Starting phenix.real_space_refine on Fri Jun 20 08:26:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f4r_28857/06_2025/8f4r_28857.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f4r_28857/06_2025/8f4r_28857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f4r_28857/06_2025/8f4r_28857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f4r_28857/06_2025/8f4r_28857.map" model { file = "/net/cci-nas-00/data/ceres_data/8f4r_28857/06_2025/8f4r_28857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f4r_28857/06_2025/8f4r_28857.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 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 132 5.16 5 C 15122 2.51 5 N 3992 2.21 5 O 4429 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23675 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7865 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 989} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 7898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7898 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 991} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7881 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 991} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LLL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.65, per 1000 atoms: 0.62 Number of scatterers: 23675 At special positions: 0 Unit cell: (124.12, 114.49, 141.24, 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 132 16.00 O 4429 8.00 N 3992 7.00 C 15122 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: 6.60 Conformation dependent library (CDL) restraints added in 3.2 seconds 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5708 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 25 sheets defined 59.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.516A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.523A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.962A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.630A pdb=" N PHE A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 359 Processing helix chain 'A' and resid 361 through 386 Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 424 removed outlier: 4.160A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 460 through 497 removed outlier: 4.554A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.774A pdb=" N LEU A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 510 through 536 Processing helix chain 'A' and resid 536 through 558 removed outlier: 3.863A pdb=" N TRP A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 601 Processing helix chain 'A' and resid 642 through 656 Processing helix chain 'A' and resid 690 through 708 removed outlier: 3.683A pdb=" N GLU A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 752 Processing helix chain 'A' and resid 775 through 778 Processing helix chain 'A' and resid 780 through 786 Processing helix chain 'A' and resid 799 through 802 No H-bonds generated for 'chain 'A' and resid 799 through 802' Processing helix chain 'A' and resid 834 through 849 Processing helix chain 'A' and resid 859 through 867 Processing helix chain 'A' and resid 869 through 891 removed outlier: 3.712A pdb=" N ALA A 873 " --> pdb=" O ALA A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.830A pdb=" N VAL A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 917 removed outlier: 3.631A pdb=" N GLY A 906 " --> pdb=" O VAL A 902 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 910 " --> pdb=" O GLY A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 953 Processing helix chain 'A' and resid 956 through 988 removed outlier: 4.549A pdb=" N ARG A 970 " --> pdb=" O ARG A 966 " (cutoff:3.500A) Proline residue: A 971 - end of helix Proline residue: A 985 - end of helix Processing helix chain 'A' and resid 993 through 1030 removed outlier: 4.271A pdb=" N TYR A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Proline residue: A1020 - end of helix Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.775A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.634A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 removed outlier: 4.056A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 removed outlier: 3.627A pdb=" N GLN B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.523A pdb=" N PHE B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 315 removed outlier: 3.702A pdb=" N GLN B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 359 Processing helix chain 'B' and resid 361 through 386 removed outlier: 3.747A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 3.662A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 424 removed outlier: 3.507A pdb=" N ILE B 402 " --> pdb=" O MET B 398 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 452 removed outlier: 3.917A pdb=" N GLY B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 459 removed outlier: 4.637A pdb=" N MET B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 459' Processing helix chain 'B' and resid 460 through 486 Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.991A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 535 removed outlier: 4.668A pdb=" N ASN B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 556 removed outlier: 4.077A pdb=" N TRP B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 Processing helix chain 'B' and resid 642 through 655 Processing helix chain 'B' and resid 690 through 708 Processing helix chain 'B' and resid 730 through 738 Processing helix chain 'B' and resid 740 through 753 Processing helix chain 'B' and resid 775 through 778 Processing helix chain 'B' and resid 780 through 786 removed outlier: 3.683A pdb=" N ILE B 784 " --> pdb=" O PRO B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 847 removed outlier: 3.571A pdb=" N LYS B 847 " --> pdb=" O GLU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 891 Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 894 through 901 Processing helix chain 'B' and resid 902 through 918 removed outlier: 3.602A pdb=" N GLY B 906 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 954 removed outlier: 4.564A pdb=" N PHE B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 968 Processing helix chain 'B' and resid 968 through 988 removed outlier: 3.588A pdb=" N ILE B 972 " --> pdb=" O ARG B 968 " (cutoff:3.500A) Proline residue: B 985 - end of helix Processing helix chain 'B' and resid 993 through 1014 removed outlier: 3.717A pdb=" N GLN B 997 " --> pdb=" O GLY B 993 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B1004 " --> pdb=" O VAL B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1030 Proline residue: B1020 - end of helix Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.559A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.527A pdb=" N ASN C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 4.139A pdb=" N SER C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.766A pdb=" N VAL C 203 " --> pdb=" O THR C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.545A pdb=" N PHE C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 315 Processing helix chain 'C' and resid 329 through 360 removed outlier: 3.622A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 387 removed outlier: 3.843A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.569A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'C' and resid 401 through 423 removed outlier: 4.176A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 459 removed outlier: 5.757A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Proline residue: C 455 - end of helix removed outlier: 3.988A pdb=" N PHE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE C 459 " --> pdb=" O PRO C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 496 removed outlier: 4.593A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 511 through 532 Processing helix chain 'C' and resid 536 through 558 removed outlier: 4.484A pdb=" N TRP C 540 " --> pdb=" O ARG C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 600 Processing helix chain 'C' and resid 642 through 657 Processing helix chain 'C' and resid 690 through 708 Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 740 through 752 Processing helix chain 'C' and resid 775 through 778 Processing helix chain 'C' and resid 780 through 786 Processing helix chain 'C' and resid 834 through 849 Processing helix chain 'C' and resid 859 through 867 Processing helix chain 'C' and resid 870 through 891 Processing helix chain 'C' and resid 894 through 901 Processing helix chain 'C' and resid 902 through 917 removed outlier: 3.998A pdb=" N GLY C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 954 removed outlier: 3.752A pdb=" N ILE C 943 " --> pdb=" O ASN C 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 988 removed outlier: 4.867A pdb=" N ARG C 970 " --> pdb=" O ARG C 966 " (cutoff:3.500A) Proline residue: C 971 - end of helix Proline residue: C 985 - end of helix Processing helix chain 'C' and resid 993 through 1030 removed outlier: 4.314A pdb=" N GLY C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C1016 " --> pdb=" O THR C1012 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Proline residue: C1020 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.718A pdb=" N ASN A 42 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 77 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 12.701A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU A 824 " --> pdb=" O HIS A 716 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N HIS A 716 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 826 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL A 714 " --> pdb=" O VAL A 826 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.718A pdb=" N ASN A 42 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 77 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 12.701A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER A 821 " --> pdb=" O ASP A 685 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP A 680 " --> pdb=" O THR A 858 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.989A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 138 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 293 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASN A 136 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE A 137 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A 328 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N THR A 139 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.989A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL A 623 " --> pdb=" O GLY A 613 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N GLY A 615 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N GLN A 621 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.364A pdb=" N TYR A 182 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS A 768 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN A 758 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 771 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR A 756 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 218 removed outlier: 3.508A pdb=" N GLY A 217 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR A 233 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE B 727 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A 235 " --> pdb=" O ILE B 727 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 729 " --> pdb=" O ASN A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA8, first strand: chain 'A' and resid 803 through 810 removed outlier: 8.563A pdb=" N ASN C 235 " --> pdb=" O PRO A 723 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 725 " --> pdb=" O ASN C 235 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB1, first strand: chain 'B' and resid 75 through 80 removed outlier: 6.984A pdb=" N SER B 93 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR B 91 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER B 80 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER B 89 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.835A pdb=" N SER B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 138 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 293 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B 136 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ILE B 137 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU B 328 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR B 139 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.251A pdb=" N SER B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.386A pdb=" N TYR B 182 " --> pdb=" O VAL B 766 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS B 768 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN B 758 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 771 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR B 756 " --> pdb=" O VAL B 771 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 219 removed outlier: 4.717A pdb=" N THR B 233 " --> pdb=" O PRO C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.841A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 711 through 716 removed outlier: 4.995A pdb=" N ARG B 713 " --> pdb=" O GLU B 828 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU B 828 " --> pdb=" O ARG B 713 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 711 through 716 removed outlier: 4.995A pdb=" N ARG B 713 " --> pdb=" O GLU B 828 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU B 828 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N SER B 821 " --> pdb=" O ASP B 685 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 788 through 790 Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.024A pdb=" N GLN C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 12.333A pdb=" N ARG C 813 " --> pdb=" O GLU C 824 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N GLU C 824 " --> pdb=" O ARG C 813 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU C 815 " --> pdb=" O ALA C 822 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU C 828 " --> pdb=" O ARG C 713 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG C 713 " --> pdb=" O GLU C 828 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.024A pdb=" N GLN C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 12.333A pdb=" N ARG C 813 " --> pdb=" O GLU C 824 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N GLU C 824 " --> pdb=" O ARG C 813 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU C 815 " --> pdb=" O ALA C 822 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.658A pdb=" N SER C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 138 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR C 139 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.290A pdb=" N SER C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.798A pdb=" N TYR C 182 " --> pdb=" O VAL C 766 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS C 768 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN C 758 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL C 771 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR C 756 " --> pdb=" O VAL C 771 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.657A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 788 through 790 1625 hydrogen bonds defined for protein. 4758 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: 10.54 Time building geometry restraints manager: 7.64 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: 7775 1.34 - 1.46: 3862 1.46 - 1.57: 12240 1.57 - 1.69: 5 1.69 - 1.81: 252 Bond restraints: 24134 Sorted by residual: bond pdb=" C51 LLL B1101 " pdb=" C61 LLL B1101 " ideal model delta sigma weight residual 1.515 1.590 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C42 LLL B1101 " pdb=" C52 LLL B1101 " ideal model delta sigma weight residual 1.529 1.601 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" CA PHE A1030 " pdb=" C PHE A1030 " ideal model delta sigma weight residual 1.532 1.511 0.022 6.50e-03 2.37e+04 1.10e+01 bond pdb=" C32 LLL B1101 " pdb=" C42 LLL B1101 " ideal model delta sigma weight residual 1.529 1.592 -0.063 2.00e-02 2.50e+03 9.93e+00 bond pdb=" C33 LLL B1101 " pdb=" C43 LLL B1101 " ideal model delta sigma weight residual 1.541 1.603 -0.062 2.00e-02 2.50e+03 9.61e+00 ... (remaining 24129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 32408 2.02 - 4.05: 324 4.05 - 6.07: 54 6.07 - 8.09: 11 8.09 - 10.12: 3 Bond angle restraints: 32800 Sorted by residual: angle pdb=" C ALA B 859 " pdb=" CA ALA B 859 " pdb=" CB ALA B 859 " ideal model delta sigma weight residual 116.54 110.06 6.48 1.15e+00 7.56e-01 3.18e+01 angle pdb=" C LEU B 500 " pdb=" CA LEU B 500 " pdb=" CB LEU B 500 " ideal model delta sigma weight residual 117.23 110.78 6.45 1.36e+00 5.41e-01 2.25e+01 angle pdb=" C ASN C 818 " pdb=" CA ASN C 818 " pdb=" CB ASN C 818 " ideal model delta sigma weight residual 116.54 111.21 5.33 1.15e+00 7.56e-01 2.15e+01 angle pdb=" C SER C 894 " pdb=" N VAL C 895 " pdb=" CA VAL C 895 " ideal model delta sigma weight residual 120.24 122.84 -2.60 6.30e-01 2.52e+00 1.70e+01 angle pdb=" CA ALA B 859 " pdb=" C ALA B 859 " pdb=" N MET B 860 " ideal model delta sigma weight residual 119.52 116.45 3.07 7.90e-01 1.60e+00 1.51e+01 ... (remaining 32795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.83: 14095 25.83 - 51.66: 301 51.66 - 77.48: 35 77.48 - 103.31: 7 103.31 - 129.14: 8 Dihedral angle restraints: 14446 sinusoidal: 5554 harmonic: 8892 Sorted by residual: dihedral pdb=" O23 LLL B1101 " pdb=" C13 LLL B1101 " pdb=" C23 LLL B1101 " pdb=" O53 LLL B1101 " ideal model delta sinusoidal sigma weight residual 178.81 -52.05 -129.14 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C11 LLL B1101 " pdb=" C51 LLL B1101 " pdb=" O51 LLL B1101 " pdb=" C61 LLL B1101 " ideal model delta sinusoidal sigma weight residual 174.24 -57.43 -128.33 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C11 LLL B1101 " pdb=" C51 LLL B1101 " pdb=" O51 LLL B1101 " pdb=" C41 LLL B1101 " ideal model delta sinusoidal sigma weight residual -60.30 64.56 -124.86 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 14443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3811 0.134 - 0.269: 5 0.269 - 0.403: 4 0.403 - 0.537: 1 0.537 - 0.671: 3 Chirality restraints: 3824 Sorted by residual: chirality pdb=" C62 LLL B1101 " pdb=" C12 LLL B1101 " pdb=" C52 LLL B1101 " pdb=" O62 LLL B1101 " both_signs ideal model delta sigma weight residual False -2.49 -3.16 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C42 LLL B1101 " pdb=" C32 LLL B1101 " pdb=" C52 LLL B1101 " pdb=" O11 LLL B1101 " both_signs ideal model delta sigma weight residual False 2.54 3.21 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C52 LLL B1101 " pdb=" C42 LLL B1101 " pdb=" C62 LLL B1101 " pdb=" O52 LLL B1101 " both_signs ideal model delta sigma weight residual False -2.47 -3.05 0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 3821 not shown) Planarity restraints: 4225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 871 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO C 872 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 872 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 872 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 426 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 427 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 830 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 831 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 831 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 831 " -0.017 5.00e-02 4.00e+02 ... (remaining 4222 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3446 2.75 - 3.29: 24065 3.29 - 3.82: 40546 3.82 - 4.36: 47331 4.36 - 4.90: 83583 Nonbonded interactions: 198971 Sorted by model distance: nonbonded pdb=" O ALA A 451 " pdb=" OG SER A 878 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A 526 " pdb=" O ILE A1016 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 759 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR C 526 " pdb=" O ILE C1016 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASP B 153 " pdb=" OH TYR B 182 " model vdw 2.276 3.040 ... (remaining 198966 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 1 through 94 or (resid 95 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 505 or ( \ resid 506 and (name N or name CA or name C or name O or name CB )) or (resid 507 \ through 509 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 10 through 1031)) selection = (chain 'B' and (resid 1 through 94 or (resid 95 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 499 or ( \ resid 500 through 502 and (name N or name CA or name C or name O or name CB )) o \ r (resid 503 through 506 and (name N or name CA or name C or name O or name CB ) \ ) or resid 507 or (resid 508 through 509 and (name N or name CA or name C or nam \ e O or name CB )) or resid 510 through 638 or (resid 639 and (name N or name CA \ or name C or name O or name CB )) or resid 640 through 657 or (resid 658 and (na \ me N or name CA or name C or name O or name CB )) or resid 659 through 1031)) selection = (chain 'C' and (resid 1 through 499 or (resid 500 through 502 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 503 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 or (resid 508 through 509 \ and (name N or name CA or name C or name O or name CB )) or resid 510 through 6 \ 57 or (resid 658 and (name N or name CA or name C or name O or name CB )) or res \ id 659 through 1031)) } 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: 3.010 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: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 57.810 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24134 Z= 0.210 Angle : 0.561 10.117 32800 Z= 0.324 Chirality : 0.044 0.671 3824 Planarity : 0.003 0.038 4225 Dihedral : 11.500 129.138 8738 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.23 % Favored : 98.74 % Rotamer: Outliers : 3.22 % Allowed : 5.53 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.15), residues: 3091 helix: 2.32 (0.12), residues: 1691 sheet: -0.26 (0.26), residues: 427 loop : 0.04 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 540 HIS 0.005 0.001 HIS A 506 PHE 0.010 0.001 PHE C 571 TYR 0.010 0.001 TYR C 862 ARG 0.005 0.000 ARG B 813 Details of bonding type rmsd hydrogen bonds : bond 0.15244 ( 1564) hydrogen bonds : angle 6.76638 ( 4758) covalent geometry : bond 0.00431 (24134) covalent geometry : angle 0.56069 (32800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 640 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 ASN cc_start: 0.7791 (m110) cc_final: 0.7572 (m110) REVERT: A 799 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8421 (t80) REVERT: B 135 THR cc_start: 0.7241 (p) cc_final: 0.6754 (p) REVERT: B 682 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7134 (tp30) REVERT: B 726 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7497 (tp40) REVERT: B 880 LEU cc_start: 0.8478 (tp) cc_final: 0.8232 (tp) REVERT: C 270 MET cc_start: 0.8061 (ttp) cc_final: 0.7677 (ttp) REVERT: C 683 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8233 (tp) REVERT: C 731 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6050 (mp10) REVERT: C 777 TYR cc_start: 0.8573 (m-80) cc_final: 0.8260 (m-80) outliers start: 81 outliers final: 25 residues processed: 696 average time/residue: 0.3505 time to fit residues: 377.5224 Evaluate side-chains 420 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 390 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 726 GLN Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 833 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 59 ASN A 81 GLN A 87 GLN A 105 GLN A 108 GLN A 124 ASN A 163 GLN A 213 GLN A 237 GLN A 437 GLN A 439 GLN A 469 GLN A 517 GLN A 583 GLN A 585 GLN A 592 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 GLN A 921 ASN A 926 GLN B 109 ASN B 163 GLN B 213 GLN B 255 GLN B 592 GLN B 700 GLN B 708 ASN B 716 HIS B 724 GLN B 726 GLN B 749 GLN B 818 ASN B 926 GLN B 951 ASN C 87 GLN C 110 GLN C 123 GLN C 194 ASN C 241 GLN C 254 ASN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 GLN C 655 ASN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 HIS C 700 GLN C 716 HIS C 735 GLN C 745 ASN C 749 GLN C 863 GLN C 967 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.095624 restraints weight = 35788.904| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.96 r_work: 0.3022 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24134 Z= 0.170 Angle : 0.561 9.330 32800 Z= 0.291 Chirality : 0.041 0.259 3824 Planarity : 0.004 0.042 4225 Dihedral : 8.097 105.793 3443 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer: Outliers : 3.90 % Allowed : 9.23 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.15), residues: 3091 helix: 2.33 (0.12), residues: 1714 sheet: -0.31 (0.25), residues: 438 loop : -0.03 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 540 HIS 0.008 0.001 HIS A 506 PHE 0.023 0.001 PHE C 511 TYR 0.014 0.001 TYR B 467 ARG 0.006 0.000 ARG B 813 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 1564) hydrogen bonds : angle 5.21724 ( 4758) covalent geometry : bond 0.00392 (24134) covalent geometry : angle 0.56060 (32800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 424 time to evaluate : 2.791 Fit side-chains revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8380 (tttp) REVERT: A 153 ASP cc_start: 0.8340 (m-30) cc_final: 0.8031 (m-30) REVERT: A 163 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7832 (mt0) REVERT: A 175 ILE cc_start: 0.8686 (pt) cc_final: 0.8392 (pt) REVERT: A 398 MET cc_start: 0.8951 (mmm) cc_final: 0.8750 (tpp) REVERT: A 450 SER cc_start: 0.9303 (t) cc_final: 0.8714 (p) REVERT: A 710 GLU cc_start: 0.7742 (mp0) cc_final: 0.7146 (mt-10) REVERT: A 799 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8713 (t80) REVERT: B 135 THR cc_start: 0.8219 (p) cc_final: 0.7792 (p) REVERT: B 168 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7252 (mpp-170) REVERT: B 682 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8572 (tp30) REVERT: B 860 MET cc_start: 0.8506 (ttm) cc_final: 0.8281 (tpp) REVERT: B 880 LEU cc_start: 0.8927 (tp) cc_final: 0.8709 (tp) REVERT: C 145 THR cc_start: 0.9037 (m) cc_final: 0.8798 (p) REVERT: C 731 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.6704 (mp10) REVERT: C 777 TYR cc_start: 0.9302 (m-80) cc_final: 0.8919 (m-80) REVERT: C 837 THR cc_start: 0.8259 (m) cc_final: 0.8040 (p) REVERT: C 938 LYS cc_start: 0.8457 (tttm) cc_final: 0.8189 (pttp) REVERT: C 953 LYS cc_start: 0.8364 (mptt) cc_final: 0.7719 (tttm) REVERT: C 1028 ARG cc_start: 0.8470 (mtt180) cc_final: 0.8063 (mtt90) outliers start: 98 outliers final: 51 residues processed: 493 average time/residue: 0.3376 time to fit residues: 266.2001 Evaluate side-chains 420 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 364 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 944 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 84 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 292 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 GLN A 517 GLN A 921 ASN ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 GLN B 686 HIS ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 HIS C 951 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.088041 restraints weight = 35500.936| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.99 r_work: 0.2930 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24134 Z= 0.197 Angle : 0.559 9.809 32800 Z= 0.286 Chirality : 0.041 0.259 3824 Planarity : 0.004 0.045 4225 Dihedral : 7.060 88.866 3424 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer: Outliers : 4.34 % Allowed : 10.62 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.15), residues: 3091 helix: 2.22 (0.12), residues: 1715 sheet: -0.41 (0.24), residues: 435 loop : -0.11 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 540 HIS 0.008 0.001 HIS A 506 PHE 0.020 0.001 PHE C 511 TYR 0.011 0.001 TYR C 526 ARG 0.005 0.000 ARG B 813 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 1564) hydrogen bonds : angle 5.00777 ( 4758) covalent geometry : bond 0.00461 (24134) covalent geometry : angle 0.55868 (32800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 381 time to evaluate : 2.756 Fit side-chains revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8629 (ttpt) cc_final: 0.8377 (tttm) REVERT: A 429 GLU cc_start: 0.8215 (tt0) cc_final: 0.8006 (mt-10) REVERT: A 450 SER cc_start: 0.9226 (t) cc_final: 0.8550 (p) REVERT: A 574 SER cc_start: 0.8990 (m) cc_final: 0.8600 (p) REVERT: A 606 MET cc_start: 0.8932 (ttm) cc_final: 0.8707 (ttp) REVERT: A 628 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8970 (mp) REVERT: A 710 GLU cc_start: 0.7634 (mp0) cc_final: 0.7078 (mt-10) REVERT: A 799 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8737 (t80) REVERT: A 824 GLU cc_start: 0.8688 (tt0) cc_final: 0.8463 (tp30) REVERT: B 135 THR cc_start: 0.8255 (p) cc_final: 0.7828 (p) REVERT: B 168 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7177 (mtp180) REVERT: B 1025 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8544 (mt) REVERT: C 145 THR cc_start: 0.9058 (m) cc_final: 0.8814 (p) REVERT: C 417 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 731 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.6640 (mp10) REVERT: C 777 TYR cc_start: 0.9269 (m-80) cc_final: 0.8845 (m-80) REVERT: C 837 THR cc_start: 0.8385 (m) cc_final: 0.8132 (p) REVERT: C 938 LYS cc_start: 0.8441 (tttm) cc_final: 0.8075 (tttt) REVERT: C 953 LYS cc_start: 0.8390 (mptt) cc_final: 0.7823 (tttm) REVERT: C 1005 MET cc_start: 0.8400 (ttm) cc_final: 0.8058 (ttm) REVERT: C 1028 ARG cc_start: 0.8459 (mtt180) cc_final: 0.8017 (mtt90) outliers start: 109 outliers final: 67 residues processed: 456 average time/residue: 0.3410 time to fit residues: 246.9791 Evaluate side-chains 418 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 346 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 805 SER Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 1009 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 98 optimal weight: 0.0770 chunk 77 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 264 optimal weight: 0.8980 chunk 181 optimal weight: 0.4980 chunk 276 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 271 optimal weight: 0.0870 chunk 153 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 319 HIS A 439 GLN A 517 GLN ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN B 3 ASN B 136 ASN B 745 ASN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.091426 restraints weight = 35357.636| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.01 r_work: 0.2984 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24134 Z= 0.112 Angle : 0.502 9.160 32800 Z= 0.256 Chirality : 0.039 0.340 3824 Planarity : 0.003 0.045 4225 Dihedral : 6.093 71.733 3421 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.13 % Favored : 98.84 % Rotamer: Outliers : 3.78 % Allowed : 11.82 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.15), residues: 3091 helix: 2.30 (0.12), residues: 1717 sheet: -0.22 (0.25), residues: 414 loop : -0.09 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 752 HIS 0.006 0.001 HIS A 506 PHE 0.016 0.001 PHE C 511 TYR 0.018 0.001 TYR C 526 ARG 0.003 0.000 ARG C 970 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 1564) hydrogen bonds : angle 4.68965 ( 4758) covalent geometry : bond 0.00237 (24134) covalent geometry : angle 0.50177 (32800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 415 time to evaluate : 2.799 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8558 (pt0) cc_final: 0.7971 (pp30) REVERT: A 182 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: A 227 LYS cc_start: 0.8607 (mttp) cc_final: 0.8277 (mmtt) REVERT: A 355 MET cc_start: 0.8882 (mmm) cc_final: 0.8671 (mmm) REVERT: A 450 SER cc_start: 0.9177 (t) cc_final: 0.8582 (p) REVERT: A 574 SER cc_start: 0.8960 (m) cc_final: 0.8535 (p) REVERT: A 710 GLU cc_start: 0.7639 (mp0) cc_final: 0.7151 (mt-10) REVERT: A 799 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8654 (t80) REVERT: A 977 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8240 (mt) REVERT: B 117 LYS cc_start: 0.9129 (mtmt) cc_final: 0.8890 (mttt) REVERT: B 135 THR cc_start: 0.8192 (p) cc_final: 0.7770 (p) REVERT: B 168 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7069 (mtp180) REVERT: B 258 SER cc_start: 0.8621 (m) cc_final: 0.8365 (p) REVERT: B 1028 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8093 (mtm-85) REVERT: C 33 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8336 (pt0) REVERT: C 115 MET cc_start: 0.8627 (mmm) cc_final: 0.8419 (mmm) REVERT: C 145 THR cc_start: 0.8998 (m) cc_final: 0.8763 (p) REVERT: C 856 GLU cc_start: 0.7616 (mp0) cc_final: 0.7049 (mp0) REVERT: C 879 LEU cc_start: 0.9007 (mt) cc_final: 0.8765 (mm) REVERT: C 911 LEU cc_start: 0.8549 (mt) cc_final: 0.8348 (mt) REVERT: C 938 LYS cc_start: 0.8382 (tttm) cc_final: 0.8113 (pttp) REVERT: C 945 GLU cc_start: 0.7944 (tp30) cc_final: 0.7398 (mm-30) REVERT: C 946 PHE cc_start: 0.8199 (t80) cc_final: 0.7987 (t80) REVERT: C 953 LYS cc_start: 0.8282 (mptt) cc_final: 0.7806 (tttm) REVERT: C 1005 MET cc_start: 0.8291 (ttm) cc_final: 0.8088 (ttm) REVERT: C 1028 ARG cc_start: 0.8403 (mtt180) cc_final: 0.7977 (mtt90) outliers start: 95 outliers final: 53 residues processed: 472 average time/residue: 0.3294 time to fit residues: 248.2465 Evaluate side-chains 426 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 368 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 855 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 75 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 191 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN B 951 ASN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.089544 restraints weight = 35610.742| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.01 r_work: 0.2953 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24134 Z= 0.152 Angle : 0.518 10.139 32800 Z= 0.265 Chirality : 0.040 0.323 3824 Planarity : 0.003 0.044 4225 Dihedral : 5.560 60.918 3415 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.13 % Favored : 98.84 % Rotamer: Outliers : 3.70 % Allowed : 12.53 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.15), residues: 3091 helix: 2.25 (0.12), residues: 1719 sheet: -0.19 (0.26), residues: 411 loop : -0.14 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 540 HIS 0.007 0.001 HIS A 506 PHE 0.014 0.001 PHE C 571 TYR 0.012 0.001 TYR C 526 ARG 0.003 0.000 ARG A 813 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 1564) hydrogen bonds : angle 4.68426 ( 4758) covalent geometry : bond 0.00354 (24134) covalent geometry : angle 0.51764 (32800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 381 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.8623 (mttp) cc_final: 0.8306 (mmtt) REVERT: A 450 SER cc_start: 0.9147 (t) cc_final: 0.8549 (p) REVERT: A 574 SER cc_start: 0.9008 (m) cc_final: 0.8609 (p) REVERT: A 628 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8942 (mp) REVERT: A 799 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8689 (t80) REVERT: A 824 GLU cc_start: 0.8700 (tt0) cc_final: 0.8479 (tp30) REVERT: A 977 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8284 (mt) REVERT: B 69 MET cc_start: 0.8725 (mmt) cc_final: 0.8486 (mmt) REVERT: B 135 THR cc_start: 0.8203 (p) cc_final: 0.7775 (p) REVERT: B 168 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7078 (mtp180) REVERT: B 211 ASN cc_start: 0.9012 (t0) cc_final: 0.8700 (t0) REVERT: B 258 SER cc_start: 0.8639 (m) cc_final: 0.8369 (p) REVERT: B 1028 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.8038 (mtm-85) REVERT: C 33 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8384 (pt0) REVERT: C 145 THR cc_start: 0.8997 (m) cc_final: 0.8759 (p) REVERT: C 417 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7697 (tm-30) REVERT: C 777 TYR cc_start: 0.9274 (m-80) cc_final: 0.8887 (m-80) REVERT: C 856 GLU cc_start: 0.7530 (mp0) cc_final: 0.6948 (mp0) REVERT: C 938 LYS cc_start: 0.8393 (tttm) cc_final: 0.8105 (pttp) REVERT: C 945 GLU cc_start: 0.7989 (tp30) cc_final: 0.7445 (mm-30) REVERT: C 946 PHE cc_start: 0.8205 (t80) cc_final: 0.7913 (t80) REVERT: C 1005 MET cc_start: 0.8348 (ttm) cc_final: 0.8126 (ttm) REVERT: C 1028 ARG cc_start: 0.8422 (mtt180) cc_final: 0.8010 (mtt90) outliers start: 93 outliers final: 63 residues processed: 441 average time/residue: 0.3366 time to fit residues: 238.1045 Evaluate side-chains 433 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 365 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 299 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 234 optimal weight: 0.0170 chunk 285 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 439 GLN A 517 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** C 415 ASN ** 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 = 0.3328 r_free = 0.3328 target = 0.106868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.091290 restraints weight = 35216.406| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.01 r_work: 0.2981 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24134 Z= 0.114 Angle : 0.501 10.518 32800 Z= 0.255 Chirality : 0.039 0.320 3824 Planarity : 0.003 0.044 4225 Dihedral : 5.304 58.439 3413 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer: Outliers : 3.22 % Allowed : 13.61 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.15), residues: 3091 helix: 2.29 (0.12), residues: 1720 sheet: -0.18 (0.25), residues: 423 loop : -0.07 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 752 HIS 0.006 0.001 HIS A 506 PHE 0.013 0.001 PHE B 979 TYR 0.011 0.001 TYR C 526 ARG 0.003 0.000 ARG C 629 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 1564) hydrogen bonds : angle 4.57050 ( 4758) covalent geometry : bond 0.00255 (24134) covalent geometry : angle 0.50145 (32800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 397 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: A 227 LYS cc_start: 0.8553 (mttp) cc_final: 0.8210 (mmtt) REVERT: A 356 TYR cc_start: 0.8791 (t80) cc_final: 0.8420 (t80) REVERT: A 450 SER cc_start: 0.9162 (t) cc_final: 0.8574 (p) REVERT: A 574 SER cc_start: 0.8964 (m) cc_final: 0.8547 (p) REVERT: A 628 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8915 (mp) REVERT: A 661 ARG cc_start: 0.8669 (ttp-170) cc_final: 0.8181 (tpt170) REVERT: A 710 GLU cc_start: 0.7613 (mp0) cc_final: 0.6879 (mt-10) REVERT: A 799 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8654 (t80) REVERT: A 824 GLU cc_start: 0.8737 (tt0) cc_final: 0.8535 (tp30) REVERT: A 977 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8189 (mt) REVERT: B 135 THR cc_start: 0.8166 (p) cc_final: 0.7732 (p) REVERT: B 168 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7017 (mtp180) REVERT: B 211 ASN cc_start: 0.8999 (t0) cc_final: 0.8690 (t0) REVERT: B 258 SER cc_start: 0.8657 (m) cc_final: 0.8451 (p) REVERT: B 274 LYS cc_start: 0.8873 (mttt) cc_final: 0.8636 (mttm) REVERT: B 1025 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8475 (mt) REVERT: B 1028 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.8013 (mtm-85) REVERT: C 145 THR cc_start: 0.8991 (m) cc_final: 0.8761 (p) REVERT: C 417 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7686 (tm-30) REVERT: C 606 MET cc_start: 0.8735 (ttm) cc_final: 0.8507 (ttt) REVERT: C 777 TYR cc_start: 0.9199 (m-80) cc_final: 0.8779 (m-80) REVERT: C 856 GLU cc_start: 0.7541 (mp0) cc_final: 0.6929 (mp0) REVERT: C 900 MET cc_start: 0.8422 (mtp) cc_final: 0.8192 (mtp) REVERT: C 911 LEU cc_start: 0.8543 (mt) cc_final: 0.8341 (mt) REVERT: C 938 LYS cc_start: 0.8369 (tttm) cc_final: 0.8065 (pttp) REVERT: C 945 GLU cc_start: 0.8007 (tp30) cc_final: 0.7484 (mm-30) REVERT: C 946 PHE cc_start: 0.8119 (t80) cc_final: 0.7818 (t80) REVERT: C 1005 MET cc_start: 0.8311 (ttm) cc_final: 0.8100 (ttm) REVERT: C 1028 ARG cc_start: 0.8370 (mtt180) cc_final: 0.7997 (mtt90) outliers start: 81 outliers final: 56 residues processed: 451 average time/residue: 0.3550 time to fit residues: 256.4651 Evaluate side-chains 432 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 370 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 289 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 517 GLN C 110 GLN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.090468 restraints weight = 35538.344| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.01 r_work: 0.2970 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 24134 Z= 0.132 Angle : 0.508 10.663 32800 Z= 0.258 Chirality : 0.039 0.296 3824 Planarity : 0.003 0.045 4225 Dihedral : 5.128 59.358 3411 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.77 % Rotamer: Outliers : 3.30 % Allowed : 14.09 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.15), residues: 3091 helix: 2.29 (0.12), residues: 1719 sheet: -0.18 (0.25), residues: 423 loop : -0.07 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 540 HIS 0.006 0.001 HIS A 506 PHE 0.015 0.001 PHE C 511 TYR 0.011 0.001 TYR C 544 ARG 0.005 0.000 ARG A1028 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 1564) hydrogen bonds : angle 4.55432 ( 4758) covalent geometry : bond 0.00304 (24134) covalent geometry : angle 0.50846 (32800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 385 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8614 (pt0) cc_final: 0.8167 (pp30) REVERT: A 182 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: A 227 LYS cc_start: 0.8456 (mttp) cc_final: 0.8125 (mmtt) REVERT: A 356 TYR cc_start: 0.8787 (t80) cc_final: 0.8432 (t80) REVERT: A 450 SER cc_start: 0.9155 (t) cc_final: 0.8576 (p) REVERT: A 574 SER cc_start: 0.8993 (m) cc_final: 0.8564 (p) REVERT: A 628 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8933 (mp) REVERT: A 661 ARG cc_start: 0.8667 (ttp-170) cc_final: 0.8189 (tpt170) REVERT: A 710 GLU cc_start: 0.7580 (mp0) cc_final: 0.6889 (mt-10) REVERT: A 799 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8663 (t80) REVERT: A 824 GLU cc_start: 0.8754 (tt0) cc_final: 0.8271 (tp30) REVERT: A 977 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8283 (mt) REVERT: B 135 THR cc_start: 0.8185 (p) cc_final: 0.7750 (p) REVERT: B 168 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7015 (mtp180) REVERT: B 211 ASN cc_start: 0.9000 (t0) cc_final: 0.8692 (t0) REVERT: B 274 LYS cc_start: 0.8871 (mttt) cc_final: 0.8626 (mttp) REVERT: B 1025 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8517 (mt) REVERT: C 115 MET cc_start: 0.9067 (tpp) cc_final: 0.8865 (mmm) REVERT: C 145 THR cc_start: 0.8995 (m) cc_final: 0.8762 (p) REVERT: C 614 SER cc_start: 0.9016 (t) cc_final: 0.8697 (p) REVERT: C 777 TYR cc_start: 0.9210 (m-80) cc_final: 0.8778 (m-80) REVERT: C 856 GLU cc_start: 0.7590 (mp0) cc_final: 0.6986 (mp0) REVERT: C 911 LEU cc_start: 0.8571 (mt) cc_final: 0.8365 (mt) REVERT: C 938 LYS cc_start: 0.8377 (tttm) cc_final: 0.8044 (pttp) REVERT: C 1005 MET cc_start: 0.8315 (ttm) cc_final: 0.8096 (ttm) REVERT: C 1028 ARG cc_start: 0.8368 (mtt180) cc_final: 0.7932 (mtt90) outliers start: 83 outliers final: 63 residues processed: 441 average time/residue: 0.4469 time to fit residues: 314.2937 Evaluate side-chains 433 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 364 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 247 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 517 GLN B 254 ASN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.090547 restraints weight = 35051.685| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.05 r_work: 0.2955 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 24134 Z= 0.129 Angle : 0.510 10.990 32800 Z= 0.257 Chirality : 0.039 0.271 3824 Planarity : 0.003 0.045 4225 Dihedral : 5.034 56.571 3411 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.77 % Rotamer: Outliers : 3.26 % Allowed : 14.37 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.15), residues: 3091 helix: 2.30 (0.12), residues: 1719 sheet: -0.24 (0.25), residues: 429 loop : -0.01 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.007 0.001 HIS A 716 PHE 0.025 0.001 PHE C 553 TYR 0.009 0.001 TYR C 526 ARG 0.005 0.000 ARG B1028 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 1564) hydrogen bonds : angle 4.51705 ( 4758) covalent geometry : bond 0.00299 (24134) covalent geometry : angle 0.50967 (32800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 377 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8646 (pt0) cc_final: 0.8160 (pp30) REVERT: A 182 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: A 227 LYS cc_start: 0.8482 (mttp) cc_final: 0.8161 (mmtt) REVERT: A 356 TYR cc_start: 0.8765 (t80) cc_final: 0.8447 (t80) REVERT: A 450 SER cc_start: 0.9133 (t) cc_final: 0.8538 (p) REVERT: A 574 SER cc_start: 0.8981 (m) cc_final: 0.8554 (p) REVERT: A 628 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8919 (mp) REVERT: A 661 ARG cc_start: 0.8635 (ttp-170) cc_final: 0.8160 (tpt170) REVERT: A 710 GLU cc_start: 0.7615 (mp0) cc_final: 0.6969 (mt-10) REVERT: A 799 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8674 (t80) REVERT: A 977 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8169 (mt) REVERT: B 135 THR cc_start: 0.8184 (p) cc_final: 0.7756 (p) REVERT: B 168 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.6975 (mtp180) REVERT: B 211 ASN cc_start: 0.9008 (t0) cc_final: 0.8686 (t0) REVERT: B 274 LYS cc_start: 0.8888 (mttt) cc_final: 0.8549 (mttm) REVERT: B 1025 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8526 (mt) REVERT: C 145 THR cc_start: 0.8983 (m) cc_final: 0.8743 (p) REVERT: C 417 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7837 (tm-30) REVERT: C 614 SER cc_start: 0.9023 (t) cc_final: 0.8710 (p) REVERT: C 777 TYR cc_start: 0.9189 (m-80) cc_final: 0.8768 (m-80) REVERT: C 856 GLU cc_start: 0.7762 (mp0) cc_final: 0.7028 (mp0) REVERT: C 911 LEU cc_start: 0.8564 (mt) cc_final: 0.8355 (mt) REVERT: C 938 LYS cc_start: 0.8310 (tttm) cc_final: 0.7973 (pttp) REVERT: C 945 GLU cc_start: 0.8027 (tp30) cc_final: 0.7595 (mm-30) REVERT: C 946 PHE cc_start: 0.8168 (t80) cc_final: 0.7934 (t80) REVERT: C 1005 MET cc_start: 0.8323 (ttm) cc_final: 0.8100 (ttm) REVERT: C 1028 ARG cc_start: 0.8397 (mtt180) cc_final: 0.7961 (mtt90) outliers start: 82 outliers final: 68 residues processed: 433 average time/residue: 0.3752 time to fit residues: 261.4563 Evaluate side-chains 444 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 370 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 848 GLN Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 58 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 127 optimal weight: 0.0470 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 182 optimal weight: 0.0010 chunk 111 optimal weight: 0.8980 chunk 307 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 517 GLN B 583 GLN B 963 HIS ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** 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 = 0.3348 r_free = 0.3348 target = 0.108807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.093294 restraints weight = 34789.117| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.06 r_work: 0.2997 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 24134 Z= 0.101 Angle : 0.499 10.787 32800 Z= 0.250 Chirality : 0.038 0.224 3824 Planarity : 0.003 0.044 4225 Dihedral : 4.872 55.461 3411 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.77 % Rotamer: Outliers : 2.90 % Allowed : 14.92 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.15), residues: 3091 helix: 2.36 (0.12), residues: 1719 sheet: -0.19 (0.25), residues: 436 loop : 0.06 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 752 HIS 0.013 0.001 HIS A 716 PHE 0.027 0.001 PHE C 553 TYR 0.011 0.001 TYR A 890 ARG 0.003 0.000 ARG A1028 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 1564) hydrogen bonds : angle 4.39508 ( 4758) covalent geometry : bond 0.00214 (24134) covalent geometry : angle 0.49876 (32800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 406 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8628 (pt0) cc_final: 0.8127 (pp30) REVERT: A 182 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: A 227 LYS cc_start: 0.8414 (mttp) cc_final: 0.8087 (mmtt) REVERT: A 356 TYR cc_start: 0.8690 (t80) cc_final: 0.8438 (t80) REVERT: A 377 MET cc_start: 0.8502 (mmp) cc_final: 0.8270 (mmm) REVERT: A 450 SER cc_start: 0.9051 (t) cc_final: 0.8478 (p) REVERT: A 574 SER cc_start: 0.8915 (m) cc_final: 0.8505 (p) REVERT: A 661 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.8145 (tpt90) REVERT: A 710 GLU cc_start: 0.7591 (mp0) cc_final: 0.6996 (mt-10) REVERT: A 799 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8709 (t80) REVERT: A 875 TYR cc_start: 0.8734 (m-80) cc_final: 0.8447 (m-10) REVERT: A 977 LEU cc_start: 0.8389 (tp) cc_final: 0.8125 (mt) REVERT: B 135 THR cc_start: 0.8167 (p) cc_final: 0.7738 (p) REVERT: B 168 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.6728 (mtp180) REVERT: B 211 ASN cc_start: 0.8974 (t0) cc_final: 0.8669 (t0) REVERT: B 274 LYS cc_start: 0.8904 (mttt) cc_final: 0.8561 (mttm) REVERT: B 874 LEU cc_start: 0.9211 (tp) cc_final: 0.8943 (tp) REVERT: B 1025 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8523 (mt) REVERT: C 145 THR cc_start: 0.8991 (m) cc_final: 0.8740 (p) REVERT: C 417 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7719 (tm-30) REVERT: C 614 SER cc_start: 0.8968 (t) cc_final: 0.8685 (p) REVERT: C 777 TYR cc_start: 0.9099 (m-80) cc_final: 0.8644 (m-80) REVERT: C 856 GLU cc_start: 0.7729 (mp0) cc_final: 0.7105 (mp0) REVERT: C 911 LEU cc_start: 0.8528 (mt) cc_final: 0.8321 (mt) REVERT: C 938 LYS cc_start: 0.8268 (tttm) cc_final: 0.7939 (pttp) REVERT: C 945 GLU cc_start: 0.8050 (tp30) cc_final: 0.7627 (mm-30) REVERT: C 946 PHE cc_start: 0.8135 (t80) cc_final: 0.7826 (t80) REVERT: C 1005 MET cc_start: 0.8215 (ttm) cc_final: 0.8002 (ttm) REVERT: C 1028 ARG cc_start: 0.8359 (mtt180) cc_final: 0.8056 (mtt90) outliers start: 73 outliers final: 56 residues processed: 458 average time/residue: 0.3749 time to fit residues: 276.6766 Evaluate side-chains 436 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 376 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 206 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 304 optimal weight: 0.2980 chunk 147 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 517 GLN B 136 ASN C 68 ASN ** C 415 ASN ** 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 = 0.3324 r_free = 0.3324 target = 0.107137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.091648 restraints weight = 35237.025| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.05 r_work: 0.2966 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 24134 Z= 0.129 Angle : 0.517 10.797 32800 Z= 0.261 Chirality : 0.039 0.264 3824 Planarity : 0.003 0.045 4225 Dihedral : 4.734 55.327 3409 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer: Outliers : 2.55 % Allowed : 15.64 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.15), residues: 3091 helix: 2.34 (0.12), residues: 1718 sheet: -0.17 (0.25), residues: 433 loop : 0.06 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.011 0.001 HIS A 716 PHE 0.029 0.001 PHE C 553 TYR 0.012 0.001 TYR A 597 ARG 0.003 0.000 ARG A1028 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 1564) hydrogen bonds : angle 4.43904 ( 4758) covalent geometry : bond 0.00302 (24134) covalent geometry : angle 0.51728 (32800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 380 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8635 (pt0) cc_final: 0.8130 (pp30) REVERT: A 112 GLN cc_start: 0.8670 (mm110) cc_final: 0.8452 (mm110) REVERT: A 182 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: A 227 LYS cc_start: 0.8411 (mttp) cc_final: 0.8106 (mmtt) REVERT: A 356 TYR cc_start: 0.8703 (t80) cc_final: 0.8476 (t80) REVERT: A 377 MET cc_start: 0.8619 (mmp) cc_final: 0.8406 (mmm) REVERT: A 450 SER cc_start: 0.9041 (t) cc_final: 0.8452 (p) REVERT: A 574 SER cc_start: 0.8930 (m) cc_final: 0.8491 (p) REVERT: A 661 ARG cc_start: 0.8664 (ttp-170) cc_final: 0.8232 (tpt170) REVERT: A 799 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8663 (t80) REVERT: A 875 TYR cc_start: 0.8754 (m-80) cc_final: 0.8437 (m-10) REVERT: A 977 LEU cc_start: 0.8416 (tp) cc_final: 0.8132 (mt) REVERT: B 135 THR cc_start: 0.8221 (p) cc_final: 0.7816 (p) REVERT: B 168 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.6864 (mtp180) REVERT: B 211 ASN cc_start: 0.8998 (t0) cc_final: 0.8679 (t0) REVERT: B 274 LYS cc_start: 0.8893 (mttt) cc_final: 0.8646 (mttp) REVERT: B 300 MET cc_start: 0.9051 (mmm) cc_final: 0.8828 (mtp) REVERT: B 839 MET cc_start: 0.8870 (mtm) cc_final: 0.8562 (mtp) REVERT: B 1025 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8542 (mt) REVERT: C 145 THR cc_start: 0.8992 (m) cc_final: 0.8749 (p) REVERT: C 417 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7900 (tm-30) REVERT: C 518 MET cc_start: 0.9200 (ttp) cc_final: 0.8886 (ppp) REVERT: C 614 SER cc_start: 0.9026 (t) cc_final: 0.8731 (p) REVERT: C 777 TYR cc_start: 0.9167 (m-80) cc_final: 0.8772 (m-80) REVERT: C 856 GLU cc_start: 0.7769 (mp0) cc_final: 0.7133 (mp0) REVERT: C 911 LEU cc_start: 0.8560 (mt) cc_final: 0.8349 (mt) REVERT: C 938 LYS cc_start: 0.8299 (tttm) cc_final: 0.7962 (pttp) REVERT: C 945 GLU cc_start: 0.8025 (tp30) cc_final: 0.7597 (mm-30) REVERT: C 946 PHE cc_start: 0.8152 (t80) cc_final: 0.7906 (t80) REVERT: C 1005 MET cc_start: 0.8237 (ttm) cc_final: 0.8036 (ttm) REVERT: C 1028 ARG cc_start: 0.8407 (mtt180) cc_final: 0.8079 (mtt90) outliers start: 64 outliers final: 57 residues processed: 421 average time/residue: 0.3724 time to fit residues: 252.2258 Evaluate side-chains 432 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 371 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 301 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 517 GLN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.091662 restraints weight = 34973.880| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.10 r_work: 0.2961 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 24134 Z= 0.190 Angle : 0.667 59.199 32800 Z= 0.374 Chirality : 0.040 0.229 3824 Planarity : 0.003 0.045 4225 Dihedral : 4.722 55.287 3408 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer: Outliers : 2.51 % Allowed : 15.88 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.15), residues: 3091 helix: 2.33 (0.12), residues: 1718 sheet: -0.17 (0.25), residues: 433 loop : 0.05 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.011 0.001 HIS A 716 PHE 0.021 0.001 PHE C 553 TYR 0.012 0.001 TYR A 597 ARG 0.003 0.000 ARG A1028 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 1564) hydrogen bonds : angle 4.43895 ( 4758) covalent geometry : bond 0.00397 (24134) covalent geometry : angle 0.66655 (32800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13214.87 seconds wall clock time: 229 minutes 54.01 seconds (13794.01 seconds total)