Starting phenix.real_space_refine on Sun Jun 15 02:53:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3m_38889/06_2025/8y3m_38889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3m_38889/06_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_38889/06_2025/8y3m_38889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3m_38889/06_2025/8y3m_38889.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3m_38889/06_2025/8y3m_38889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3m_38889/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.82, per 1000 atoms: 0.58 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: 3.67 Conformation dependent library (CDL) restraints added in 2.1 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: 1.92 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: 4.94 Time building geometry restraints manager: 4.46 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: 2.580 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 36.930 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.990 ------------------------------------------------------------------------------- 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= 0.310 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 Details of bonding type rmsd hydrogen bonds : bond 0.20421 ( 647) hydrogen bonds : angle 9.71142 ( 1887) covalent geometry : bond 0.00661 (17175) covalent geometry : angle 1.17000 (23141) *********************** 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 : 1.782 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: 0.3221 time to fit residues: 138.1137 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 : 1.742 ------------------------------------------------------------------------------- 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 = 0.172986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.151374 restraints weight = 39734.623| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 2.78 r_work: 0.4145 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 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= 0.154 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 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 647) hydrogen bonds : angle 5.36821 ( 1887) covalent geometry : bond 0.00336 (17175) covalent geometry : angle 0.71937 (23141) *********************** 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 : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.8301 (m-10) cc_final: 0.8085 (m-80) REVERT: A 585 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8337 (tt) REVERT: A 978 HIS cc_start: 0.7943 (t70) cc_final: 0.7705 (t-90) REVERT: A 994 LYS cc_start: 0.7996 (pttm) cc_final: 0.7427 (pttm) REVERT: B 45 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: B 98 MET cc_start: 0.3508 (tpp) cc_final: 0.3137 (pmm) REVERT: B 359 ARG cc_start: 0.7742 (tpp-160) cc_final: 0.7302 (ttm170) REVERT: B 509 ASP cc_start: 0.3545 (p0) cc_final: 0.3334 (m-30) REVERT: B 616 MET cc_start: -0.1780 (mmm) cc_final: -0.2184 (tpt) REVERT: B 936 MET cc_start: 0.0451 (ptm) cc_final: -0.0889 (tpt) REVERT: B 962 TYR cc_start: 0.2413 (m-10) cc_final: 0.1513 (m-10) REVERT: C 30 ASP cc_start: 0.7427 (m-30) cc_final: 0.7053 (m-30) REVERT: C 52 ARG cc_start: 0.6911 (ttm-80) cc_final: 0.6711 (ttm110) REVERT: C 59 PHE cc_start: 0.6033 (m-80) cc_final: 0.5594 (m-10) REVERT: C 85 LYS cc_start: 0.7882 (tptp) cc_final: 0.7441 (tptp) outliers start: 20 outliers final: 11 residues processed: 206 average time/residue: 0.2919 time to fit residues: 91.5930 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 : 1.719 ------------------------------------------------------------------------------- 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: 0.2980 chunk 140 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 182 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 195 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.167644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.144903 restraints weight = 38370.857| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.68 r_work: 0.4028 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17175 Z= 0.150 Angle : 0.669 11.146 23141 Z= 0.356 Chirality : 0.043 0.225 2472 Planarity : 0.003 0.031 2945 Dihedral : 6.224 54.130 2212 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.05 % Favored : 89.60 % Rotamer: Outliers : 2.05 % Allowed : 10.52 % Favored : 87.43 % 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: -2.92 (0.17), residues: 1991 helix: -1.14 (0.15), residues: 1143 sheet: -1.86 (0.80), residues: 36 loop : -3.11 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 25 HIS 0.007 0.001 HIS A 118 PHE 0.033 0.002 PHE C 81 TYR 0.023 0.002 TYR B 552 ARG 0.006 0.001 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 647) hydrogen bonds : angle 4.90037 ( 1887) covalent geometry : bond 0.00334 (17175) covalent geometry : angle 0.66884 (23141) *********************** 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 210 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.8423 (m-10) cc_final: 0.8160 (m-80) REVERT: A 576 PHE cc_start: 0.6152 (t80) cc_final: 0.5912 (t80) REVERT: A 994 LYS cc_start: 0.8019 (pttm) cc_final: 0.7382 (pttm) REVERT: B 44 PHE cc_start: 0.6830 (m-10) cc_final: 0.6104 (m-10) REVERT: B 45 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7117 (m-80) REVERT: B 329 ASP cc_start: 0.4896 (m-30) cc_final: 0.4497 (m-30) REVERT: B 359 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.7558 (mtm180) REVERT: B 509 ASP cc_start: 0.4311 (p0) cc_final: 0.4040 (m-30) REVERT: B 511 PHE cc_start: 0.5715 (OUTLIER) cc_final: 0.5264 (m-80) REVERT: B 542 LEU cc_start: -0.0520 (OUTLIER) cc_final: -0.0768 (pp) REVERT: B 880 GLU cc_start: 0.5470 (pp20) cc_final: 0.5163 (tm-30) REVERT: B 962 TYR cc_start: 0.3210 (m-10) cc_final: 0.1936 (m-10) REVERT: C 30 ASP cc_start: 0.7627 (m-30) cc_final: 0.7224 (m-30) REVERT: C 52 ARG cc_start: 0.7095 (ttm-80) cc_final: 0.6885 (ttm110) REVERT: C 85 LYS cc_start: 0.8051 (tptp) cc_final: 0.7721 (tptm) REVERT: C 98 ILE cc_start: 0.8279 (mp) cc_final: 0.7950 (mm) outliers start: 38 outliers final: 16 residues processed: 197 average time/residue: 0.2845 time to fit residues: 85.2691 Evaluate side-chains 160 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 740 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain B residue 45 PHE 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 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 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: 0.5980 chunk 67 optimal weight: 0.6980 chunk 112 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 103 optimal weight: 0.0060 chunk 109 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 ASN A 926 ASN ** B 118 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.165144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.142443 restraints weight = 37987.512| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.93 r_work: 0.4002 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17175 Z= 0.127 Angle : 0.612 10.793 23141 Z= 0.326 Chirality : 0.042 0.203 2472 Planarity : 0.003 0.029 2945 Dihedral : 5.909 54.345 2212 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.10 % Favored : 89.60 % Rotamer: Outliers : 2.43 % Allowed : 11.27 % Favored : 86.30 % 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: -2.42 (0.18), residues: 1991 helix: -0.71 (0.16), residues: 1138 sheet: -1.69 (0.86), residues: 36 loop : -2.92 (0.19), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 25 HIS 0.006 0.001 HIS B 609 PHE 0.031 0.001 PHE C 81 TYR 0.017 0.001 TYR B 552 ARG 0.004 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 647) hydrogen bonds : angle 4.56739 ( 1887) covalent geometry : bond 0.00279 (17175) covalent geometry : angle 0.61245 (23141) *********************** 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 205 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.8403 (m-10) cc_final: 0.8153 (m-80) REVERT: A 576 PHE cc_start: 0.6418 (t80) cc_final: 0.6123 (t80) REVERT: A 994 LYS cc_start: 0.8064 (pttm) cc_final: 0.7403 (pttm) REVERT: B 21 MET cc_start: 0.5914 (tpt) cc_final: 0.5425 (tpt) REVERT: B 44 PHE cc_start: 0.7338 (m-10) cc_final: 0.6668 (m-10) REVERT: B 45 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: B 268 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8472 (mp) REVERT: B 295 GLU cc_start: 0.1786 (OUTLIER) cc_final: 0.0438 (pp20) REVERT: B 329 ASP cc_start: 0.5571 (m-30) cc_final: 0.5315 (m-30) REVERT: B 359 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7567 (mtm-85) REVERT: B 407 ILE cc_start: 0.5966 (OUTLIER) cc_final: 0.5746 (pp) REVERT: B 511 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.5498 (m-80) REVERT: B 616 MET cc_start: -0.1085 (mmm) cc_final: -0.2251 (tpt) REVERT: B 880 GLU cc_start: 0.5795 (pp20) cc_final: 0.5440 (tm-30) REVERT: B 962 TYR cc_start: 0.3104 (m-10) cc_final: 0.2243 (m-10) REVERT: C 28 GLU cc_start: 0.7316 (mp0) cc_final: 0.7105 (mp0) REVERT: C 30 ASP cc_start: 0.7571 (m-30) cc_final: 0.7352 (m-30) outliers start: 45 outliers final: 22 residues processed: 194 average time/residue: 0.2723 time to fit residues: 81.3919 Evaluate side-chains 168 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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 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 84 TYR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 295 GLU 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 Chi-restraints excluded: chain C residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 167 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 175 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 89 optimal weight: 0.0870 chunk 163 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 797 ASN A 926 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN ** B 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.164136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.140857 restraints weight = 38312.553| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.92 r_work: 0.3979 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.5713 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= 0.117 Angle : 0.587 8.745 23141 Z= 0.313 Chirality : 0.042 0.176 2472 Planarity : 0.003 0.024 2945 Dihedral : 5.670 53.176 2212 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.84 % Favored : 89.80 % Rotamer: Outliers : 2.48 % Allowed : 12.35 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.15 (0.18), residues: 1991 helix: -0.44 (0.16), residues: 1148 sheet: -2.11 (0.74), residues: 48 loop : -2.88 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 25 HIS 0.008 0.001 HIS B 609 PHE 0.030 0.001 PHE C 81 TYR 0.015 0.001 TYR C 51 ARG 0.004 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 647) hydrogen bonds : angle 4.37096 ( 1887) covalent geometry : bond 0.00258 (17175) covalent geometry : angle 0.58700 (23141) *********************** 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: 46 poor density : 166 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 VAL cc_start: 0.9039 (t) cc_final: 0.8810 (t) REVERT: A 576 PHE cc_start: 0.6527 (t80) cc_final: 0.6229 (t80) REVERT: A 674 ASP cc_start: 0.6366 (p0) cc_final: 0.6134 (m-30) REVERT: A 994 LYS cc_start: 0.8052 (pttm) cc_final: 0.7312 (pttm) REVERT: B 44 PHE cc_start: 0.7702 (m-10) cc_final: 0.7293 (m-80) REVERT: B 45 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: B 152 ILE cc_start: 0.4325 (mt) cc_final: 0.3646 (mt) REVERT: B 268 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8462 (mp) REVERT: B 407 ILE cc_start: 0.6369 (OUTLIER) cc_final: 0.6140 (pp) REVERT: B 511 PHE cc_start: 0.6129 (OUTLIER) cc_final: 0.5426 (m-80) REVERT: B 583 VAL cc_start: 0.5043 (p) cc_final: 0.4741 (t) REVERT: B 773 SER cc_start: 0.7573 (m) cc_final: 0.7362 (t) REVERT: B 962 TYR cc_start: 0.3143 (m-10) cc_final: 0.1846 (m-10) REVERT: C 30 ASP cc_start: 0.7524 (m-30) cc_final: 0.7257 (m-30) outliers start: 46 outliers final: 21 residues processed: 201 average time/residue: 0.2609 time to fit residues: 81.6475 Evaluate side-chains 181 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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 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 118 HIS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 455 TYR 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 744 PHE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 113 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 182 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 609 HIS A 789 GLN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 457 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.158588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.135715 restraints weight = 37536.884| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 3.13 r_work: 0.3828 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17175 Z= 0.155 Angle : 0.656 14.391 23141 Z= 0.346 Chirality : 0.043 0.179 2472 Planarity : 0.003 0.030 2945 Dihedral : 5.801 53.583 2212 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.89 % Favored : 89.75 % Rotamer: Outliers : 2.43 % Allowed : 12.94 % 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: -2.05 (0.18), residues: 1991 helix: -0.41 (0.16), residues: 1154 sheet: -1.85 (0.88), residues: 36 loop : -2.77 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 757 HIS 0.011 0.001 HIS B 609 PHE 0.031 0.002 PHE B 608 TYR 0.019 0.002 TYR B 418 ARG 0.004 0.000 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 647) hydrogen bonds : angle 4.50119 ( 1887) covalent geometry : bond 0.00352 (17175) covalent geometry : angle 0.65581 (23141) *********************** 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 213 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.8395 (m-10) cc_final: 0.8146 (m-80) REVERT: A 280 TYR cc_start: 0.7809 (m-80) cc_final: 0.7584 (m-80) REVERT: A 576 PHE cc_start: 0.6611 (t80) cc_final: 0.6271 (t80) REVERT: A 869 ILE cc_start: 0.8817 (mt) cc_final: 0.8598 (mt) REVERT: A 920 TYR cc_start: 0.8033 (t80) cc_final: 0.7805 (t80) REVERT: A 952 LYS cc_start: 0.8372 (tppt) cc_final: 0.7964 (tptt) REVERT: A 994 LYS cc_start: 0.8040 (pttm) cc_final: 0.7351 (pttm) REVERT: B 21 MET cc_start: 0.6516 (tpt) cc_final: 0.6170 (tpt) REVERT: B 45 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: B 46 VAL cc_start: 0.8114 (t) cc_final: 0.7618 (m) REVERT: B 98 MET cc_start: 0.4532 (tpp) cc_final: 0.4142 (pmm) REVERT: B 186 LYS cc_start: 0.2684 (mttm) cc_final: 0.2461 (mttm) REVERT: B 279 GLU cc_start: 0.6001 (tp30) cc_final: 0.5569 (tp30) REVERT: B 295 GLU cc_start: 0.2059 (OUTLIER) cc_final: 0.1144 (pp20) REVERT: B 407 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6271 (tt) REVERT: B 511 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.5171 (m-80) REVERT: B 744 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7511 (m-80) REVERT: B 962 TYR cc_start: 0.3856 (m-10) cc_final: 0.2407 (m-10) REVERT: C 28 GLU cc_start: 0.7279 (mp0) cc_final: 0.7037 (mp0) REVERT: C 30 ASP cc_start: 0.7605 (m-30) cc_final: 0.7365 (m-30) REVERT: C 83 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7908 (pt) outliers start: 45 outliers final: 23 residues processed: 199 average time/residue: 0.2654 time to fit residues: 82.0587 Evaluate side-chains 181 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 289 VAL Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 605 PHE 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 19 PHE 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 403 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 28 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 121 optimal weight: 0.0020 chunk 171 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.158040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.135728 restraints weight = 37300.318| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.89 r_work: 0.3845 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17175 Z= 0.128 Angle : 0.610 10.232 23141 Z= 0.325 Chirality : 0.043 0.200 2472 Planarity : 0.003 0.025 2945 Dihedral : 5.623 54.052 2212 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.69 % Favored : 89.95 % Rotamer: Outliers : 1.94 % Allowed : 13.70 % Favored : 84.36 % 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: -1.86 (0.19), residues: 1991 helix: -0.23 (0.16), residues: 1155 sheet: -2.15 (0.75), residues: 48 loop : -2.72 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 919 HIS 0.005 0.001 HIS B 609 PHE 0.027 0.001 PHE C 81 TYR 0.017 0.001 TYR B 197 ARG 0.003 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 647) hydrogen bonds : angle 4.35377 ( 1887) covalent geometry : bond 0.00287 (17175) covalent geometry : angle 0.61010 (23141) *********************** 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 194 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: A 280 TYR cc_start: 0.7768 (m-80) cc_final: 0.7566 (m-80) REVERT: A 576 PHE cc_start: 0.6640 (t80) cc_final: 0.6275 (t80) REVERT: A 674 ASP cc_start: 0.6639 (p0) cc_final: 0.6378 (m-30) REVERT: A 869 ILE cc_start: 0.8825 (mt) cc_final: 0.8615 (mt) REVERT: A 952 LYS cc_start: 0.8367 (tppt) cc_final: 0.8059 (tptt) REVERT: A 994 LYS cc_start: 0.7992 (pttm) cc_final: 0.7279 (pttm) REVERT: B 21 MET cc_start: 0.6760 (tpt) cc_final: 0.6415 (tpt) REVERT: B 45 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.7563 (m-80) REVERT: B 46 VAL cc_start: 0.8119 (t) cc_final: 0.7659 (m) REVERT: B 98 MET cc_start: 0.4584 (tpp) cc_final: 0.4131 (pmm) REVERT: B 295 GLU cc_start: 0.2163 (OUTLIER) cc_final: 0.0732 (pt0) REVERT: B 455 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6125 (m-10) REVERT: B 511 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5217 (m-80) REVERT: B 744 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.6127 (t80) REVERT: B 962 TYR cc_start: 0.3707 (m-10) cc_final: 0.2401 (m-10) REVERT: C 83 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7855 (pt) outliers start: 36 outliers final: 20 residues processed: 187 average time/residue: 0.2711 time to fit residues: 79.3694 Evaluate side-chains 166 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 107 PHE 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 84 TYR Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 303 THR 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 617 SER Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 758 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 83 ILE Chi-restraints excluded: chain C residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 113 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 196 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.154401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.131510 restraints weight = 36976.318| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 3.12 r_work: 0.3786 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.7743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17175 Z= 0.156 Angle : 0.665 14.873 23141 Z= 0.350 Chirality : 0.044 0.182 2472 Planarity : 0.003 0.034 2945 Dihedral : 5.683 54.084 2212 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.50 % Favored : 89.15 % Rotamer: Outliers : 1.83 % Allowed : 13.81 % Favored : 84.36 % 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: -1.80 (0.19), residues: 1991 helix: -0.21 (0.16), residues: 1167 sheet: -1.73 (0.91), residues: 36 loop : -2.69 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 919 HIS 0.009 0.001 HIS B 609 PHE 0.033 0.002 PHE B 699 TYR 0.013 0.001 TYR B 414 ARG 0.004 0.000 ARG B 326 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 647) hydrogen bonds : angle 4.46186 ( 1887) covalent geometry : bond 0.00359 (17175) covalent geometry : angle 0.66498 (23141) *********************** 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 197 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 PHE cc_start: 0.6675 (t80) cc_final: 0.6303 (t80) REVERT: A 674 ASP cc_start: 0.6891 (p0) cc_final: 0.6494 (m-30) REVERT: A 869 ILE cc_start: 0.8849 (mt) cc_final: 0.8638 (mt) REVERT: A 952 LYS cc_start: 0.8453 (tppt) cc_final: 0.8164 (tptt) REVERT: A 994 LYS cc_start: 0.7991 (pttm) cc_final: 0.7305 (pttm) REVERT: B 21 MET cc_start: 0.6882 (tpt) cc_final: 0.6603 (tpt) REVERT: B 98 MET cc_start: 0.4950 (tpp) cc_final: 0.4380 (pmm) REVERT: B 186 LYS cc_start: 0.2508 (mttm) cc_final: 0.2283 (mttm) REVERT: B 295 GLU cc_start: 0.2489 (OUTLIER) cc_final: 0.1110 (pt0) REVERT: B 359 ARG cc_start: 0.8519 (tpp-160) cc_final: 0.8248 (tpp-160) REVERT: B 511 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.5327 (m-80) REVERT: B 706 VAL cc_start: 0.7928 (m) cc_final: 0.7684 (p) REVERT: B 744 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.6013 (t80) REVERT: B 758 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7362 (tp) REVERT: B 962 TYR cc_start: 0.3838 (m-10) cc_final: 0.2078 (m-10) REVERT: C 83 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7938 (pt) REVERT: C 97 GLU cc_start: 0.7000 (mp0) cc_final: 0.6726 (mp0) outliers start: 34 outliers final: 16 residues processed: 190 average time/residue: 0.2956 time to fit residues: 86.3351 Evaluate side-chains 168 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 84 TYR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 100 LEU 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: 2.9990 chunk 48 optimal weight: 0.8980 chunk 166 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 598 ASN B 610 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.150372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.127182 restraints weight = 37212.035| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 3.33 r_work: 0.3708 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.8458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17175 Z= 0.198 Angle : 0.717 14.451 23141 Z= 0.380 Chirality : 0.045 0.176 2472 Planarity : 0.004 0.047 2945 Dihedral : 5.946 53.358 2212 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.10 % Favored : 89.55 % Rotamer: Outliers : 1.94 % Allowed : 14.02 % Favored : 84.03 % 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: -1.87 (0.18), residues: 1991 helix: -0.31 (0.16), residues: 1158 sheet: -1.96 (0.93), residues: 36 loop : -2.60 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 919 HIS 0.024 0.002 HIS B 609 PHE 0.036 0.002 PHE B 722 TYR 0.060 0.002 TYR B 721 ARG 0.008 0.001 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 647) hydrogen bonds : angle 4.64934 ( 1887) covalent geometry : bond 0.00467 (17175) covalent geometry : angle 0.71697 (23141) *********************** 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 195 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 PHE cc_start: 0.6726 (t80) cc_final: 0.6358 (t80) REVERT: A 674 ASP cc_start: 0.7172 (p0) cc_final: 0.6604 (m-30) REVERT: A 677 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.6162 (ptt-90) REVERT: A 920 TYR cc_start: 0.8091 (t80) cc_final: 0.7886 (t80) REVERT: A 952 LYS cc_start: 0.8527 (tppt) cc_final: 0.8208 (tptt) REVERT: A 994 LYS cc_start: 0.8098 (pttm) cc_final: 0.7342 (pttm) REVERT: B 21 MET cc_start: 0.6968 (tpt) cc_final: 0.6765 (tpt) REVERT: B 98 MET cc_start: 0.4780 (tpp) cc_final: 0.4252 (pmm) REVERT: B 186 LYS cc_start: 0.2493 (mttm) cc_final: 0.2117 (mttm) REVERT: B 195 GLN cc_start: 0.8433 (pp30) cc_final: 0.8204 (pp30) REVERT: B 295 GLU cc_start: 0.2200 (OUTLIER) cc_final: 0.1138 (pt0) REVERT: B 407 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6708 (tt) REVERT: B 511 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.5550 (m-80) REVERT: B 706 VAL cc_start: 0.8180 (m) cc_final: 0.7922 (p) REVERT: B 744 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.5851 (t80) REVERT: B 758 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7456 (tp) REVERT: B 962 TYR cc_start: 0.3918 (m-10) cc_final: 0.3244 (m-10) REVERT: C 28 GLU cc_start: 0.7427 (mp0) cc_final: 0.7133 (mp0) REVERT: C 83 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7824 (pt) REVERT: C 103 SER cc_start: 0.8027 (m) cc_final: 0.7648 (p) outliers start: 36 outliers final: 23 residues processed: 184 average time/residue: 0.2836 time to fit residues: 80.4546 Evaluate side-chains 182 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 6 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 511 PHE 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 758 LEU Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 162 optimal weight: 0.0870 chunk 46 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4362 r_free = 0.4362 target = 0.150865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.128350 restraints weight = 36968.667| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.28 r_work: 0.3719 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.8739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17175 Z= 0.147 Angle : 0.678 16.785 23141 Z= 0.353 Chirality : 0.044 0.284 2472 Planarity : 0.003 0.026 2945 Dihedral : 5.734 52.553 2212 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.99 % Favored : 89.65 % Rotamer: Outliers : 1.46 % Allowed : 14.99 % Favored : 83.55 % 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: -1.67 (0.19), residues: 1991 helix: -0.12 (0.16), residues: 1162 sheet: -1.97 (0.91), residues: 36 loop : -2.59 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 919 HIS 0.015 0.001 HIS B 609 PHE 0.027 0.002 PHE B 646 TYR 0.022 0.001 TYR B 611 ARG 0.004 0.000 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 647) hydrogen bonds : angle 4.50881 ( 1887) covalent geometry : bond 0.00338 (17175) covalent geometry : angle 0.67800 (23141) ********************** 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 183 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.964 Fit side-chains revert: symmetry clash REVERT: A 576 PHE cc_start: 0.6739 (t80) cc_final: 0.6366 (t80) REVERT: A 674 ASP cc_start: 0.7118 (p0) cc_final: 0.6622 (m-30) REVERT: A 952 LYS cc_start: 0.8515 (tppt) cc_final: 0.8308 (tppt) REVERT: A 994 LYS cc_start: 0.8136 (pttm) cc_final: 0.7391 (pttm) REVERT: B 21 MET cc_start: 0.7048 (tpt) cc_final: 0.6738 (tpt) REVERT: B 98 MET cc_start: 0.4998 (tpp) cc_final: 0.4476 (pmm) REVERT: B 160 ASN cc_start: 0.6634 (m-40) cc_final: 0.5945 (p0) REVERT: B 186 LYS cc_start: 0.2344 (mttm) cc_final: 0.1835 (mttm) REVERT: B 295 GLU cc_start: 0.2015 (OUTLIER) cc_final: 0.1323 (pp20) REVERT: B 328 ILE cc_start: 0.8809 (mt) cc_final: 0.8593 (mt) REVERT: B 511 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.5586 (m-80) REVERT: B 610 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7405 (pt0) REVERT: B 704 MET cc_start: 0.5113 (mpp) cc_final: 0.4534 (tmm) REVERT: B 706 VAL cc_start: 0.8157 (m) cc_final: 0.7916 (p) REVERT: B 744 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.6153 (t80) REVERT: B 758 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7422 (tp) REVERT: B 962 TYR cc_start: 0.3934 (m-10) cc_final: 0.2007 (m-10) REVERT: C 28 GLU cc_start: 0.7409 (mp0) cc_final: 0.7126 (mp0) REVERT: C 97 GLU cc_start: 0.7276 (mp0) cc_final: 0.6998 (mp0) REVERT: C 103 SER cc_start: 0.8024 (m) cc_final: 0.7655 (p) outliers start: 27 outliers final: 17 residues processed: 175 average time/residue: 0.3095 time to fit residues: 84.3628 Evaluate side-chains 168 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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 740 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 511 PHE 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 758 LEU Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain C residue 100 LEU 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: 0.7980 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 164 optimal weight: 0.9990 chunk 26 optimal weight: 0.0050 chunk 5 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4362 r_free = 0.4362 target = 0.150688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.128545 restraints weight = 36964.762| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.16 r_work: 0.3728 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.8778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.246 17175 Z= 0.201 Angle : 0.899 59.196 23141 Z= 0.490 Chirality : 0.046 0.400 2472 Planarity : 0.004 0.066 2945 Dihedral : 5.725 52.538 2212 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.05 % Favored : 89.60 % Rotamer: Outliers : 1.29 % Allowed : 15.43 % Favored : 83.28 % Cbeta Deviations : 0.05 % 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: -1.67 (0.19), residues: 1991 helix: -0.12 (0.16), residues: 1162 sheet: -1.97 (0.91), residues: 36 loop : -2.58 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 919 HIS 0.023 0.001 HIS B 609 PHE 0.102 0.002 PHE B 149 TYR 0.016 0.001 TYR B 625 ARG 0.021 0.000 ARG B 613 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 647) hydrogen bonds : angle 4.50561 ( 1887) covalent geometry : bond 0.00489 (17175) covalent geometry : angle 0.89906 (23141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8186.06 seconds wall clock time: 142 minutes 20.97 seconds (8540.97 seconds total)