Starting phenix.real_space_refine on Thu Sep 18 12:44:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3m_38889/09_2025/8y3m_38889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3m_38889/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y3m_38889/09_2025/8y3m_38889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3m_38889/09_2025/8y3m_38889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y3m_38889/09_2025/8y3m_38889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3m_38889/09_2025/8y3m_38889.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.57, per 1000 atoms: 0.21 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: 0.83 Conformation dependent library (CDL) restraints added in 716.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.68 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: 2.30 Time building geometry restraints manager: 1.16 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: 4.920 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.010 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.018 0.001 ARG B 987 TYR 0.027 0.003 TYR A 804 PHE 0.058 0.004 PHE C 81 TRP 0.062 0.005 TRP B 757 HIS 0.024 0.003 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00661 (17175) covalent geometry : angle 1.17000 (23141) hydrogen bonds : bond 0.20421 ( 647) hydrogen bonds : angle 9.71142 ( 1887) *********************** 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 : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 PHE cc_start: 0.5867 (t80) cc_final: 0.5647 (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: 0.7065 (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: 0.1143 (m-10) REVERT: B 969 LYS cc_start: 0.6956 (mttm) cc_final: 0.6400 (tttm) REVERT: C 30 ASP cc_start: 0.7061 (m-30) cc_final: 0.6836 (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: 0.7872 (tptm) outliers start: 2 outliers final: 0 residues processed: 295 average time/residue: 0.1480 time to fit residues: 63.5822 Evaluate side-chains 170 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 609 HIS A 658 HIS A 698 GLN A 790 ASN A 881 HIS A 895 ASN A 926 ASN A 973 ASN A 990 ASN A 992 ASN B 457 ASN B 467 ASN B 591 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.171263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.148869 restraints weight = 39252.129| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 2.79 r_work: 0.4111 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 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 : 0.004 0.054 17175 Z= 0.175 Angle : 0.730 10.489 23141 Z= 0.391 Chirality : 0.045 0.247 2472 Planarity : 0.004 0.039 2945 Dihedral : 6.817 54.959 2212 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.64 % Favored : 89.85 % Rotamer: Outliers : 1.08 % Allowed : 8.31 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.87 (0.16), residues: 1991 helix: -2.04 (0.13), residues: 1154 sheet: -1.71 (0.99), residues: 24 loop : -3.32 (0.18), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 380 TYR 0.029 0.002 TYR B 552 PHE 0.026 0.002 PHE C 81 TRP 0.022 0.002 TRP C 25 HIS 0.011 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00383 (17175) covalent geometry : angle 0.73014 (23141) hydrogen bonds : bond 0.04411 ( 647) hydrogen bonds : angle 5.50521 ( 1887) *********************** 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 217 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.8334 (m-10) cc_final: 0.8126 (m-80) REVERT: A 585 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8402 (tt) REVERT: A 978 HIS cc_start: 0.8010 (t70) cc_final: 0.7723 (t-90) REVERT: A 994 LYS cc_start: 0.8016 (pttm) cc_final: 0.7402 (pttm) REVERT: B 45 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.6751 (m-80) REVERT: B 98 MET cc_start: 0.3411 (tpp) cc_final: 0.2940 (pmm) REVERT: B 509 ASP cc_start: 0.3747 (p0) cc_final: 0.3544 (m-30) REVERT: B 616 MET cc_start: -0.2161 (mmm) cc_final: -0.2526 (tpt) REVERT: B 733 LEU cc_start: 0.5052 (mm) cc_final: 0.4648 (mt) REVERT: B 936 MET cc_start: 0.0735 (ptm) cc_final: -0.0798 (tpt) REVERT: B 962 TYR cc_start: 0.2518 (m-10) cc_final: 0.1253 (m-10) REVERT: B 969 LYS cc_start: 0.6624 (mttm) cc_final: 0.6373 (tttp) REVERT: C 30 ASP cc_start: 0.7404 (m-30) cc_final: 0.7061 (m-30) REVERT: C 59 PHE cc_start: 0.6077 (m-80) cc_final: 0.5621 (m-10) REVERT: C 85 LYS cc_start: 0.7904 (tptp) cc_final: 0.7534 (tptm) outliers start: 20 outliers final: 10 residues processed: 211 average time/residue: 0.1263 time to fit residues: 40.4639 Evaluate side-chains 161 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 42 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 145 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 491 GLN A 926 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 230 ASN B 339 HIS B 349 HIS ** B 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 HIS ** B 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.168657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.145260 restraints weight = 38780.225| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 3.32 r_work: 0.3914 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17175 Z= 0.169 Angle : 0.702 10.124 23141 Z= 0.375 Chirality : 0.044 0.230 2472 Planarity : 0.004 0.043 2945 Dihedral : 6.300 54.866 2212 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.05 % Favored : 89.55 % Rotamer: Outliers : 2.10 % Allowed : 11.06 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.17), residues: 1991 helix: -1.10 (0.15), residues: 1146 sheet: -1.82 (0.82), residues: 36 loop : -3.13 (0.18), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 566 TYR 0.027 0.002 TYR B 452 PHE 0.033 0.002 PHE C 81 TRP 0.027 0.002 TRP C 25 HIS 0.007 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00381 (17175) covalent geometry : angle 0.70187 (23141) hydrogen bonds : bond 0.04375 ( 647) hydrogen bonds : angle 4.90540 ( 1887) *********************** 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 218 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.8446 (m-10) cc_final: 0.8217 (m-80) REVERT: A 576 PHE cc_start: 0.6352 (t80) cc_final: 0.5873 (t80) REVERT: A 994 LYS cc_start: 0.8131 (pttm) cc_final: 0.7472 (pttm) REVERT: B 44 PHE cc_start: 0.7323 (m-10) cc_final: 0.6745 (m-10) REVERT: B 45 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: B 227 MET cc_start: 0.6888 (mtm) cc_final: 0.6684 (mtm) REVERT: B 326 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7501 (mtm180) REVERT: B 511 PHE cc_start: 0.5567 (OUTLIER) cc_final: 0.5093 (m-80) REVERT: B 591 ASN cc_start: 0.3940 (OUTLIER) cc_final: 0.3505 (m-40) REVERT: B 733 LEU cc_start: 0.6253 (mm) cc_final: 0.5843 (mt) REVERT: B 880 GLU cc_start: 0.5556 (pp20) cc_final: 0.5283 (tm-30) REVERT: B 962 TYR cc_start: 0.3800 (m-10) cc_final: 0.2229 (m-10) REVERT: C 30 ASP cc_start: 0.7722 (m-30) cc_final: 0.7335 (m-30) REVERT: C 85 LYS cc_start: 0.8086 (tptp) cc_final: 0.7753 (tptm) REVERT: C 98 ILE cc_start: 0.8369 (mp) cc_final: 0.8062 (mm) outliers start: 39 outliers final: 13 residues processed: 207 average time/residue: 0.1334 time to fit residues: 42.0660 Evaluate side-chains 164 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 TYR 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 B residue 45 PHE Chi-restraints excluded: chain B residue 326 ARG 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 591 ASN Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain C residue 11 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 145 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 184 optimal weight: 4.9990 chunk 70 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 HIS A 698 GLN A 797 ASN A 926 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.161583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.138508 restraints weight = 37791.606| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 3.20 r_work: 0.3913 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17175 Z= 0.141 Angle : 0.632 9.980 23141 Z= 0.336 Chirality : 0.043 0.201 2472 Planarity : 0.003 0.054 2945 Dihedral : 6.039 55.035 2212 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.79 % Favored : 89.90 % Rotamer: Outliers : 2.70 % Allowed : 12.08 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.18), residues: 1991 helix: -0.77 (0.15), residues: 1149 sheet: -1.85 (0.86), residues: 36 loop : -3.01 (0.18), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 870 TYR 0.017 0.001 TYR B 552 PHE 0.032 0.002 PHE C 81 TRP 0.012 0.001 TRP C 25 HIS 0.013 0.001 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00319 (17175) covalent geometry : angle 0.63216 (23141) hydrogen bonds : bond 0.03675 ( 647) hydrogen bonds : angle 4.61030 ( 1887) *********************** 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 218 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.6405 (tpt170) cc_final: 0.6050 (tpt170) REVERT: A 280 TYR cc_start: 0.8092 (m-10) cc_final: 0.7868 (m-80) REVERT: A 576 PHE cc_start: 0.6422 (t80) cc_final: 0.6099 (t80) REVERT: A 952 LYS cc_start: 0.8239 (tppt) cc_final: 0.7925 (tptt) REVERT: A 994 LYS cc_start: 0.8043 (pttm) cc_final: 0.7322 (pttm) REVERT: B 44 PHE cc_start: 0.7812 (m-10) cc_final: 0.7550 (m-80) REVERT: B 45 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: B 46 VAL cc_start: 0.7586 (t) cc_final: 0.7094 (m) REVERT: B 69 GLU cc_start: 0.2424 (OUTLIER) cc_final: 0.2018 (mt-10) REVERT: B 295 GLU cc_start: 0.2144 (OUTLIER) cc_final: 0.0860 (pp20) REVERT: B 407 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.6236 (tt) REVERT: B 455 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.6515 (m-80) REVERT: B 583 VAL cc_start: 0.5141 (p) cc_final: 0.4851 (t) REVERT: B 616 MET cc_start: -0.0999 (mmm) cc_final: -0.2050 (tpt) REVERT: B 733 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6038 (mt) REVERT: B 773 SER cc_start: 0.7770 (m) cc_final: 0.7541 (t) REVERT: B 962 TYR cc_start: 0.3440 (m-10) cc_final: 0.1987 (m-10) REVERT: C 30 ASP cc_start: 0.7607 (m-30) cc_final: 0.7390 (m-30) outliers start: 50 outliers final: 21 residues processed: 207 average time/residue: 0.1137 time to fit residues: 36.7880 Evaluate side-chains 177 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 707 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 295 GLU 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 617 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 91 THR 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 22 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 172 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 391 ASN A 797 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN B 457 ASN ** 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 = 0.4458 r_free = 0.4458 target = 0.158367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.135508 restraints weight = 37154.718| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 3.14 r_work: 0.3830 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.6602 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= 0.153 Angle : 0.649 9.745 23141 Z= 0.347 Chirality : 0.043 0.186 2472 Planarity : 0.003 0.042 2945 Dihedral : 5.952 54.438 2212 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.25 % Favored : 89.40 % Rotamer: Outliers : 2.70 % Allowed : 12.19 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.18), residues: 1991 helix: -0.61 (0.15), residues: 1148 sheet: -2.01 (0.86), residues: 36 loop : -2.88 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 870 TYR 0.024 0.002 TYR B 197 PHE 0.031 0.002 PHE C 81 TRP 0.025 0.002 TRP A 143 HIS 0.008 0.001 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00350 (17175) covalent geometry : angle 0.64919 (23141) hydrogen bonds : bond 0.03869 ( 647) hydrogen bonds : angle 4.56203 ( 1887) *********************** 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 224 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.8347 (m-10) cc_final: 0.8114 (m-80) REVERT: A 576 PHE cc_start: 0.6565 (t80) cc_final: 0.6179 (t80) REVERT: A 952 LYS cc_start: 0.8343 (tppt) cc_final: 0.8056 (tptt) REVERT: A 994 LYS cc_start: 0.8018 (pttm) cc_final: 0.7332 (pttm) REVERT: B 6 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5973 (tp) REVERT: B 21 MET cc_start: 0.6391 (tpt) cc_final: 0.6002 (tpt) REVERT: B 45 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7584 (m-80) REVERT: B 46 VAL cc_start: 0.8099 (t) cc_final: 0.7613 (m) REVERT: B 69 GLU cc_start: 0.2382 (OUTLIER) cc_final: 0.2140 (mt-10) REVERT: B 186 LYS cc_start: 0.2292 (mttm) cc_final: 0.1835 (mttm) REVERT: B 407 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6498 (tt) REVERT: B 419 ASP cc_start: 0.6356 (t0) cc_final: 0.6135 (t0) REVERT: B 455 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.6984 (m-10) REVERT: B 511 PHE cc_start: 0.6301 (OUTLIER) cc_final: 0.5181 (m-80) REVERT: B 722 PHE cc_start: 0.6660 (m-10) cc_final: 0.6365 (m-10) REVERT: B 744 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: B 758 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7121 (tp) REVERT: B 880 GLU cc_start: 0.6117 (pp20) cc_final: 0.5866 (tm-30) REVERT: B 962 TYR cc_start: 0.3800 (m-10) cc_final: 0.2520 (m-10) REVERT: C 30 ASP cc_start: 0.7605 (m-30) cc_final: 0.7310 (m-30) REVERT: C 52 ARG cc_start: 0.7299 (ttm110) cc_final: 0.7018 (ttm110) outliers start: 50 outliers final: 23 residues processed: 214 average time/residue: 0.1160 time to fit residues: 38.4092 Evaluate side-chains 183 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 289 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 6 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 232 VAL 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 744 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 863 ASN Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 79 PHE 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 107 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 119 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 391 ASN ** B 118 HIS ** 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 = 0.4431 r_free = 0.4431 target = 0.156170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.132919 restraints weight = 37082.707| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 3.11 r_work: 0.3805 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17175 Z= 0.151 Angle : 0.646 14.577 23141 Z= 0.343 Chirality : 0.044 0.232 2472 Planarity : 0.003 0.043 2945 Dihedral : 5.877 55.053 2212 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.84 % Favored : 89.75 % Rotamer: Outliers : 2.64 % Allowed : 12.51 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.18), residues: 1991 helix: -0.51 (0.15), residues: 1159 sheet: -2.24 (0.75), residues: 48 loop : -2.81 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 613 TYR 0.018 0.001 TYR B 721 PHE 0.028 0.002 PHE C 81 TRP 0.009 0.001 TRP A 143 HIS 0.005 0.001 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00348 (17175) covalent geometry : angle 0.64597 (23141) hydrogen bonds : bond 0.03738 ( 647) hydrogen bonds : angle 4.54232 ( 1887) *********************** 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 210 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 PHE cc_start: 0.6586 (t80) cc_final: 0.6197 (t80) REVERT: A 994 LYS cc_start: 0.8048 (pttm) cc_final: 0.7348 (pttm) REVERT: B 6 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5966 (tp) REVERT: B 21 MET cc_start: 0.6750 (tpt) cc_final: 0.6274 (tpt) REVERT: B 45 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: B 46 VAL cc_start: 0.8316 (t) cc_final: 0.7871 (m) REVERT: B 69 GLU cc_start: 0.2676 (OUTLIER) cc_final: 0.2370 (mt-10) REVERT: B 195 GLN cc_start: 0.7860 (pp30) cc_final: 0.7562 (pp30) REVERT: B 295 GLU cc_start: 0.2394 (OUTLIER) cc_final: 0.0821 (pt0) REVERT: B 455 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6831 (m-10) REVERT: B 511 PHE cc_start: 0.6426 (OUTLIER) cc_final: 0.5253 (m-80) REVERT: B 706 VAL cc_start: 0.7956 (m) cc_final: 0.7618 (p) REVERT: B 744 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: B 758 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7183 (tp) REVERT: B 880 GLU cc_start: 0.6200 (pp20) cc_final: 0.5953 (tm-30) REVERT: B 962 TYR cc_start: 0.4045 (m-10) cc_final: 0.2809 (m-10) REVERT: C 30 ASP cc_start: 0.7628 (m-30) cc_final: 0.7403 (m-30) REVERT: C 59 PHE cc_start: 0.7735 (m-80) cc_final: 0.7485 (m-80) outliers start: 49 outliers final: 22 residues processed: 199 average time/residue: 0.1188 time to fit residues: 36.9241 Evaluate side-chains 181 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 391 ASN 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 6 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 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 863 ASN Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 79 PHE 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 47 optimal weight: 0.1980 chunk 162 optimal weight: 0.0770 chunk 111 optimal weight: 1.9990 chunk 157 optimal weight: 0.0970 chunk 145 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.157394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.133965 restraints weight = 37072.063| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.11 r_work: 0.3844 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.7425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17175 Z= 0.118 Angle : 0.608 11.201 23141 Z= 0.323 Chirality : 0.042 0.206 2472 Planarity : 0.003 0.046 2945 Dihedral : 5.662 55.250 2212 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.49 % Favored : 90.16 % Rotamer: Outliers : 2.05 % Allowed : 13.05 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.18), residues: 1991 helix: -0.22 (0.16), residues: 1150 sheet: -2.02 (0.76), residues: 48 loop : -2.73 (0.19), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 802 TYR 0.019 0.001 TYR B 725 PHE 0.028 0.001 PHE C 81 TRP 0.008 0.001 TRP A 60 HIS 0.005 0.001 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00252 (17175) covalent geometry : angle 0.60821 (23141) hydrogen bonds : bond 0.03404 ( 647) hydrogen bonds : angle 4.34947 ( 1887) *********************** 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: 38 poor density : 156 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 PHE cc_start: 0.6609 (t80) cc_final: 0.6166 (t80) REVERT: A 674 ASP cc_start: 0.6701 (p0) cc_final: 0.6433 (m-30) REVERT: A 994 LYS cc_start: 0.8029 (pttm) cc_final: 0.7286 (pttm) REVERT: B 21 MET cc_start: 0.6856 (tpt) cc_final: 0.6547 (tpt) REVERT: B 45 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: B 46 VAL cc_start: 0.8188 (t) cc_final: 0.7692 (m) REVERT: B 195 GLN cc_start: 0.7885 (pp30) cc_final: 0.7434 (pp30) REVERT: B 232 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8663 (p) REVERT: B 295 GLU cc_start: 0.1924 (OUTLIER) cc_final: 0.0118 (pt0) REVERT: B 511 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.5305 (m-80) REVERT: B 542 LEU cc_start: -0.0598 (OUTLIER) cc_final: -0.0892 (pp) REVERT: B 659 PHE cc_start: 0.5123 (m-10) cc_final: 0.4905 (m-80) REVERT: B 758 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7242 (tp) REVERT: B 880 GLU cc_start: 0.6141 (pp20) cc_final: 0.5911 (tm-30) REVERT: B 913 MET cc_start: -0.2118 (mmp) cc_final: -0.2364 (mmm) REVERT: B 962 TYR cc_start: 0.3665 (m-10) cc_final: 0.2581 (m-10) REVERT: C 59 PHE cc_start: 0.7608 (m-80) cc_final: 0.7385 (m-80) outliers start: 38 outliers final: 18 residues processed: 186 average time/residue: 0.1153 time to fit residues: 34.4099 Evaluate side-chains 168 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 223 TYR 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 693 GLU 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 45 PHE Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 79 PHE 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 34 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 175 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 171 optimal weight: 0.0970 chunk 189 optimal weight: 0.4980 chunk 131 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 391 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.156250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.133286 restraints weight = 37071.478| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.27 r_work: 0.3833 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.7782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17175 Z= 0.119 Angle : 0.609 15.057 23141 Z= 0.321 Chirality : 0.042 0.177 2472 Planarity : 0.003 0.032 2945 Dihedral : 5.546 54.178 2212 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.34 % Favored : 90.31 % Rotamer: Outliers : 2.00 % Allowed : 13.38 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.19), residues: 1991 helix: -0.04 (0.16), residues: 1151 sheet: -1.86 (0.79), residues: 48 loop : -2.58 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 72 TYR 0.017 0.001 TYR B 418 PHE 0.025 0.001 PHE C 81 TRP 0.009 0.001 TRP C 25 HIS 0.005 0.001 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00263 (17175) covalent geometry : angle 0.60933 (23141) hydrogen bonds : bond 0.03343 ( 647) hydrogen bonds : angle 4.28019 ( 1887) *********************** 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 200 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 PHE cc_start: 0.6663 (t80) cc_final: 0.6169 (t80) REVERT: A 674 ASP cc_start: 0.6836 (p0) cc_final: 0.6502 (m-30) REVERT: A 677 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6183 (ptt-90) REVERT: A 994 LYS cc_start: 0.8061 (pttm) cc_final: 0.7297 (pttm) REVERT: B 21 MET cc_start: 0.6635 (tpt) cc_final: 0.6368 (tpt) REVERT: B 45 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: B 46 VAL cc_start: 0.8261 (t) cc_final: 0.7754 (m) REVERT: B 69 GLU cc_start: 0.2042 (OUTLIER) cc_final: 0.1841 (mt-10) REVERT: B 232 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8740 (p) REVERT: B 295 GLU cc_start: 0.1826 (OUTLIER) cc_final: 0.0776 (pt0) REVERT: B 511 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.5237 (m-80) REVERT: B 542 LEU cc_start: -0.0631 (OUTLIER) cc_final: -0.0954 (pp) REVERT: B 659 PHE cc_start: 0.5473 (m-10) cc_final: 0.5181 (m-80) REVERT: B 758 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7273 (tp) REVERT: B 880 GLU cc_start: 0.6255 (pp20) cc_final: 0.5999 (tm-30) REVERT: B 962 TYR cc_start: 0.3523 (m-10) cc_final: 0.2687 (m-10) REVERT: C 59 PHE cc_start: 0.7616 (m-80) cc_final: 0.7406 (m-80) outliers start: 37 outliers final: 17 residues processed: 190 average time/residue: 0.1226 time to fit residues: 36.9272 Evaluate side-chains 171 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 677 ARG Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 592 LEU 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 C residue 11 THR Chi-restraints excluded: chain C residue 39 LEU 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 87 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 129 optimal weight: 0.0470 chunk 52 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 391 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.153831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.130548 restraints weight = 36903.103| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 3.35 r_work: 0.3767 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.8184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17175 Z= 0.141 Angle : 0.635 13.350 23141 Z= 0.336 Chirality : 0.043 0.191 2472 Planarity : 0.003 0.059 2945 Dihedral : 5.579 54.382 2212 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.74 % Favored : 89.85 % Rotamer: Outliers : 1.62 % Allowed : 14.13 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.19), residues: 1991 helix: -0.02 (0.16), residues: 1155 sheet: -1.95 (0.79), residues: 48 loop : -2.51 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 760 TYR 0.016 0.001 TYR B 725 PHE 0.026 0.002 PHE C 81 TRP 0.011 0.001 TRP B 919 HIS 0.027 0.002 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00320 (17175) covalent geometry : angle 0.63461 (23141) hydrogen bonds : bond 0.03624 ( 647) hydrogen bonds : angle 4.34948 ( 1887) *********************** 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 174 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 PHE cc_start: 0.6626 (t80) cc_final: 0.6180 (t80) REVERT: A 674 ASP cc_start: 0.7074 (p0) cc_final: 0.6615 (m-30) REVERT: A 994 LYS cc_start: 0.8042 (pttm) cc_final: 0.7258 (pttm) REVERT: B 21 MET cc_start: 0.6859 (tpt) cc_final: 0.6440 (tpt) REVERT: B 232 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8931 (p) REVERT: B 295 GLU cc_start: 0.1827 (OUTLIER) cc_final: 0.0777 (pt0) REVERT: B 332 HIS cc_start: 0.7738 (m-70) cc_final: 0.7436 (m90) REVERT: B 511 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.5359 (m-80) REVERT: B 744 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.6071 (t80) REVERT: B 758 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7187 (tp) REVERT: B 880 GLU cc_start: 0.6248 (pp20) cc_final: 0.5975 (tm-30) REVERT: B 962 TYR cc_start: 0.3579 (m-10) cc_final: -0.0006 (m-10) REVERT: C 103 SER cc_start: 0.8072 (m) cc_final: 0.7665 (p) outliers start: 30 outliers final: 20 residues processed: 169 average time/residue: 0.1214 time to fit residues: 32.4758 Evaluate side-chains 168 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 391 ASN 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 6 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 592 LEU 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 C residue 39 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 163 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 133 optimal weight: 0.2980 chunk 118 optimal weight: 0.0170 chunk 123 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 overall best weight: 0.3218 ------------------------------------------------------------------------------- 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 391 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.155065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.132503 restraints weight = 36820.733| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 3.03 r_work: 0.3808 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.8334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 17175 Z= 0.113 Angle : 0.620 15.960 23141 Z= 0.323 Chirality : 0.042 0.167 2472 Planarity : 0.003 0.032 2945 Dihedral : 5.480 54.615 2212 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.39 % Favored : 90.26 % Rotamer: Outliers : 1.56 % Allowed : 14.19 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.19), residues: 1991 helix: 0.05 (0.16), residues: 1165 sheet: -1.87 (0.79), residues: 48 loop : -2.44 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 892 TYR 0.018 0.001 TYR B 356 PHE 0.019 0.001 PHE B 722 TRP 0.008 0.001 TRP A 60 HIS 0.013 0.001 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00247 (17175) covalent geometry : angle 0.61983 (23141) hydrogen bonds : bond 0.03302 ( 647) hydrogen bonds : angle 4.27360 ( 1887) ********************** 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 179 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.7230 (t80) REVERT: A 576 PHE cc_start: 0.6791 (t80) cc_final: 0.6200 (t80) REVERT: A 605 PHE cc_start: 0.7747 (p90) cc_final: 0.7451 (p90) REVERT: A 674 ASP cc_start: 0.6845 (p0) cc_final: 0.6565 (m-30) REVERT: A 994 LYS cc_start: 0.7930 (pttm) cc_final: 0.7225 (pttm) REVERT: B 21 MET cc_start: 0.6969 (tpt) cc_final: 0.6600 (tpt) REVERT: B 186 LYS cc_start: 0.2175 (mmtt) cc_final: 0.1549 (mttm) REVERT: B 295 GLU cc_start: 0.1701 (OUTLIER) cc_final: 0.0668 (pt0) REVERT: B 332 HIS cc_start: 0.7741 (m-70) cc_final: 0.7522 (m-70) REVERT: B 511 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.5323 (m-80) REVERT: B 610 GLN cc_start: 0.7863 (pp30) cc_final: 0.7576 (pt0) REVERT: B 744 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.6387 (t80) REVERT: B 758 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7164 (tp) REVERT: B 866 MET cc_start: 0.5150 (tmm) cc_final: 0.4760 (ppp) REVERT: B 880 GLU cc_start: 0.6139 (pp20) cc_final: 0.5839 (tm-30) REVERT: B 962 TYR cc_start: 0.3408 (m-10) cc_final: -0.0202 (m-10) REVERT: C 65 ASP cc_start: 0.7444 (t70) cc_final: 0.7223 (t70) REVERT: C 103 SER cc_start: 0.8097 (m) cc_final: 0.7717 (p) outliers start: 29 outliers final: 19 residues processed: 173 average time/residue: 0.1133 time to fit residues: 30.7620 Evaluate side-chains 168 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 391 ASN 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 869 ILE Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain B residue 6 LEU 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 511 PHE Chi-restraints excluded: chain B residue 592 LEU 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 823 ILE Chi-restraints excluded: chain C residue 39 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 111 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 119 optimal weight: 0.4980 chunk 115 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 391 ASN ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.153019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.129711 restraints weight = 36777.538| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.38 r_work: 0.3741 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.8577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17175 Z= 0.135 Angle : 0.636 14.024 23141 Z= 0.333 Chirality : 0.043 0.187 2472 Planarity : 0.003 0.033 2945 Dihedral : 5.477 53.837 2212 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.59 % Favored : 90.06 % Rotamer: Outliers : 1.51 % Allowed : 14.19 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.19), residues: 1991 helix: 0.09 (0.16), residues: 1159 sheet: -1.99 (0.77), residues: 48 loop : -2.42 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 802 TYR 0.018 0.001 TYR A 709 PHE 0.024 0.002 PHE C 81 TRP 0.012 0.001 TRP B 919 HIS 0.016 0.001 HIS B 609 Details of bonding type rmsd covalent geometry : bond 0.00310 (17175) covalent geometry : angle 0.63560 (23141) hydrogen bonds : bond 0.03581 ( 647) hydrogen bonds : angle 4.32755 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3747.93 seconds wall clock time: 65 minutes 2.79 seconds (3902.79 seconds total)