real_space_refine on Tue Jan 21 12:42:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3m_38889/01_2025/8y3m_38889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3m_38889/01_2025/8y3m_38889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3m_38889/01_2025/8y3m_38889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3m_38889/01_2025/8y3m_38889.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3m_38889/01_2025/8y3m_38889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3m_38889/01_2025/8y3m_38889.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.079 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 65 5.16 5 C 10877 2.51 5 N 2705 2.21 5 O 3146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16793 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7968 Classifications: {'peptide': 957} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 937} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 7996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7996 Classifications: {'peptide': 958} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 938} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 829 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.72, per 1000 atoms: 0.64 Number of scatterers: 16793 At special positions: 0 Unit cell: (103.421, 131.431, 150.822, 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 65 16.00 O 3146 8.00 N 2705 7.00 C 10877 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: 3.93 Conformation dependent library (CDL) restraints added in 2.2 seconds 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 7 sheets defined 57.2% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 23 through 40 removed outlier: 3.939A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 28 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.608A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 removed outlier: 3.754A pdb=" N ILE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.159A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 197 through 209 removed outlier: 3.921A pdb=" N SER A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.564A pdb=" N ASN A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.686A pdb=" N TYR A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.845A pdb=" N PHE A 320 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 317 through 321' Processing helix chain 'A' and resid 326 through 334 removed outlier: 4.375A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.513A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.798A pdb=" N GLU A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 392 removed outlier: 3.646A pdb=" N GLY A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.799A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 470 through 490 Processing helix chain 'A' and resid 510 through 519 removed outlier: 3.585A pdb=" N ARG A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 4.268A pdb=" N PHE A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 524 through 529' Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.556A pdb=" N LYS A 537 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 533 through 538' Processing helix chain 'A' and resid 551 through 557 Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 580 through 589 removed outlier: 3.957A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 598 removed outlier: 3.829A pdb=" N LEU A 595 " --> pdb=" O ASN A 591 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 626 removed outlier: 4.132A pdb=" N HIS A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A 610 " --> pdb=" O HIS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 removed outlier: 3.709A pdb=" N VAL A 653 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 672 through 676 removed outlier: 3.683A pdb=" N LYS A 675 " --> pdb=" O SER A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 699 removed outlier: 3.636A pdb=" N GLU A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 722 removed outlier: 3.789A pdb=" N THR A 710 " --> pdb=" O VAL A 706 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 753 through 765 removed outlier: 4.248A pdb=" N TRP A 757 " --> pdb=" O LYS A 753 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 785 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.870A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 831 through 841 Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 854 Processing helix chain 'A' and resid 861 through 872 removed outlier: 4.035A pdb=" N ARG A 870 " --> pdb=" O MET A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 898 removed outlier: 4.009A pdb=" N GLU A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 883 " --> pdb=" O PRO A 879 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 922 removed outlier: 3.761A pdb=" N TRP A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.880A pdb=" N PHE A 933 " --> pdb=" O MET A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 944 removed outlier: 3.685A pdb=" N PHE A 943 " --> pdb=" O GLN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 990 removed outlier: 3.893A pdb=" N GLU A 982 " --> pdb=" O HIS A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.527A pdb=" N GLU A 998 " --> pdb=" O LYS A 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 21 removed outlier: 3.585A pdb=" N GLY B 12 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 removed outlier: 3.939A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.609A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 removed outlier: 3.753A pdb=" N ILE B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 154 through 158 removed outlier: 4.159A pdb=" N VAL B 158 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 197 through 209 removed outlier: 3.920A pdb=" N SER B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 202 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.564A pdb=" N ASN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 removed outlier: 3.685A pdb=" N TYR B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.845A pdb=" N PHE B 320 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 317 through 321' Processing helix chain 'B' and resid 326 through 334 removed outlier: 4.374A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 removed outlier: 3.513A pdb=" N GLU B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.798A pdb=" N GLU B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 392 removed outlier: 3.646A pdb=" N GLY B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.800A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 470 through 493 removed outlier: 3.871A pdb=" N GLN B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 519 removed outlier: 3.585A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 529 removed outlier: 4.267A pdb=" N PHE B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 529' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.555A pdb=" N LYS B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 538 " --> pdb=" O GLU B 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 533 through 538' Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 558 through 565 Processing helix chain 'B' and resid 580 through 589 removed outlier: 3.958A pdb=" N VAL B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 removed outlier: 3.829A pdb=" N LEU B 595 " --> pdb=" O ASN B 591 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 626 removed outlier: 4.134A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 610 " --> pdb=" O HIS B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 659 removed outlier: 3.708A pdb=" N VAL B 653 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE B 655 " --> pdb=" O ASP B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.682A pdb=" N LYS B 675 " --> pdb=" O SER B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 699 removed outlier: 3.637A pdb=" N GLU B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 722 removed outlier: 3.789A pdb=" N THR B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 722 " --> pdb=" O ALA B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 735 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 753 through 765 removed outlier: 4.247A pdb=" N TRP B 757 " --> pdb=" O LYS B 753 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 785 Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.870A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 Processing helix chain 'B' and resid 831 through 841 Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 846 through 854 Processing helix chain 'B' and resid 861 through 872 removed outlier: 4.036A pdb=" N ARG B 870 " --> pdb=" O MET B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 898 removed outlier: 4.009A pdb=" N GLU B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 883 " --> pdb=" O PRO B 879 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 922 removed outlier: 3.760A pdb=" N TRP B 919 " --> pdb=" O THR B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.879A pdb=" N PHE B 933 " --> pdb=" O MET B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 944 removed outlier: 3.686A pdb=" N PHE B 943 " --> pdb=" O GLN B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 990 removed outlier: 3.893A pdb=" N GLU B 982 " --> pdb=" O HIS B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1003 removed outlier: 3.528A pdb=" N GLU B 998 " --> pdb=" O LYS B 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.274A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 44 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 340 removed outlier: 3.551A pdb=" N VAL A 347 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 575 Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.274A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 44 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 339 through 340 removed outlier: 3.551A pdb=" N VAL B 347 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 28 removed outlier: 3.590A pdb=" N VAL C 87 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 647 hydrogen bonds defined for protein. 1887 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: 5.00 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5020 1.34 - 1.46: 3544 1.46 - 1.58: 8503 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 17175 Sorted by residual: bond pdb=" C TYR B 56 " pdb=" N PRO B 57 " ideal model delta sigma weight residual 1.332 1.368 -0.036 1.12e-02 7.97e+03 1.05e+01 bond pdb=" C TYR A 56 " pdb=" N PRO A 57 " ideal model delta sigma weight residual 1.332 1.368 -0.036 1.12e-02 7.97e+03 1.03e+01 bond pdb=" C ILE A 955 " pdb=" N PRO A 956 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.51e-02 4.39e+03 9.39e+00 bond pdb=" C ILE B 955 " pdb=" N PRO B 956 " ideal model delta sigma weight residual 1.334 1.379 -0.045 1.51e-02 4.39e+03 8.98e+00 bond pdb=" CB VAL C 61 " pdb=" CG2 VAL C 61 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.73e+00 ... (remaining 17170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 21439 2.03 - 4.06: 1433 4.06 - 6.08: 181 6.08 - 8.11: 65 8.11 - 10.14: 23 Bond angle restraints: 23141 Sorted by residual: angle pdb=" N GLY C 70 " pdb=" CA GLY C 70 " pdb=" C GLY C 70 " ideal model delta sigma weight residual 111.95 105.61 6.34 9.50e-01 1.11e+00 4.45e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 114.75 107.77 6.98 1.26e+00 6.30e-01 3.06e+01 angle pdb=" N ASP A 291 " pdb=" CA ASP A 291 " pdb=" C ASP A 291 " ideal model delta sigma weight residual 114.75 107.81 6.94 1.26e+00 6.30e-01 3.04e+01 angle pdb=" C LYS C 93 " pdb=" N ASP C 94 " pdb=" CA ASP C 94 " ideal model delta sigma weight residual 121.54 131.56 -10.02 1.91e+00 2.74e-01 2.75e+01 angle pdb=" C ASN C 80 " pdb=" N PHE C 81 " pdb=" CA PHE C 81 " ideal model delta sigma weight residual 121.54 131.35 -9.81 1.91e+00 2.74e-01 2.64e+01 ... (remaining 23136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 9499 15.43 - 30.86: 561 30.86 - 46.29: 145 46.29 - 61.72: 18 61.72 - 77.14: 14 Dihedral angle restraints: 10237 sinusoidal: 4248 harmonic: 5989 Sorted by residual: dihedral pdb=" CA ILE B 631 " pdb=" C ILE B 631 " pdb=" N ASP B 632 " pdb=" CA ASP B 632 " ideal model delta harmonic sigma weight residual 180.00 120.38 59.62 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA ASP B 632 " pdb=" C ASP B 632 " pdb=" N GLU B 633 " pdb=" CA GLU B 633 " ideal model delta harmonic sigma weight residual -180.00 -121.16 -58.84 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA LYS B 364 " pdb=" C LYS B 364 " pdb=" N GLU B 365 " pdb=" CA GLU B 365 " ideal model delta harmonic sigma weight residual -180.00 -133.30 -46.70 0 5.00e+00 4.00e-02 8.72e+01 ... (remaining 10234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2203 0.090 - 0.180: 251 0.180 - 0.271: 16 0.271 - 0.361: 0 0.361 - 0.451: 2 Chirality restraints: 2472 Sorted by residual: chirality pdb=" CB VAL C 95 " pdb=" CA VAL C 95 " pdb=" CG1 VAL C 95 " pdb=" CG2 VAL C 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA PHE C 81 " pdb=" N PHE C 81 " pdb=" C PHE C 81 " pdb=" CB PHE C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB ILE B 955 " pdb=" CA ILE B 955 " pdb=" CG1 ILE B 955 " pdb=" CG2 ILE B 955 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 2469 not shown) Planarity restraints: 2945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 757 " -0.028 2.00e-02 2.50e+03 2.41e-02 1.45e+01 pdb=" CG TRP B 757 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 757 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 757 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 757 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 757 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 757 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 757 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 757 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 757 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 757 " 0.028 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP A 757 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 757 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 757 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 757 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 757 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 757 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 757 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 757 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 757 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 80 " 0.018 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ASN C 80 " -0.065 2.00e-02 2.50e+03 pdb=" O ASN C 80 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE C 81 " 0.022 2.00e-02 2.50e+03 ... (remaining 2942 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4989 2.82 - 3.34: 15186 3.34 - 3.86: 26602 3.86 - 4.38: 32411 4.38 - 4.90: 53992 Nonbonded interactions: 133180 Sorted by model distance: nonbonded pdb=" OG1 THR B 828 " pdb=" OD1 ASP B 830 " model vdw 2.299 3.040 nonbonded pdb=" OG1 THR A 828 " pdb=" OD1 ASP A 830 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 589 " pdb=" OD1 ASP A 651 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR B 589 " pdb=" OD1 ASP B 651 " model vdw 2.313 3.040 nonbonded pdb=" O TYR B 611 " pdb=" OG SER B 615 " model vdw 2.321 3.040 ... (remaining 133175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 376 or (resid 377 and (name N or name CA or nam \ e C or name O or name CB )) or resid 378 through 565 or resid 577 through 898 or \ resid 912 through 1005)) selection = (chain 'B' and (resid 12 through 491 or resid 506 through 628 or (resid 629 and \ (name N or name CA or name C or name O or name CB )) or resid 630 through 631 or \ resid 644 through 986 or (resid 987 and (name N or name CA or name C or name O \ or name CB )) or resid 988 through 1005)) } 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: 2.630 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 37.880 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 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 : 0.007 0.089 17175 Z= 0.420 Angle : 1.170 10.140 23141 Z= 0.707 Chirality : 0.058 0.451 2472 Planarity : 0.006 0.063 2945 Dihedral : 11.370 77.145 6381 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.60 % Allowed : 11.10 % Favored : 88.30 % Rotamer: Outliers : 0.11 % Allowed : 4.15 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.87 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.56 (0.13), residues: 1991 helix: -3.57 (0.10), residues: 1151 sheet: -1.24 (0.98), residues: 24 loop : -3.81 (0.16), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.005 TRP B 757 HIS 0.024 0.003 HIS A 118 PHE 0.058 0.004 PHE C 81 TYR 0.027 0.003 TYR A 804 ARG 0.018 0.001 ARG B 987 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 PHE cc_start: 0.5867 (t80) cc_final: 0.5646 (t80) REVERT: A 978 HIS cc_start: 0.7595 (t70) cc_final: 0.7278 (t-90) REVERT: A 994 LYS cc_start: 0.7935 (pttm) cc_final: 0.7067 (pttm) REVERT: B 152 ILE cc_start: 0.2659 (mt) cc_final: 0.2233 (mt) REVERT: B 962 TYR cc_start: 0.2187 (m-10) cc_final: 0.1144 (m-10) REVERT: B 969 LYS cc_start: 0.6956 (mttm) cc_final: 0.6399 (tttm) REVERT: C 30 ASP cc_start: 0.7061 (m-30) cc_final: 0.6769 (m-30) REVERT: C 39 LEU cc_start: 0.7669 (mp) cc_final: 0.7407 (mt) REVERT: C 85 LYS cc_start: 0.8153 (tptp) cc_final: 0.7683 (tptp) outliers start: 2 outliers final: 0 residues processed: 295 average time/residue: 0.3364 time to fit residues: 144.1693 Evaluate side-chains 167 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 84 optimal weight: 0.0870 chunk 51 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 HIS A 467 ASN A 491 GLN A 609 HIS A 658 HIS A 698 GLN A 790 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN A 926 ASN A 973 ASN A 990 ASN A 992 ASN B 457 ASN B 467 ASN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN B 810 HIS ** B 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 GLN B 973 ASN B 990 ASN B 992 ASN C 17 HIS C 21 ASN C 54 ASN C 88 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.172999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.151376 restraints weight = 39732.929| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 2.78 r_work: 0.4147 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17175 Z= 0.211 Angle : 0.719 10.739 23141 Z= 0.383 Chirality : 0.045 0.243 2472 Planarity : 0.004 0.036 2945 Dihedral : 6.725 54.897 2212 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.49 % Favored : 90.11 % Rotamer: Outliers : 1.08 % Allowed : 8.25 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.16), residues: 1991 helix: -1.97 (0.14), residues: 1149 sheet: -1.72 (0.98), residues: 24 loop : -3.23 (0.18), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 25 HIS 0.012 0.001 HIS C 88 PHE 0.026 0.002 PHE C 81 TYR 0.020 0.002 TYR A 338 ARG 0.005 0.001 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.8302 (m-10) cc_final: 0.8088 (m-80) REVERT: A 585 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8337 (tt) REVERT: A 978 HIS cc_start: 0.7916 (t70) cc_final: 0.7686 (t-90) REVERT: A 994 LYS cc_start: 0.7996 (pttm) cc_final: 0.7428 (pttm) REVERT: B 45 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: B 98 MET cc_start: 0.3525 (tpp) cc_final: 0.3168 (pmm) REVERT: B 359 ARG cc_start: 0.7735 (tpp-160) cc_final: 0.7319 (ttm170) REVERT: B 616 MET cc_start: -0.1761 (mmm) cc_final: -0.2174 (tpt) REVERT: B 936 MET cc_start: 0.0439 (ptm) cc_final: -0.0903 (tpt) REVERT: B 962 TYR cc_start: 0.2413 (m-10) cc_final: 0.1511 (m-10) REVERT: C 30 ASP cc_start: 0.7420 (m-30) cc_final: 0.7051 (m-30) REVERT: C 59 PHE cc_start: 0.6030 (m-80) cc_final: 0.5597 (m-10) REVERT: C 85 LYS cc_start: 0.7876 (tptp) cc_final: 0.7435 (tptp) outliers start: 20 outliers final: 11 residues processed: 206 average time/residue: 0.2922 time to fit residues: 91.7622 Evaluate side-chains 160 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain C residue 11 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 chunk 140 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 182 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 195 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 339 HIS B 349 HIS B 591 ASN ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 HIS ** B 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.169115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.146150 restraints weight = 38545.068| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 2.74 r_work: 0.4050 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17175 Z= 0.189 Angle : 0.648 11.072 23141 Z= 0.347 Chirality : 0.042 0.225 2472 Planarity : 0.003 0.029 2945 Dihedral : 6.171 54.216 2212 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.84 % Favored : 89.75 % Rotamer: Outliers : 2.16 % Allowed : 10.09 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.17), residues: 1991 helix: -1.11 (0.15), residues: 1144 sheet: -1.88 (0.79), residues: 36 loop : -3.09 (0.18), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 25 HIS 0.007 0.001 HIS A 118 PHE 0.033 0.002 PHE C 81 TYR 0.022 0.001 TYR B 552 ARG 0.006 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.8371 (m-10) cc_final: 0.8105 (m-80) REVERT: A 576 PHE cc_start: 0.6114 (t80) cc_final: 0.5839 (t80) REVERT: A 994 LYS cc_start: 0.8016 (pttm) cc_final: 0.7371 (pttm) REVERT: B 44 PHE cc_start: 0.6500 (m-10) cc_final: 0.5706 (m-10) REVERT: B 45 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: B 227 MET cc_start: 0.6480 (mtm) cc_final: 0.6217 (mtm) REVERT: B 329 ASP cc_start: 0.4826 (m-30) cc_final: 0.4527 (m-30) REVERT: B 359 ARG cc_start: 0.7840 (tpp-160) cc_final: 0.7477 (mtm180) REVERT: B 511 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.5304 (m-80) REVERT: B 880 GLU cc_start: 0.5471 (pp20) cc_final: 0.5159 (tm-30) REVERT: B 962 TYR cc_start: 0.2851 (m-10) cc_final: 0.1693 (m-10) REVERT: C 30 ASP cc_start: 0.7597 (m-30) cc_final: 0.7206 (m-30) REVERT: C 85 LYS cc_start: 0.8055 (tptp) cc_final: 0.7710 (tptm) REVERT: C 98 ILE cc_start: 0.8266 (mp) cc_final: 0.7944 (mm) outliers start: 40 outliers final: 16 residues processed: 195 average time/residue: 0.3034 time to fit residues: 89.7286 Evaluate side-chains 158 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain C residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 187 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 103 optimal weight: 0.0270 chunk 109 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN A 881 HIS A 926 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.164072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.141187 restraints weight = 38008.967| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.95 r_work: 0.3971 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17175 Z= 0.202 Angle : 0.645 11.077 23141 Z= 0.342 Chirality : 0.043 0.191 2472 Planarity : 0.003 0.036 2945 Dihedral : 5.877 54.068 2212 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.35 % Favored : 89.30 % Rotamer: Outliers : 2.37 % Allowed : 11.54 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.18), residues: 1991 helix: -0.70 (0.15), residues: 1147 sheet: -1.49 (0.90), residues: 35 loop : -2.96 (0.18), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 25 HIS 0.009 0.001 HIS B 609 PHE 0.028 0.002 PHE C 81 TYR 0.020 0.001 TYR B 725 ARG 0.005 0.001 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 VAL cc_start: 0.7915 (t) cc_final: 0.7549 (m) REVERT: A 576 PHE cc_start: 0.6409 (t80) cc_final: 0.6128 (t80) REVERT: A 994 LYS cc_start: 0.8055 (pttm) cc_final: 0.7333 (pttm) REVERT: B 21 MET cc_start: 0.6057 (tpt) cc_final: 0.5510 (tpt) REVERT: B 44 PHE cc_start: 0.7680 (m-10) cc_final: 0.7306 (m-80) REVERT: B 45 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: B 186 LYS cc_start: 0.2599 (mttm) cc_final: 0.2256 (mttm) REVERT: B 227 MET cc_start: 0.6960 (mtm) cc_final: 0.6758 (mtm) REVERT: B 268 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8469 (mp) REVERT: B 295 GLU cc_start: 0.1756 (OUTLIER) cc_final: 0.0332 (pp20) REVERT: B 359 ARG cc_start: 0.8116 (tpp-160) cc_final: 0.7569 (mtm-85) REVERT: B 407 ILE cc_start: 0.6398 (OUTLIER) cc_final: 0.6130 (pp) REVERT: B 511 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.5476 (m-80) REVERT: B 583 VAL cc_start: 0.5180 (p) cc_final: 0.4853 (t) REVERT: B 616 MET cc_start: -0.1187 (mmm) cc_final: -0.2115 (tpt) REVERT: B 880 GLU cc_start: 0.5813 (pp20) cc_final: 0.5550 (tm-30) REVERT: B 962 TYR cc_start: 0.2924 (m-10) cc_final: 0.2101 (m-10) REVERT: C 30 ASP cc_start: 0.7443 (m-30) cc_final: 0.7170 (m-30) outliers start: 44 outliers final: 19 residues processed: 212 average time/residue: 0.2786 time to fit residues: 91.4386 Evaluate side-chains 181 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 863 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 167 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 163 optimal weight: 0.9980 chunk 133 optimal weight: 0.0370 chunk 191 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 926 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 391 ASN B 457 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.160763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.138165 restraints weight = 37630.229| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 2.92 r_work: 0.3890 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17175 Z= 0.195 Angle : 0.623 9.168 23141 Z= 0.332 Chirality : 0.042 0.173 2472 Planarity : 0.003 0.028 2945 Dihedral : 5.725 53.991 2212 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.59 % Favored : 90.06 % Rotamer: Outliers : 2.27 % Allowed : 12.84 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.18), residues: 1991 helix: -0.48 (0.16), residues: 1152 sheet: -1.79 (0.87), residues: 36 loop : -2.81 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 757 HIS 0.008 0.001 HIS B 609 PHE 0.030 0.002 PHE C 81 TYR 0.022 0.001 TYR B 452 ARG 0.003 0.000 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 TYR cc_start: 0.7771 (m-80) cc_final: 0.7560 (m-80) REVERT: A 333 VAL cc_start: 0.9037 (t) cc_final: 0.8820 (t) REVERT: A 576 PHE cc_start: 0.6507 (t80) cc_final: 0.6149 (t80) REVERT: A 674 ASP cc_start: 0.6612 (p0) cc_final: 0.6381 (m-30) REVERT: A 869 ILE cc_start: 0.8776 (mt) cc_final: 0.8567 (mt) REVERT: A 994 LYS cc_start: 0.8019 (pttm) cc_final: 0.7300 (pttm) REVERT: B 21 MET cc_start: 0.6286 (tpt) cc_final: 0.5974 (tpt) REVERT: B 45 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: B 69 GLU cc_start: 0.2506 (OUTLIER) cc_final: 0.1964 (mt-10) REVERT: B 152 ILE cc_start: 0.4732 (mt) cc_final: 0.4042 (mt) REVERT: B 268 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8366 (mp) REVERT: B 326 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7844 (mtm-85) REVERT: B 419 ASP cc_start: 0.6212 (t0) cc_final: 0.5988 (t0) REVERT: B 542 LEU cc_start: -0.0290 (OUTLIER) cc_final: -0.0609 (pp) REVERT: B 583 VAL cc_start: 0.5473 (p) cc_final: 0.5213 (t) REVERT: B 589 TYR cc_start: 0.7344 (m-10) cc_final: 0.7113 (m-10) REVERT: B 880 GLU cc_start: 0.6038 (pp20) cc_final: 0.5792 (tm-30) REVERT: B 962 TYR cc_start: 0.3487 (m-10) cc_final: 0.2019 (m-10) REVERT: C 30 ASP cc_start: 0.7477 (m-30) cc_final: 0.7147 (m-30) outliers start: 42 outliers final: 23 residues processed: 205 average time/residue: 0.3093 time to fit residues: 98.7615 Evaluate side-chains 175 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 113 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 182 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 195 optimal weight: 0.0670 chunk 181 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 GLN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.158486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.136262 restraints weight = 37671.115| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 3.22 r_work: 0.3829 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.6899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17175 Z= 0.204 Angle : 0.631 15.225 23141 Z= 0.332 Chirality : 0.043 0.177 2472 Planarity : 0.003 0.028 2945 Dihedral : 5.685 54.231 2212 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.79 % Favored : 89.85 % Rotamer: Outliers : 2.21 % Allowed : 13.48 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.18), residues: 1991 helix: -0.34 (0.16), residues: 1159 sheet: -1.75 (0.89), residues: 36 loop : -2.69 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 143 HIS 0.005 0.001 HIS B 609 PHE 0.028 0.002 PHE B 608 TYR 0.019 0.001 TYR B 197 ARG 0.003 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 TYR cc_start: 0.7875 (m-80) cc_final: 0.7662 (m-80) REVERT: A 576 PHE cc_start: 0.6461 (t80) cc_final: 0.6116 (t80) REVERT: A 869 ILE cc_start: 0.8791 (mt) cc_final: 0.8562 (mt) REVERT: A 952 LYS cc_start: 0.8359 (tppt) cc_final: 0.8037 (tptt) REVERT: A 994 LYS cc_start: 0.8035 (pttm) cc_final: 0.7361 (pttm) REVERT: B 21 MET cc_start: 0.6783 (tpt) cc_final: 0.6356 (tpt) REVERT: B 45 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: B 46 VAL cc_start: 0.8162 (t) cc_final: 0.7689 (m) REVERT: B 69 GLU cc_start: 0.2718 (OUTLIER) cc_final: 0.2301 (mt-10) REVERT: B 295 GLU cc_start: 0.2174 (OUTLIER) cc_final: 0.0151 (pt0) REVERT: B 419 ASP cc_start: 0.6313 (t0) cc_final: 0.6018 (t0) REVERT: B 455 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.7072 (m-10) REVERT: B 542 LEU cc_start: -0.0191 (OUTLIER) cc_final: -0.0537 (pp) REVERT: B 589 TYR cc_start: 0.7746 (m-10) cc_final: 0.7534 (m-10) REVERT: B 744 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: B 880 GLU cc_start: 0.6178 (pp20) cc_final: 0.5963 (tm-30) REVERT: B 962 TYR cc_start: 0.3815 (m-10) cc_final: 0.2877 (m-10) REVERT: C 30 ASP cc_start: 0.7572 (m-30) cc_final: 0.7365 (m-30) outliers start: 41 outliers final: 23 residues processed: 194 average time/residue: 0.2769 time to fit residues: 83.8269 Evaluate side-chains 178 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 83 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 0.0470 chunk 86 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 171 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.4686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.157907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.135730 restraints weight = 37181.569| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.92 r_work: 0.3856 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.7251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17175 Z= 0.171 Angle : 0.598 11.606 23141 Z= 0.317 Chirality : 0.042 0.174 2472 Planarity : 0.003 0.029 2945 Dihedral : 5.517 54.752 2212 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.69 % Favored : 89.95 % Rotamer: Outliers : 1.62 % Allowed : 13.81 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.19), residues: 1991 helix: -0.13 (0.16), residues: 1162 sheet: -2.02 (0.77), residues: 48 loop : -2.61 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 143 HIS 0.004 0.001 HIS B 609 PHE 0.028 0.001 PHE C 81 TYR 0.015 0.001 TYR B 452 ARG 0.003 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 TYR cc_start: 0.7794 (m-80) cc_final: 0.7588 (m-80) REVERT: A 576 PHE cc_start: 0.6431 (t80) cc_final: 0.6044 (t80) REVERT: A 674 ASP cc_start: 0.6695 (p0) cc_final: 0.6469 (m-30) REVERT: A 869 ILE cc_start: 0.8823 (mt) cc_final: 0.8617 (mt) REVERT: A 952 LYS cc_start: 0.8428 (tppt) cc_final: 0.7960 (tptt) REVERT: A 994 LYS cc_start: 0.7975 (pttm) cc_final: 0.7249 (pttm) REVERT: B 21 MET cc_start: 0.6771 (tpt) cc_final: 0.6462 (tpt) REVERT: B 45 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: B 46 VAL cc_start: 0.8149 (t) cc_final: 0.7626 (m) REVERT: B 69 GLU cc_start: 0.2550 (OUTLIER) cc_final: 0.1948 (mt-10) REVERT: B 152 ILE cc_start: 0.5394 (mt) cc_final: 0.4816 (mt) REVERT: B 195 GLN cc_start: 0.7625 (pp30) cc_final: 0.7248 (pp30) REVERT: B 290 MET cc_start: 0.4758 (mmp) cc_final: 0.4326 (mmp) REVERT: B 295 GLU cc_start: 0.2235 (OUTLIER) cc_final: 0.0197 (pt0) REVERT: B 356 TYR cc_start: 0.6633 (p90) cc_final: 0.6415 (p90) REVERT: B 455 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.6510 (m-10) REVERT: B 511 PHE cc_start: 0.6382 (OUTLIER) cc_final: 0.5271 (m-80) REVERT: B 542 LEU cc_start: -0.0522 (OUTLIER) cc_final: -0.0765 (pp) REVERT: B 744 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.6057 (t80) REVERT: B 789 GLN cc_start: 0.6912 (mp10) cc_final: 0.6662 (mp10) REVERT: B 962 TYR cc_start: 0.3664 (m-10) cc_final: 0.1831 (m-10) REVERT: C 30 ASP cc_start: 0.7484 (m-30) cc_final: 0.7278 (m-30) outliers start: 30 outliers final: 15 residues processed: 185 average time/residue: 0.2795 time to fit residues: 80.6170 Evaluate side-chains 170 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain C residue 39 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 113 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 136 ASN B 548 ASN B 939 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.152153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.128775 restraints weight = 36788.669| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 3.33 r_work: 0.3712 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.8081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 17175 Z= 0.268 Angle : 0.702 19.144 23141 Z= 0.367 Chirality : 0.045 0.243 2472 Planarity : 0.003 0.043 2945 Dihedral : 5.828 55.525 2212 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.65 % Favored : 89.00 % Rotamer: Outliers : 2.00 % Allowed : 13.38 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.19), residues: 1991 helix: -0.25 (0.16), residues: 1164 sheet: -1.75 (0.94), residues: 36 loop : -2.55 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 919 HIS 0.012 0.001 HIS B 609 PHE 0.032 0.002 PHE B 646 TYR 0.018 0.002 TYR B 414 ARG 0.005 0.001 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 PHE cc_start: 0.6586 (t80) cc_final: 0.6174 (t80) REVERT: A 646 PHE cc_start: 0.6925 (t80) cc_final: 0.6521 (t80) REVERT: A 674 ASP cc_start: 0.7064 (p0) cc_final: 0.6576 (m-30) REVERT: A 677 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.5861 (ptt-90) REVERT: A 952 LYS cc_start: 0.8525 (tppt) cc_final: 0.8189 (tptt) REVERT: A 994 LYS cc_start: 0.8120 (pttm) cc_final: 0.7352 (pttm) REVERT: B 21 MET cc_start: 0.7366 (tpt) cc_final: 0.7097 (tpp) REVERT: B 69 GLU cc_start: 0.3157 (OUTLIER) cc_final: 0.2266 (mt-10) REVERT: B 186 LYS cc_start: 0.1928 (mttm) cc_final: 0.1555 (mttm) REVERT: B 195 GLN cc_start: 0.8158 (pp30) cc_final: 0.7553 (pp30) REVERT: B 295 GLU cc_start: 0.2484 (OUTLIER) cc_final: 0.1035 (pt0) REVERT: B 455 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.5906 (m-10) REVERT: B 511 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.5731 (m-80) REVERT: B 542 LEU cc_start: 0.0001 (OUTLIER) cc_final: -0.0210 (pp) REVERT: B 744 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.5817 (t80) REVERT: B 962 TYR cc_start: 0.3584 (m-10) cc_final: 0.0324 (m-10) REVERT: C 30 ASP cc_start: 0.7559 (m-30) cc_final: 0.7326 (m-30) REVERT: C 103 SER cc_start: 0.8093 (m) cc_final: 0.7730 (p) outliers start: 37 outliers final: 18 residues processed: 192 average time/residue: 0.2780 time to fit residues: 82.7110 Evaluate side-chains 176 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain C residue 83 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 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 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.151525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.128174 restraints weight = 37101.064| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 3.30 r_work: 0.3713 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.8453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17175 Z= 0.221 Angle : 0.648 14.793 23141 Z= 0.342 Chirality : 0.044 0.199 2472 Planarity : 0.003 0.030 2945 Dihedral : 5.690 54.488 2212 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.54 % Favored : 90.11 % Rotamer: Outliers : 1.46 % Allowed : 14.08 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.19), residues: 1991 helix: -0.15 (0.16), residues: 1168 sheet: -1.93 (0.93), residues: 36 loop : -2.50 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 919 HIS 0.013 0.001 HIS B 606 PHE 0.027 0.002 PHE C 81 TYR 0.017 0.001 TYR B 134 ARG 0.003 0.000 ARG B 587 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 PHE cc_start: 0.6605 (t80) cc_final: 0.6115 (t80) REVERT: A 674 ASP cc_start: 0.7054 (p0) cc_final: 0.6587 (m-30) REVERT: A 677 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.6047 (ptt-90) REVERT: A 920 TYR cc_start: 0.8025 (t80) cc_final: 0.7789 (t80) REVERT: A 952 LYS cc_start: 0.8575 (tppt) cc_final: 0.8294 (tptt) REVERT: A 994 LYS cc_start: 0.8128 (pttm) cc_final: 0.7362 (pttm) REVERT: B 15 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6877 (tp) REVERT: B 21 MET cc_start: 0.7411 (tpt) cc_final: 0.7131 (tpt) REVERT: B 69 GLU cc_start: 0.3167 (OUTLIER) cc_final: 0.2487 (mt-10) REVERT: B 160 ASN cc_start: 0.6520 (m-40) cc_final: 0.5942 (p0) REVERT: B 195 GLN cc_start: 0.8119 (pp30) cc_final: 0.7617 (pp30) REVERT: B 279 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6674 (tm-30) REVERT: B 295 GLU cc_start: 0.2276 (OUTLIER) cc_final: 0.0757 (pt0) REVERT: B 610 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7309 (pt0) REVERT: B 744 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.5848 (t80) REVERT: B 930 MET cc_start: -0.3037 (tpt) cc_final: -0.3247 (tpt) REVERT: B 962 TYR cc_start: 0.3507 (m-10) cc_final: 0.0223 (m-10) REVERT: C 103 SER cc_start: 0.8106 (m) cc_final: 0.7731 (p) REVERT: C 115 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7670 (mm-30) outliers start: 27 outliers final: 14 residues processed: 173 average time/residue: 0.2896 time to fit residues: 77.7109 Evaluate side-chains 165 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain C residue 83 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 129 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 162 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.150842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.127697 restraints weight = 36710.822| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 3.30 r_work: 0.3727 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.8834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17175 Z= 0.203 Angle : 0.652 19.030 23141 Z= 0.340 Chirality : 0.044 0.214 2472 Planarity : 0.003 0.029 2945 Dihedral : 5.552 53.290 2212 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.74 % Favored : 89.90 % Rotamer: Outliers : 1.40 % Allowed : 14.40 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.19), residues: 1991 helix: 0.01 (0.16), residues: 1168 sheet: -2.30 (0.77), residues: 48 loop : -2.43 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 919 HIS 0.012 0.001 HIS B 609 PHE 0.030 0.002 PHE A 385 TYR 0.016 0.001 TYR B 134 ARG 0.005 0.000 ARG A 566 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3982 Ramachandran restraints generated. 1991 Oldfield, 0 Emsley, 1991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 MET cc_start: 0.7744 (mmm) cc_final: 0.7538 (mmt) REVERT: A 576 PHE cc_start: 0.6516 (t80) cc_final: 0.6004 (t80) REVERT: A 646 PHE cc_start: 0.6784 (t80) cc_final: 0.6542 (t80) REVERT: A 674 ASP cc_start: 0.7196 (p0) cc_final: 0.6712 (m-30) REVERT: A 677 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6107 (ptt-90) REVERT: A 693 GLU cc_start: 0.7882 (pp20) cc_final: 0.7482 (tm-30) REVERT: A 994 LYS cc_start: 0.8001 (pttm) cc_final: 0.7228 (pttm) REVERT: B 21 MET cc_start: 0.7560 (tpt) cc_final: 0.7333 (tpp) REVERT: B 69 GLU cc_start: 0.2976 (OUTLIER) cc_final: 0.2313 (mt-10) REVERT: B 160 ASN cc_start: 0.6748 (m-40) cc_final: 0.6183 (p0) REVERT: B 279 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6680 (tm-30) REVERT: B 295 GLU cc_start: 0.2072 (OUTLIER) cc_final: 0.0704 (pt0) REVERT: B 610 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: B 744 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.6068 (t80) REVERT: B 930 MET cc_start: -0.2930 (tpt) cc_final: -0.3167 (tpt) REVERT: B 962 TYR cc_start: 0.3412 (m-10) cc_final: 0.0223 (m-10) REVERT: C 103 SER cc_start: 0.8195 (m) cc_final: 0.7843 (p) REVERT: C 115 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7597 (mm-30) outliers start: 26 outliers final: 17 residues processed: 172 average time/residue: 0.2827 time to fit residues: 76.2269 Evaluate side-chains 162 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain C residue 83 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 126 optimal weight: 1.9990 chunk 38 optimal weight: 0.0020 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 182 optimal weight: 0.0770 chunk 120 optimal weight: 0.6980 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.151030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.128218 restraints weight = 36848.003| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.23 r_work: 0.3714 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.8985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17175 Z= 0.176 Angle : 0.617 14.340 23141 Z= 0.325 Chirality : 0.043 0.169 2472 Planarity : 0.003 0.035 2945 Dihedral : 5.460 52.755 2212 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.19 % Favored : 90.46 % Rotamer: Outliers : 1.24 % Allowed : 14.99 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.19), residues: 1991 helix: 0.08 (0.16), residues: 1170 sheet: -2.32 (0.75), residues: 48 loop : -2.37 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 919 HIS 0.003 0.001 HIS A 339 PHE 0.028 0.001 PHE C 81 TYR 0.018 0.001 TYR A 709 ARG 0.005 0.000 ARG B 613 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7700.64 seconds wall clock time: 138 minutes 4.79 seconds (8284.79 seconds total)