Starting phenix.real_space_refine on Thu Aug 6 19:56:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wuk_66262/08_2026/9wuk_66262.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wuk_66262/08_2026/9wuk_66262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wuk_66262/08_2026/9wuk_66262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wuk_66262/08_2026/9wuk_66262.map" model { file = "/net/cci-nas-00/data/ceres_data/9wuk_66262/08_2026/9wuk_66262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wuk_66262/08_2026/9wuk_66262.cif" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.070 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 6 5.49 5 S 68 5.16 5 C 10536 2.51 5 N 2859 2.21 5 O 3157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16628 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8178 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 1 Chain: "B" Number of atoms: 8194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8194 Classifications: {'peptide': 1026} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 1 Chain: "A" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'FAD': 1, 'FMN': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'FAD': 1, 'FMN': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3259 SG CYS A 404 77.968 34.024 41.159 1.00 30.24 S ATOM 11437 SG CYS B 404 25.809 36.064 85.580 1.00 38.32 S Time building chain proxies: 3.40, per 1000 atoms: 0.20 Number of scatterers: 16628 At special positions: 0 Unit cell: (106.02, 112.53, 128.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 68 16.00 P 6 15.00 O 3157 8.00 N 2859 7.00 C 10536 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 677.5 milliseconds 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 20 sheets defined 51.0% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 26 through 39 removed outlier: 3.707A pdb=" N SER A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 75 through 85 removed outlier: 4.275A pdb=" N ALA A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.672A pdb=" N ARG A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 removed outlier: 3.619A pdb=" N SER A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 111 through 112 No H-bonds generated for 'chain 'A' and resid 111 through 112' Processing helix chain 'A' and resid 113 through 134 removed outlier: 3.891A pdb=" N TYR A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N MET A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 173 through 191 removed outlier: 3.751A pdb=" N GLN A 191 " --> pdb=" O MET A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 200 through 227 removed outlier: 3.599A pdb=" N LYS A 204 " --> pdb=" O MET A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 253 through 286 removed outlier: 4.647A pdb=" N GLU A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N THR A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'A' and resid 314 through 328 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 399 through 403 removed outlier: 3.576A pdb=" N ARG A 402 " --> pdb=" O ASN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 424 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 503 through 506 removed outlier: 3.694A pdb=" N ILE A 506 " --> pdb=" O ASN A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 530 through 540 Processing helix chain 'A' and resid 565 through 578 Processing helix chain 'A' and resid 594 through 615 removed outlier: 4.156A pdb=" N GLU A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 705 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 761 through 771 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 795 Processing helix chain 'A' and resid 801 through 809 Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 891 through 894 Processing helix chain 'A' and resid 895 through 911 removed outlier: 3.618A pdb=" N GLY A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 930 Processing helix chain 'A' and resid 932 through 942 Processing helix chain 'A' and resid 961 through 969 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'A' and resid 991 through 1009 Processing helix chain 'A' and resid 1011 through 1026 removed outlier: 3.524A pdb=" N GLN A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 39 removed outlier: 3.747A pdb=" N SER B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.822A pdb=" N LYS B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 107 through 110 removed outlier: 3.684A pdb=" N SER B 110 " --> pdb=" O PRO B 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 135 removed outlier: 4.398A pdb=" N ASP B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 173 through 191 removed outlier: 3.617A pdb=" N GLN B 191 " --> pdb=" O MET B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 227 Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 253 through 282 removed outlier: 4.487A pdb=" N GLU B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 307 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 379 through 384 removed outlier: 3.508A pdb=" N PHE B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 403 removed outlier: 3.709A pdb=" N ARG B 402 " --> pdb=" O ASN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 424 Processing helix chain 'B' and resid 477 through 493 Processing helix chain 'B' and resid 503 through 506 removed outlier: 3.655A pdb=" N ILE B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 503 through 506' Processing helix chain 'B' and resid 530 through 540 Processing helix chain 'B' and resid 560 through 564 removed outlier: 3.543A pdb=" N TYR B 564 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 578 Processing helix chain 'B' and resid 594 through 615 removed outlier: 3.793A pdb=" N GLU B 612 " --> pdb=" O SER B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 661 through 665 removed outlier: 3.950A pdb=" N GLY B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 705 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 748 through 758 Processing helix chain 'B' and resid 761 through 771 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 795 Processing helix chain 'B' and resid 801 through 809 Processing helix chain 'B' and resid 850 through 858 Processing helix chain 'B' and resid 891 through 894 Processing helix chain 'B' and resid 895 through 911 removed outlier: 3.545A pdb=" N GLY B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 930 Processing helix chain 'B' and resid 932 through 942 Processing helix chain 'B' and resid 961 through 969 removed outlier: 3.601A pdb=" N VAL B 965 " --> pdb=" O TYR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 980 Processing helix chain 'B' and resid 991 through 1008 removed outlier: 3.577A pdb=" N GLU B 995 " --> pdb=" O ARG B 991 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1025 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 removed outlier: 7.068A pdb=" N SER A 50 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR A 358 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE A 52 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 360 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 54 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 334 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA3, first strand: chain 'A' and resid 342 through 344 Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 439 Processing sheet with id=AA5, first strand: chain 'A' and resid 497 through 501 Processing sheet with id=AA6, first strand: chain 'A' and resid 497 through 501 removed outlier: 9.314A pdb=" N GLY A 587 " --> pdb=" O TYR A 550 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 552 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLY A 589 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY A 554 " --> pdb=" O GLY A 589 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 629 through 634 removed outlier: 4.191A pdb=" N GLN B 712 " --> pdb=" O VAL A 634 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 815 through 818 removed outlier: 3.624A pdb=" N LYS A 652 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU A 672 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN A 656 " --> pdb=" O HIS A 670 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N HIS A 670 " --> pdb=" O ASN A 656 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU A 658 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR A 668 " --> pdb=" O GLU A 658 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 731 through 732 removed outlier: 4.288A pdb=" N GLN A 712 " --> pdb=" O VAL B 634 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 838 through 840 Processing sheet with id=AB2, first strand: chain 'A' and resid 946 through 951 removed outlier: 6.779A pdb=" N ALA A 918 " --> pdb=" O THR A 946 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TYR A 948 " --> pdb=" O ALA A 918 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 920 " --> pdb=" O TYR A 948 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ALA A 950 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE A 922 " --> pdb=" O ALA A 950 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 886 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N TYR A 921 " --> pdb=" O ILE A 886 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET A 888 " --> pdb=" O TYR A 921 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLY A 923 " --> pdb=" O MET A 888 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 887 " --> pdb=" O TYR A 984 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N CYS A 986 " --> pdb=" O ILE A 887 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 889 " --> pdb=" O CYS A 986 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP A 988 " --> pdb=" O VAL A 889 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 983 " --> pdb=" O ALA A1029 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASP A1031 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE A 985 " --> pdb=" O ASP A1031 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP A1033 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY A 987 " --> pdb=" O TRP A1033 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 41 through 45 removed outlier: 7.182A pdb=" N SER B 50 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR B 358 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE B 52 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 360 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 54 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B 334 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AB5, first strand: chain 'B' and resid 342 through 344 Processing sheet with id=AB6, first strand: chain 'B' and resid 437 through 439 Processing sheet with id=AB7, first strand: chain 'B' and resid 497 through 501 removed outlier: 6.435A pdb=" N VAL B 515 " --> pdb=" O ALA B 551 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE B 553 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE B 517 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N CYS B 555 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 519 " --> pdb=" O CYS B 555 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 497 through 501 removed outlier: 6.435A pdb=" N VAL B 515 " --> pdb=" O ALA B 551 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE B 553 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE B 517 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N CYS B 555 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 519 " --> pdb=" O CYS B 555 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N GLY B 587 " --> pdb=" O TYR B 550 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 552 " --> pdb=" O GLY B 587 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLY B 589 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY B 554 " --> pdb=" O GLY B 589 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 815 through 818 removed outlier: 3.536A pdb=" N LYS B 652 " --> pdb=" O THR B 674 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU B 672 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN B 656 " --> pdb=" O HIS B 670 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N HIS B 670 " --> pdb=" O ASN B 656 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU B 658 " --> pdb=" O THR B 668 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR B 668 " --> pdb=" O GLU B 658 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER B 667 " --> pdb=" O VAL B 836 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 838 through 840 Processing sheet with id=AC2, first strand: chain 'B' and resid 946 through 949 removed outlier: 6.631A pdb=" N ILE B 886 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N TYR B 921 " --> pdb=" O ILE B 886 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET B 888 " --> pdb=" O TYR B 921 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE B 887 " --> pdb=" O TYR B 984 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N CYS B 986 " --> pdb=" O ILE B 887 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL B 889 " --> pdb=" O CYS B 986 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP B 988 " --> pdb=" O VAL B 889 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 983 " --> pdb=" O ALA B1029 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASP B1031 " --> pdb=" O LEU B 983 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE B 985 " --> pdb=" O ASP B1031 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TRP B1033 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY B 987 " --> pdb=" O TRP B1033 " (cutoff:3.500A) 822 hydrogen bonds defined for protein. 2337 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 6095 1.38 - 1.55: 10773 1.55 - 1.72: 16 1.72 - 1.89: 118 1.89 - 2.05: 8 Bond restraints: 17010 Sorted by residual: bond pdb=" C4 FMN B1103 " pdb=" C4A FMN B1103 " ideal model delta sigma weight residual 1.485 1.387 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C4 FMN A1102 " pdb=" C4A FMN A1102 " ideal model delta sigma weight residual 1.485 1.388 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C4A FMN A1102 " pdb=" N5 FMN A1102 " ideal model delta sigma weight residual 1.300 1.377 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C4A FMN B1103 " pdb=" N5 FMN B1103 " ideal model delta sigma weight residual 1.300 1.376 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" O5' FMN A1102 " pdb=" P FMN A1102 " ideal model delta sigma weight residual 1.676 1.607 0.069 2.00e-02 2.50e+03 1.21e+01 ... (remaining 17005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 22673 1.69 - 3.37: 304 3.37 - 5.06: 73 5.06 - 6.75: 13 6.75 - 8.43: 5 Bond angle restraints: 23068 Sorted by residual: angle pdb=" N VAL A 781 " pdb=" CA VAL A 781 " pdb=" C VAL A 781 " ideal model delta sigma weight residual 111.62 109.41 2.21 7.90e-01 1.60e+00 7.85e+00 angle pdb=" N GLU B 353 " pdb=" CA GLU B 353 " pdb=" CB GLU B 353 " ideal model delta sigma weight residual 113.65 109.83 3.82 1.47e+00 4.63e-01 6.75e+00 angle pdb=" O3P FMN A1102 " pdb=" P FMN A1102 " pdb=" O5' FMN A1102 " ideal model delta sigma weight residual 102.33 109.70 -7.37 3.00e+00 1.11e-01 6.03e+00 angle pdb=" CA LEU A 441 " pdb=" CB LEU A 441 " pdb=" CG LEU A 441 " ideal model delta sigma weight residual 116.30 124.73 -8.43 3.50e+00 8.16e-02 5.80e+00 angle pdb=" CA LEU B 441 " pdb=" CB LEU B 441 " pdb=" CG LEU B 441 " ideal model delta sigma weight residual 116.30 124.66 -8.36 3.50e+00 8.16e-02 5.70e+00 ... (remaining 23063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 9322 17.74 - 35.49: 662 35.49 - 53.23: 211 53.23 - 70.98: 54 70.98 - 88.72: 23 Dihedral angle restraints: 10272 sinusoidal: 4334 harmonic: 5938 Sorted by residual: dihedral pdb=" CA GLN B 439 " pdb=" C GLN B 439 " pdb=" N THR B 440 " pdb=" CA THR B 440 " ideal model delta harmonic sigma weight residual 180.00 158.29 21.71 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA TYR B 281 " pdb=" C TYR B 281 " pdb=" N PHE B 282 " pdb=" CA PHE B 282 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CG ARG A 112 " pdb=" CD ARG A 112 " pdb=" NE ARG A 112 " pdb=" CZ ARG A 112 " ideal model delta sinusoidal sigma weight residual 90.00 41.07 48.93 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 10269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1335 0.024 - 0.049: 693 0.049 - 0.073: 240 0.073 - 0.098: 126 0.098 - 0.122: 73 Chirality restraints: 2467 Sorted by residual: chirality pdb=" CA ILE B 618 " pdb=" N ILE B 618 " pdb=" C ILE B 618 " pdb=" CB ILE B 618 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA VAL B 141 " pdb=" N VAL B 141 " pdb=" C VAL B 141 " pdb=" CB VAL B 141 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA ILE B 786 " pdb=" N ILE B 786 " pdb=" C ILE B 786 " pdb=" CB ILE B 786 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 2464 not shown) Planarity restraints: 2987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 451 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" CD GLN A 451 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLN A 451 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN A 451 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 348 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO A 349 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 349 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 349 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 761 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO A 762 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 762 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 762 " -0.022 5.00e-02 4.00e+02 ... (remaining 2984 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 10370 3.05 - 3.51: 17774 3.51 - 3.97: 29619 3.97 - 4.44: 35532 4.44 - 4.90: 53194 Nonbonded interactions: 146489 Sorted by model distance: nonbonded pdb=" N ASP B 253 " pdb=" OD1 ASP B 253 " model vdw 2.583 3.120 nonbonded pdb=" O SER A 608 " pdb=" OE1 GLU A 612 " model vdw 2.591 3.040 nonbonded pdb=" OG1 THR B 108 " pdb=" OH TYR B 117 " model vdw 2.606 3.040 nonbonded pdb=" CAA HEM A1101 " pdb=" O2A HEM A1101 " model vdw 2.615 2.752 nonbonded pdb=" O GLU B 323 " pdb=" O ARG B 326 " model vdw 2.622 3.040 ... (remaining 146484 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 5 through 1101) selection = (chain 'B' and (resid 5 through 456 or resid 465 through 1101)) } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 15.240 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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: 0.020 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.003 0.098 17012 Z= 0.151 Angle : 0.548 8.432 23068 Z= 0.271 Chirality : 0.039 0.122 2467 Planarity : 0.004 0.049 2987 Dihedral : 14.769 88.719 6460 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.68 % Allowed : 11.45 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 2042 helix: 1.28 (0.17), residues: 921 sheet: -0.78 (0.31), residues: 281 loop : 0.22 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 466 TYR 0.011 0.001 TYR A 168 PHE 0.014 0.001 PHE B 898 TRP 0.020 0.001 TRP B 98 HIS 0.006 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (17010) covalent geometry : angle 0.54772 / 0.27 (23068) hydrogen bonds : bond 0.12821 / 8.66 ( 796) hydrogen bonds : angle 6.52507 / 4.79 ( 2337) Misc. bond : bond 0.00661 / 0.32 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 270 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.6964 (mt0) cc_final: 0.6534 (mt0) REVERT: A 58 GLU cc_start: 0.6589 (mm-30) cc_final: 0.6186 (pm20) REVERT: A 130 GLN cc_start: 0.7422 (mt0) cc_final: 0.7061 (mt0) REVERT: A 134 ARG cc_start: 0.7401 (mmt90) cc_final: 0.7179 (mmt90) REVERT: A 187 MET cc_start: 0.7333 (ttp) cc_final: 0.6500 (mmp) REVERT: A 194 ASP cc_start: 0.7655 (m-30) cc_final: 0.7400 (m-30) REVERT: A 196 GLN cc_start: 0.6425 (mt0) cc_final: 0.5903 (tt0) REVERT: A 250 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6242 (pt0) REVERT: A 270 GLU cc_start: 0.7429 (tt0) cc_final: 0.6992 (pt0) REVERT: A 350 VAL cc_start: 0.7465 (p) cc_final: 0.7247 (t) REVERT: A 352 LYS cc_start: 0.7686 (tttm) cc_final: 0.7332 (ttmt) REVERT: A 373 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6198 (mm-30) REVERT: A 388 LYS cc_start: 0.7244 (mttp) cc_final: 0.6879 (mtmm) REVERT: A 423 ARG cc_start: 0.6739 (mmm160) cc_final: 0.6319 (tpt90) REVERT: A 444 LYS cc_start: 0.7511 (ttpt) cc_final: 0.6986 (ptpp) REVERT: A 485 GLU cc_start: 0.7490 (tt0) cc_final: 0.6437 (mm-30) REVERT: A 498 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: A 573 LYS cc_start: 0.8298 (tttt) cc_final: 0.7926 (ttmm) REVERT: A 604 GLU cc_start: 0.7032 (pt0) cc_final: 0.6597 (pp20) REVERT: A 644 ARG cc_start: 0.7553 (mmt90) cc_final: 0.6778 (mmp-170) REVERT: A 682 GLN cc_start: 0.7953 (pt0) cc_final: 0.7088 (mm110) REVERT: A 774 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6810 (tp30) REVERT: A 783 LYS cc_start: 0.7777 (tmmt) cc_final: 0.7156 (tppt) REVERT: A 804 ARG cc_start: 0.7730 (tpt-90) cc_final: 0.6285 (mmt180) REVERT: A 860 LYS cc_start: 0.7259 (mttt) cc_final: 0.6706 (mmtm) REVERT: A 990 SER cc_start: 0.8042 (p) cc_final: 0.7370 (m) REVERT: A 1019 LEU cc_start: 0.6317 (tp) cc_final: 0.6109 (tp) REVERT: A 1023 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.6137 (mt0) REVERT: B 11 LYS cc_start: 0.7213 (mtmm) cc_final: 0.6680 (tttt) REVERT: B 12 THR cc_start: 0.8228 (p) cc_final: 0.7974 (m) REVERT: B 24 LYS cc_start: 0.7303 (pttm) cc_final: 0.6788 (mttp) REVERT: B 58 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6762 (mp0) REVERT: B 115 LYS cc_start: 0.6821 (mttt) cc_final: 0.6511 (mtpp) REVERT: B 170 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7431 (mp0) REVERT: B 187 MET cc_start: 0.7895 (ttp) cc_final: 0.6783 (tpp) REVERT: B 198 LYS cc_start: 0.7759 (mttt) cc_final: 0.7257 (pttt) REVERT: B 295 GLU cc_start: 0.6748 (tt0) cc_final: 0.6007 (mt-10) REVERT: B 315 LYS cc_start: 0.7038 (mmtp) cc_final: 0.6211 (mtpt) REVERT: B 354 GLN cc_start: 0.7168 (mt0) cc_final: 0.6440 (mm-40) REVERT: B 356 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7969 (ttp-110) REVERT: B 379 ARG cc_start: 0.6876 (ttp80) cc_final: 0.6422 (ttt180) REVERT: B 444 LYS cc_start: 0.8253 (pttt) cc_final: 0.7703 (ptpp) REVERT: B 454 PRO cc_start: 0.7983 (Cg_exo) cc_final: 0.7717 (Cg_endo) REVERT: B 485 GLU cc_start: 0.7975 (tt0) cc_final: 0.7164 (tp30) REVERT: B 512 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7025 (mm-30) REVERT: B 573 LYS cc_start: 0.8149 (tttt) cc_final: 0.7876 (ttpp) REVERT: B 597 GLU cc_start: 0.7469 (tt0) cc_final: 0.6507 (tp30) REVERT: B 627 ASN cc_start: 0.7581 (m-40) cc_final: 0.7118 (m-40) REVERT: B 632 GLN cc_start: 0.8591 (tt0) cc_final: 0.8170 (tm-30) REVERT: B 652 LYS cc_start: 0.8086 (tttt) cc_final: 0.7620 (ttmm) REVERT: B 666 ARG cc_start: 0.7029 (mmt180) cc_final: 0.6436 (mmm160) REVERT: B 783 LYS cc_start: 0.7674 (mttm) cc_final: 0.6979 (tttp) REVERT: B 796 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7909 (mt-10) REVERT: B 804 ARG cc_start: 0.7432 (mmp80) cc_final: 0.7216 (mmp80) REVERT: B 813 LYS cc_start: 0.8133 (mtmp) cc_final: 0.7617 (mmtm) outliers start: 12 outliers final: 8 residues processed: 278 average time/residue: 0.8076 time to fit residues: 244.5462 Evaluate side-chains 252 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 242 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1023 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 577 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 ASN A 598 GLN A 780 GLN A1005 GLN ** A1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.164006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.131740 restraints weight = 17089.606| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.78 r_work: 0.3395 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17012 Z= 0.127 Angle : 0.522 8.298 23068 Z= 0.263 Chirality : 0.040 0.131 2467 Planarity : 0.004 0.042 2987 Dihedral : 7.826 85.098 2394 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.21 % Allowed : 10.32 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 2042 helix: 1.36 (0.17), residues: 931 sheet: -0.77 (0.30), residues: 282 loop : 0.14 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 991 TYR 0.012 0.001 TYR B 817 PHE 0.017 0.002 PHE B 160 TRP 0.021 0.001 TRP A 98 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (17010) covalent geometry : angle 0.52228 / 0.26 (23068) hydrogen bonds : bond 0.04255 / 2.82 ( 796) hydrogen bonds : angle 4.94798 / 3.61 ( 2337) Misc. bond : bond 0.00798 / 0.40 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7318 (m-30) cc_final: 0.6841 (t0) REVERT: A 45 GLN cc_start: 0.7001 (mt0) cc_final: 0.6552 (mt0) REVERT: A 58 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6227 (pm20) REVERT: A 187 MET cc_start: 0.7717 (ttp) cc_final: 0.6772 (mmp) REVERT: A 194 ASP cc_start: 0.7688 (m-30) cc_final: 0.7454 (m-30) REVERT: A 196 GLN cc_start: 0.6397 (mt0) cc_final: 0.5898 (tt0) REVERT: A 217 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7931 (tm) REVERT: A 224 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6236 (tp30) REVERT: A 250 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6420 (pt0) REVERT: A 270 GLU cc_start: 0.7521 (tt0) cc_final: 0.6975 (pt0) REVERT: A 343 ILE cc_start: 0.6924 (mm) cc_final: 0.6636 (pt) REVERT: A 350 VAL cc_start: 0.7476 (p) cc_final: 0.7263 (t) REVERT: A 373 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6256 (mm-30) REVERT: A 388 LYS cc_start: 0.7241 (mttp) cc_final: 0.6890 (mtmm) REVERT: A 423 ARG cc_start: 0.6775 (mmm160) cc_final: 0.6405 (tpt90) REVERT: A 485 GLU cc_start: 0.7619 (tt0) cc_final: 0.6602 (mm-30) REVERT: A 573 LYS cc_start: 0.8243 (tttt) cc_final: 0.7866 (ttmm) REVERT: A 604 GLU cc_start: 0.7199 (pt0) cc_final: 0.6738 (pp20) REVERT: A 644 ARG cc_start: 0.7740 (mmt90) cc_final: 0.6877 (mmp-170) REVERT: A 774 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6714 (tp30) REVERT: A 783 LYS cc_start: 0.7923 (tmmt) cc_final: 0.7302 (tppt) REVERT: A 799 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7330 (mt-10) REVERT: A 804 ARG cc_start: 0.7751 (tpt-90) cc_final: 0.6253 (mmt180) REVERT: A 860 LYS cc_start: 0.7443 (mttt) cc_final: 0.6869 (mmtm) REVERT: A 990 SER cc_start: 0.8059 (p) cc_final: 0.7675 (m) REVERT: B 11 LYS cc_start: 0.7381 (mtmm) cc_final: 0.6981 (tttt) REVERT: B 23 ASP cc_start: 0.7548 (t70) cc_final: 0.7087 (t0) REVERT: B 24 LYS cc_start: 0.7473 (pttm) cc_final: 0.6854 (mttp) REVERT: B 32 MET cc_start: 0.8253 (mtm) cc_final: 0.7899 (mtp) REVERT: B 58 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6952 (mp0) REVERT: B 115 LYS cc_start: 0.6900 (mttt) cc_final: 0.6583 (mtpp) REVERT: B 187 MET cc_start: 0.8056 (ttp) cc_final: 0.6857 (tpp) REVERT: B 198 LYS cc_start: 0.7789 (mttt) cc_final: 0.7275 (pttt) REVERT: B 251 LYS cc_start: 0.7800 (mttt) cc_final: 0.7434 (mttt) REVERT: B 295 GLU cc_start: 0.6771 (tt0) cc_final: 0.6000 (mt-10) REVERT: B 315 LYS cc_start: 0.7142 (mmtp) cc_final: 0.6345 (mtpt) REVERT: B 354 GLN cc_start: 0.7382 (mt0) cc_final: 0.6709 (mm-40) REVERT: B 379 ARG cc_start: 0.7414 (ttp80) cc_final: 0.6947 (ttp-170) REVERT: B 444 LYS cc_start: 0.8473 (pttt) cc_final: 0.7835 (ptpp) REVERT: B 454 PRO cc_start: 0.7893 (Cg_exo) cc_final: 0.7626 (Cg_endo) REVERT: B 485 GLU cc_start: 0.8032 (tt0) cc_final: 0.7267 (tp30) REVERT: B 512 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7055 (mm-30) REVERT: B 573 LYS cc_start: 0.8181 (tttt) cc_final: 0.7921 (ttpp) REVERT: B 597 GLU cc_start: 0.7611 (tt0) cc_final: 0.6702 (tp30) REVERT: B 627 ASN cc_start: 0.7699 (m-40) cc_final: 0.7217 (m-40) REVERT: B 652 LYS cc_start: 0.8266 (tttt) cc_final: 0.7768 (ttmm) REVERT: B 666 ARG cc_start: 0.7043 (mmt180) cc_final: 0.6228 (mmm-85) REVERT: B 734 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7373 (ttp-110) REVERT: B 744 GLN cc_start: 0.8265 (mt0) cc_final: 0.7900 (mt0) REVERT: B 783 LYS cc_start: 0.7841 (mttm) cc_final: 0.7112 (tttp) REVERT: B 796 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7965 (mt-10) REVERT: B 799 GLU cc_start: 0.7229 (mp0) cc_final: 0.6941 (mp0) REVERT: B 813 LYS cc_start: 0.8255 (mtmp) cc_final: 0.7730 (mmtm) REVERT: B 888 MET cc_start: 0.7390 (mtt) cc_final: 0.7034 (mtt) REVERT: B 933 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6787 (ttt90) REVERT: B 949 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6304 (mm) outliers start: 39 outliers final: 8 residues processed: 277 average time/residue: 0.7691 time to fit residues: 233.2734 Evaluate side-chains 246 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 234 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 933 ARG Chi-restraints excluded: chain B residue 949 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 82 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 163 optimal weight: 0.3980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 627 ASN A 682 GLN A 780 GLN A1005 GLN ** A1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.160369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128024 restraints weight = 17390.532| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.79 r_work: 0.3359 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17012 Z= 0.146 Angle : 0.541 8.922 23068 Z= 0.273 Chirality : 0.041 0.135 2467 Planarity : 0.005 0.050 2987 Dihedral : 7.170 88.773 2374 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.15 % Allowed : 11.17 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 2042 helix: 1.35 (0.17), residues: 926 sheet: -0.69 (0.30), residues: 283 loop : 0.12 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 112 TYR 0.017 0.001 TYR B 817 PHE 0.017 0.002 PHE B 160 TRP 0.022 0.002 TRP A 98 HIS 0.006 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (17010) covalent geometry : angle 0.54102 / 0.27 (23068) hydrogen bonds : bond 0.04426 / 2.94 ( 796) hydrogen bonds : angle 4.88485 / 3.57 ( 2337) Misc. bond : bond 0.01000 / 0.49 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7282 (m-30) cc_final: 0.6776 (t0) REVERT: A 45 GLN cc_start: 0.7234 (mt0) cc_final: 0.6786 (mt0) REVERT: A 50 SER cc_start: 0.7400 (t) cc_final: 0.6970 (p) REVERT: A 58 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6335 (pm20) REVERT: A 187 MET cc_start: 0.8014 (ttp) cc_final: 0.6955 (mmm) REVERT: A 194 ASP cc_start: 0.7876 (m-30) cc_final: 0.7606 (m-30) REVERT: A 196 GLN cc_start: 0.6534 (mt0) cc_final: 0.6167 (tt0) REVERT: A 217 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8067 (tm) REVERT: A 224 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6308 (tp30) REVERT: A 250 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6539 (pt0) REVERT: A 270 GLU cc_start: 0.7451 (tt0) cc_final: 0.6843 (pt0) REVERT: A 343 ILE cc_start: 0.6954 (mm) cc_final: 0.6654 (pt) REVERT: A 373 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6285 (mm-30) REVERT: A 388 LYS cc_start: 0.7289 (mttp) cc_final: 0.6929 (mtmm) REVERT: A 423 ARG cc_start: 0.6644 (mmm160) cc_final: 0.6394 (tpt90) REVERT: A 485 GLU cc_start: 0.7662 (tt0) cc_final: 0.6634 (mm-30) REVERT: A 498 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8240 (tt0) REVERT: A 573 LYS cc_start: 0.8312 (tttt) cc_final: 0.7923 (ttmm) REVERT: A 604 GLU cc_start: 0.7381 (pt0) cc_final: 0.6836 (pp20) REVERT: A 612 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6601 (pm20) REVERT: A 644 ARG cc_start: 0.8019 (mmt90) cc_final: 0.7104 (mmp-170) REVERT: A 774 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6737 (tp30) REVERT: A 783 LYS cc_start: 0.8216 (tmmt) cc_final: 0.7515 (tppt) REVERT: A 799 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7364 (mt-10) REVERT: A 804 ARG cc_start: 0.7799 (tpt-90) cc_final: 0.6310 (mmt180) REVERT: A 860 LYS cc_start: 0.7570 (mttt) cc_final: 0.6994 (mmtm) REVERT: A 867 MET cc_start: 0.9098 (pp-130) cc_final: 0.8683 (ppp) REVERT: A 910 GLN cc_start: 0.7357 (mm110) cc_final: 0.7105 (mm-40) REVERT: A 934 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7397 (mmtt) REVERT: A 990 SER cc_start: 0.8104 (p) cc_final: 0.7858 (m) REVERT: B 11 LYS cc_start: 0.7567 (mtmm) cc_final: 0.7319 (tttt) REVERT: B 23 ASP cc_start: 0.7665 (t70) cc_final: 0.6739 (t0) REVERT: B 24 LYS cc_start: 0.7665 (pttm) cc_final: 0.6874 (mttp) REVERT: B 25 ASP cc_start: 0.7403 (m-30) cc_final: 0.7161 (m-30) REVERT: B 61 LYS cc_start: 0.7459 (ttmt) cc_final: 0.7151 (ttpp) REVERT: B 120 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7599 (mtt) REVERT: B 187 MET cc_start: 0.8030 (ttp) cc_final: 0.6880 (tpp) REVERT: B 198 LYS cc_start: 0.7757 (mttt) cc_final: 0.7210 (pttt) REVERT: B 295 GLU cc_start: 0.6750 (tt0) cc_final: 0.5928 (mt-10) REVERT: B 315 LYS cc_start: 0.7260 (mmtp) cc_final: 0.6476 (mtpt) REVERT: B 354 GLN cc_start: 0.7704 (mt0) cc_final: 0.7013 (mm-40) REVERT: B 379 ARG cc_start: 0.7454 (ttp80) cc_final: 0.7091 (ttp-110) REVERT: B 434 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.5878 (mp10) REVERT: B 444 LYS cc_start: 0.8537 (pttt) cc_final: 0.7878 (ptpp) REVERT: B 454 PRO cc_start: 0.7962 (Cg_exo) cc_final: 0.7664 (Cg_endo) REVERT: B 466 ARG cc_start: 0.6714 (mtt-85) cc_final: 0.6268 (mtt90) REVERT: B 485 GLU cc_start: 0.8082 (tt0) cc_final: 0.7321 (tp30) REVERT: B 512 GLU cc_start: 0.7663 (mt-10) cc_final: 0.6954 (tp30) REVERT: B 573 LYS cc_start: 0.8256 (tttt) cc_final: 0.7970 (ttpp) REVERT: B 597 GLU cc_start: 0.7608 (tt0) cc_final: 0.6622 (tp30) REVERT: B 627 ASN cc_start: 0.7851 (m-40) cc_final: 0.7601 (m-40) REVERT: B 652 LYS cc_start: 0.8254 (tttt) cc_final: 0.7842 (ttmm) REVERT: B 666 ARG cc_start: 0.7086 (mmt180) cc_final: 0.6540 (mmm160) REVERT: B 734 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7324 (ttp-110) REVERT: B 744 GLN cc_start: 0.8304 (mt0) cc_final: 0.8005 (mt0) REVERT: B 783 LYS cc_start: 0.7730 (mttm) cc_final: 0.7145 (tttp) REVERT: B 813 LYS cc_start: 0.8492 (mtmp) cc_final: 0.7916 (mmtm) REVERT: B 933 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6859 (ttt90) REVERT: B 949 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6465 (mm) REVERT: B 1027 GLN cc_start: 0.7407 (mt0) cc_final: 0.7169 (mt0) outliers start: 38 outliers final: 13 residues processed: 291 average time/residue: 0.6593 time to fit residues: 209.9514 Evaluate side-chains 263 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 933 ARG Chi-restraints excluded: chain B residue 949 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 123 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 181 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN A 780 GLN A 964 HIS A1005 GLN B 191 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.163547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.131436 restraints weight = 17058.543| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.74 r_work: 0.3402 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17012 Z= 0.108 Angle : 0.496 8.817 23068 Z= 0.250 Chirality : 0.039 0.129 2467 Planarity : 0.004 0.049 2987 Dihedral : 7.024 87.871 2374 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.21 % Allowed : 12.41 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 2042 helix: 1.45 (0.17), residues: 944 sheet: -0.75 (0.30), residues: 282 loop : 0.04 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 112 TYR 0.012 0.001 TYR B 817 PHE 0.014 0.001 PHE B 160 TRP 0.020 0.001 TRP A 98 HIS 0.004 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (17010) covalent geometry : angle 0.49561 / 0.25 (23068) hydrogen bonds : bond 0.03789 / 2.50 ( 796) hydrogen bonds : angle 4.63926 / 3.38 ( 2337) Misc. bond : bond 0.00533 / 0.27 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7291 (m-30) cc_final: 0.6799 (t0) REVERT: A 45 GLN cc_start: 0.7206 (mt0) cc_final: 0.6814 (mt0) REVERT: A 50 SER cc_start: 0.7345 (t) cc_final: 0.6922 (p) REVERT: A 58 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6359 (pm20) REVERT: A 187 MET cc_start: 0.7920 (ttp) cc_final: 0.6859 (mmp) REVERT: A 194 ASP cc_start: 0.7835 (m-30) cc_final: 0.7577 (m-30) REVERT: A 196 GLN cc_start: 0.6488 (mt0) cc_final: 0.6171 (tt0) REVERT: A 217 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8039 (tm) REVERT: A 224 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6312 (tp30) REVERT: A 250 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6564 (pt0) REVERT: A 270 GLU cc_start: 0.7418 (tt0) cc_final: 0.6832 (pt0) REVERT: A 288 ASP cc_start: 0.6654 (p0) cc_final: 0.6409 (p0) REVERT: A 295 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6277 (mt-10) REVERT: A 343 ILE cc_start: 0.6991 (mm) cc_final: 0.6606 (pt) REVERT: A 373 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6317 (mm-30) REVERT: A 388 LYS cc_start: 0.7311 (mttp) cc_final: 0.6972 (mtmm) REVERT: A 423 ARG cc_start: 0.6625 (mmm160) cc_final: 0.6408 (tpt90) REVERT: A 485 GLU cc_start: 0.7659 (tt0) cc_final: 0.6647 (mm-30) REVERT: A 541 GLN cc_start: 0.6769 (mm-40) cc_final: 0.6389 (mm-40) REVERT: A 573 LYS cc_start: 0.8264 (tttt) cc_final: 0.7867 (ttmm) REVERT: A 604 GLU cc_start: 0.7339 (pt0) cc_final: 0.6830 (pp20) REVERT: A 612 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6764 (pm20) REVERT: A 644 ARG cc_start: 0.8095 (mmt90) cc_final: 0.7128 (mmp-170) REVERT: A 783 LYS cc_start: 0.8227 (tmmt) cc_final: 0.7524 (tppt) REVERT: A 799 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7350 (mt-10) REVERT: A 804 ARG cc_start: 0.7791 (tpt-90) cc_final: 0.6311 (mmt180) REVERT: A 860 LYS cc_start: 0.7557 (mttt) cc_final: 0.7028 (mmtm) REVERT: A 867 MET cc_start: 0.9136 (pp-130) cc_final: 0.8708 (ppp) REVERT: A 910 GLN cc_start: 0.7428 (mm110) cc_final: 0.7034 (mm-40) REVERT: A 934 LYS cc_start: 0.7782 (mmtt) cc_final: 0.7486 (mmtt) REVERT: A 945 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8017 (pmt) REVERT: A 990 SER cc_start: 0.8185 (p) cc_final: 0.7828 (m) REVERT: A 1012 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5285 (mm-30) REVERT: B 11 LYS cc_start: 0.7578 (mtmm) cc_final: 0.7338 (tttt) REVERT: B 23 ASP cc_start: 0.7583 (t70) cc_final: 0.6718 (t0) REVERT: B 24 LYS cc_start: 0.7662 (pttm) cc_final: 0.6896 (mttp) REVERT: B 61 LYS cc_start: 0.7526 (ttmt) cc_final: 0.7187 (ttpp) REVERT: B 120 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7657 (mtt) REVERT: B 187 MET cc_start: 0.8048 (ttp) cc_final: 0.6871 (tpp) REVERT: B 198 LYS cc_start: 0.7781 (mttt) cc_final: 0.7216 (pptt) REVERT: B 251 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7676 (mttt) REVERT: B 288 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.6146 (p0) REVERT: B 295 GLU cc_start: 0.6782 (tt0) cc_final: 0.6009 (mt-10) REVERT: B 309 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.5889 (ttpp) REVERT: B 315 LYS cc_start: 0.7477 (mmtp) cc_final: 0.6634 (mtpt) REVERT: B 354 GLN cc_start: 0.7659 (mt0) cc_final: 0.7016 (mm-40) REVERT: B 379 ARG cc_start: 0.7506 (ttp80) cc_final: 0.7186 (ttp-170) REVERT: B 444 LYS cc_start: 0.8520 (pttt) cc_final: 0.7874 (ptpp) REVERT: B 454 PRO cc_start: 0.7820 (Cg_exo) cc_final: 0.7514 (Cg_endo) REVERT: B 466 ARG cc_start: 0.6757 (mtt-85) cc_final: 0.6398 (mtt90) REVERT: B 485 GLU cc_start: 0.8088 (tt0) cc_final: 0.7328 (tp30) REVERT: B 512 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7110 (tp30) REVERT: B 573 LYS cc_start: 0.8210 (tttt) cc_final: 0.7936 (ttpp) REVERT: B 597 GLU cc_start: 0.7643 (tt0) cc_final: 0.6680 (tp30) REVERT: B 627 ASN cc_start: 0.7756 (m-40) cc_final: 0.7471 (m-40) REVERT: B 652 LYS cc_start: 0.8224 (tttt) cc_final: 0.7828 (ttmm) REVERT: B 666 ARG cc_start: 0.7033 (mmt180) cc_final: 0.6320 (mmm-85) REVERT: B 709 GLU cc_start: 0.7637 (pt0) cc_final: 0.7416 (mp0) REVERT: B 734 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7330 (ttm110) REVERT: B 744 GLN cc_start: 0.8229 (mt0) cc_final: 0.7849 (mt0) REVERT: B 783 LYS cc_start: 0.7825 (mttm) cc_final: 0.7225 (tttp) REVERT: B 813 LYS cc_start: 0.8482 (mtmp) cc_final: 0.7947 (mmtm) REVERT: B 933 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7009 (ttt90) REVERT: B 949 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6524 (mm) REVERT: B 959 LYS cc_start: 0.7273 (tttt) cc_final: 0.6771 (tppt) REVERT: B 1027 GLN cc_start: 0.7435 (mt0) cc_final: 0.7225 (mt0) outliers start: 39 outliers final: 15 residues processed: 278 average time/residue: 0.8067 time to fit residues: 244.4114 Evaluate side-chains 272 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 933 ARG Chi-restraints excluded: chain B residue 949 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 31 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 124 optimal weight: 0.0370 chunk 86 optimal weight: 3.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 HIS A 627 ASN A 780 GLN A 964 HIS A1005 GLN B 408 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.161106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128611 restraints weight = 17071.518| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.74 r_work: 0.3359 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17012 Z= 0.141 Angle : 0.534 9.007 23068 Z= 0.268 Chirality : 0.040 0.133 2467 Planarity : 0.004 0.047 2987 Dihedral : 7.114 89.789 2374 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.32 % Allowed : 12.53 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 2042 helix: 1.35 (0.17), residues: 939 sheet: -0.62 (0.30), residues: 281 loop : 0.01 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 112 TYR 0.016 0.001 TYR B 817 PHE 0.016 0.002 PHE B 160 TRP 0.022 0.002 TRP A 98 HIS 0.006 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (17010) covalent geometry : angle 0.53359 / 0.27 (23068) hydrogen bonds : bond 0.04181 / 2.77 ( 796) hydrogen bonds : angle 4.72505 / 3.44 ( 2337) Misc. bond : bond 0.00949 / 0.48 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 254 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7309 (m-30) cc_final: 0.6819 (t0) REVERT: A 45 GLN cc_start: 0.7291 (mt0) cc_final: 0.6855 (mm-40) REVERT: A 50 SER cc_start: 0.7440 (t) cc_final: 0.7055 (p) REVERT: A 58 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6567 (pm20) REVERT: A 187 MET cc_start: 0.8020 (ttp) cc_final: 0.6876 (mmm) REVERT: A 194 ASP cc_start: 0.7860 (m-30) cc_final: 0.7594 (m-30) REVERT: A 196 GLN cc_start: 0.6516 (mt0) cc_final: 0.6198 (tt0) REVERT: A 217 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8080 (tm) REVERT: A 224 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6271 (tp30) REVERT: A 250 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6647 (pt0) REVERT: A 270 GLU cc_start: 0.7405 (tt0) cc_final: 0.6783 (pt0) REVERT: A 288 ASP cc_start: 0.6755 (p0) cc_final: 0.6504 (p0) REVERT: A 295 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6278 (mt-10) REVERT: A 343 ILE cc_start: 0.7072 (mm) cc_final: 0.6567 (pp) REVERT: A 352 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7289 (tttp) REVERT: A 373 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6262 (mm-30) REVERT: A 388 LYS cc_start: 0.7343 (mttp) cc_final: 0.7000 (mtmm) REVERT: A 423 ARG cc_start: 0.6658 (mmm160) cc_final: 0.6431 (tpt90) REVERT: A 485 GLU cc_start: 0.7728 (tt0) cc_final: 0.6656 (mm-30) REVERT: A 541 GLN cc_start: 0.6823 (mm-40) cc_final: 0.6397 (mm-40) REVERT: A 573 LYS cc_start: 0.8266 (tttt) cc_final: 0.7865 (ttmm) REVERT: A 604 GLU cc_start: 0.7352 (pt0) cc_final: 0.6798 (pp20) REVERT: A 612 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6830 (pm20) REVERT: A 644 ARG cc_start: 0.8122 (mmt90) cc_final: 0.7150 (mmp-170) REVERT: A 774 GLU cc_start: 0.7111 (tp30) cc_final: 0.6785 (tt0) REVERT: A 783 LYS cc_start: 0.8251 (tmmt) cc_final: 0.7530 (tppt) REVERT: A 799 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7529 (mt-10) REVERT: A 804 ARG cc_start: 0.7796 (tpt-90) cc_final: 0.6338 (mmt180) REVERT: A 860 LYS cc_start: 0.7554 (mttt) cc_final: 0.7015 (mmtm) REVERT: A 867 MET cc_start: 0.9105 (pp-130) cc_final: 0.8590 (ppp) REVERT: A 910 GLN cc_start: 0.7489 (mm110) cc_final: 0.7152 (mm-40) REVERT: A 934 LYS cc_start: 0.7783 (mmtt) cc_final: 0.7486 (mmtt) REVERT: A 990 SER cc_start: 0.8195 (p) cc_final: 0.7708 (m) REVERT: A 1012 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5392 (mm-30) REVERT: A 1027 GLN cc_start: 0.8518 (tt0) cc_final: 0.8217 (tt0) REVERT: B 11 LYS cc_start: 0.7546 (mtmm) cc_final: 0.7336 (tttt) REVERT: B 23 ASP cc_start: 0.7648 (t70) cc_final: 0.6826 (t0) REVERT: B 24 LYS cc_start: 0.7594 (pttm) cc_final: 0.6801 (mttp) REVERT: B 61 LYS cc_start: 0.7408 (ttmt) cc_final: 0.7118 (ttpp) REVERT: B 62 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7462 (tp30) REVERT: B 120 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7627 (mtt) REVERT: B 187 MET cc_start: 0.8024 (ttp) cc_final: 0.6917 (tpp) REVERT: B 198 LYS cc_start: 0.7774 (mttt) cc_final: 0.7181 (pttt) REVERT: B 251 LYS cc_start: 0.8070 (mttt) cc_final: 0.7857 (mttt) REVERT: B 288 ASP cc_start: 0.6508 (OUTLIER) cc_final: 0.6134 (p0) REVERT: B 295 GLU cc_start: 0.6796 (tt0) cc_final: 0.5978 (mt-10) REVERT: B 309 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.5880 (ttpp) REVERT: B 315 LYS cc_start: 0.7446 (mmtp) cc_final: 0.6603 (mtpt) REVERT: B 354 GLN cc_start: 0.7717 (mt0) cc_final: 0.7129 (mm-40) REVERT: B 379 ARG cc_start: 0.7466 (ttp80) cc_final: 0.7104 (ttp-170) REVERT: B 434 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.5897 (mp10) REVERT: B 444 LYS cc_start: 0.8534 (pttt) cc_final: 0.7856 (ptpp) REVERT: B 454 PRO cc_start: 0.7933 (Cg_exo) cc_final: 0.7616 (Cg_endo) REVERT: B 485 GLU cc_start: 0.8024 (tt0) cc_final: 0.7315 (tp30) REVERT: B 512 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7209 (tp30) REVERT: B 573 LYS cc_start: 0.8223 (tttt) cc_final: 0.7934 (ttpp) REVERT: B 597 GLU cc_start: 0.7634 (tt0) cc_final: 0.6641 (tp30) REVERT: B 627 ASN cc_start: 0.7877 (m-40) cc_final: 0.7529 (m-40) REVERT: B 652 LYS cc_start: 0.8315 (tttt) cc_final: 0.7838 (ttmm) REVERT: B 666 ARG cc_start: 0.7064 (mmt180) cc_final: 0.6314 (mmm-85) REVERT: B 734 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7293 (ttp-110) REVERT: B 744 GLN cc_start: 0.8283 (mt0) cc_final: 0.7986 (mt0) REVERT: B 780 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6114 (mp10) REVERT: B 783 LYS cc_start: 0.7884 (mttm) cc_final: 0.7270 (tttp) REVERT: B 813 LYS cc_start: 0.8549 (mtmp) cc_final: 0.7952 (mmtm) REVERT: B 933 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6985 (ttt90) REVERT: B 949 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6593 (mm) REVERT: B 959 LYS cc_start: 0.7271 (tttt) cc_final: 0.6882 (tttp) outliers start: 41 outliers final: 20 residues processed: 282 average time/residue: 0.7872 time to fit residues: 242.2937 Evaluate side-chains 279 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 933 ARG Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 965 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 39 optimal weight: 0.0370 chunk 63 optimal weight: 8.9990 chunk 156 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 363 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 HIS A 627 ASN A 780 GLN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.162101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.129752 restraints weight = 17025.632| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.74 r_work: 0.3374 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17012 Z= 0.124 Angle : 0.511 9.061 23068 Z= 0.257 Chirality : 0.040 0.130 2467 Planarity : 0.004 0.048 2987 Dihedral : 7.069 89.697 2374 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.27 % Allowed : 12.87 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 2042 helix: 1.43 (0.17), residues: 939 sheet: -0.62 (0.31), residues: 280 loop : 0.01 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 112 TYR 0.015 0.001 TYR B 817 PHE 0.015 0.001 PHE B 160 TRP 0.021 0.001 TRP A 98 HIS 0.005 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (17010) covalent geometry : angle 0.51146 / 0.26 (23068) hydrogen bonds : bond 0.03946 / 2.61 ( 796) hydrogen bonds : angle 4.63758 / 3.38 ( 2337) Misc. bond : bond 0.00602 / 0.31 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7304 (m-30) cc_final: 0.6809 (t0) REVERT: A 45 GLN cc_start: 0.7311 (mt0) cc_final: 0.6883 (mm-40) REVERT: A 50 SER cc_start: 0.7385 (t) cc_final: 0.6992 (p) REVERT: A 58 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6497 (pm20) REVERT: A 187 MET cc_start: 0.7936 (ttp) cc_final: 0.6841 (mmm) REVERT: A 194 ASP cc_start: 0.7827 (m-30) cc_final: 0.7560 (m-30) REVERT: A 196 GLN cc_start: 0.6433 (mt0) cc_final: 0.6141 (tt0) REVERT: A 217 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8083 (tm) REVERT: A 224 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6279 (tp30) REVERT: A 250 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6617 (pt0) REVERT: A 270 GLU cc_start: 0.7400 (tt0) cc_final: 0.6768 (pt0) REVERT: A 288 ASP cc_start: 0.6730 (p0) cc_final: 0.6496 (p0) REVERT: A 295 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6246 (mt-10) REVERT: A 343 ILE cc_start: 0.7024 (mm) cc_final: 0.6564 (pp) REVERT: A 373 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6231 (mm-30) REVERT: A 388 LYS cc_start: 0.7284 (mttp) cc_final: 0.6986 (mtmm) REVERT: A 423 ARG cc_start: 0.6642 (mmm160) cc_final: 0.6428 (tpt90) REVERT: A 485 GLU cc_start: 0.7723 (tt0) cc_final: 0.6665 (mm-30) REVERT: A 541 GLN cc_start: 0.6801 (mm-40) cc_final: 0.6398 (mm-40) REVERT: A 573 LYS cc_start: 0.8255 (tttt) cc_final: 0.7851 (ttmm) REVERT: A 604 GLU cc_start: 0.7352 (pt0) cc_final: 0.6798 (pp20) REVERT: A 612 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6813 (pm20) REVERT: A 644 ARG cc_start: 0.8123 (mmt90) cc_final: 0.7139 (mmp-170) REVERT: A 783 LYS cc_start: 0.8259 (tmmt) cc_final: 0.7527 (tppt) REVERT: A 799 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7519 (mt-10) REVERT: A 804 ARG cc_start: 0.7778 (tpt-90) cc_final: 0.6297 (mmt180) REVERT: A 860 LYS cc_start: 0.7561 (mttt) cc_final: 0.7018 (mmtm) REVERT: A 867 MET cc_start: 0.9152 (pp-130) cc_final: 0.8616 (ppp) REVERT: A 910 GLN cc_start: 0.7467 (mm110) cc_final: 0.7037 (mm-40) REVERT: A 934 LYS cc_start: 0.7808 (mmtt) cc_final: 0.7500 (mmtt) REVERT: A 990 SER cc_start: 0.8024 (p) cc_final: 0.7666 (m) REVERT: A 1012 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5372 (mm-30) REVERT: A 1027 GLN cc_start: 0.8501 (tt0) cc_final: 0.8196 (tt0) REVERT: B 23 ASP cc_start: 0.7636 (t70) cc_final: 0.6732 (t0) REVERT: B 24 LYS cc_start: 0.7568 (pttm) cc_final: 0.6774 (mttp) REVERT: B 61 LYS cc_start: 0.7394 (ttmt) cc_final: 0.7090 (ttpp) REVERT: B 120 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7674 (mtt) REVERT: B 187 MET cc_start: 0.7978 (ttp) cc_final: 0.6877 (tpp) REVERT: B 198 LYS cc_start: 0.7819 (mttt) cc_final: 0.7206 (pttt) REVERT: B 288 ASP cc_start: 0.6486 (OUTLIER) cc_final: 0.6137 (p0) REVERT: B 295 GLU cc_start: 0.6767 (tt0) cc_final: 0.5980 (mt-10) REVERT: B 309 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.5861 (ttpp) REVERT: B 315 LYS cc_start: 0.7453 (mmtp) cc_final: 0.6589 (mtpt) REVERT: B 354 GLN cc_start: 0.7741 (mt0) cc_final: 0.7206 (mm-40) REVERT: B 379 ARG cc_start: 0.7500 (ttp80) cc_final: 0.7078 (ttp-170) REVERT: B 434 GLN cc_start: 0.6696 (OUTLIER) cc_final: 0.5900 (mp10) REVERT: B 444 LYS cc_start: 0.8425 (pttt) cc_final: 0.7772 (ptpp) REVERT: B 454 PRO cc_start: 0.7905 (Cg_exo) cc_final: 0.7586 (Cg_endo) REVERT: B 485 GLU cc_start: 0.7989 (tt0) cc_final: 0.7283 (tp30) REVERT: B 512 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7205 (tp30) REVERT: B 525 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8405 (mptm) REVERT: B 573 LYS cc_start: 0.8177 (tttt) cc_final: 0.7885 (ttpp) REVERT: B 597 GLU cc_start: 0.7639 (tt0) cc_final: 0.6660 (tp30) REVERT: B 627 ASN cc_start: 0.7825 (m-40) cc_final: 0.7513 (m-40) REVERT: B 652 LYS cc_start: 0.8315 (tttt) cc_final: 0.7844 (ttmm) REVERT: B 666 ARG cc_start: 0.7034 (mmt180) cc_final: 0.6347 (mmm-85) REVERT: B 734 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7308 (ttp-110) REVERT: B 744 GLN cc_start: 0.8267 (mt0) cc_final: 0.7953 (mt0) REVERT: B 780 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6126 (mp10) REVERT: B 783 LYS cc_start: 0.7880 (mttm) cc_final: 0.7256 (tttp) REVERT: B 813 LYS cc_start: 0.8552 (mtmp) cc_final: 0.7938 (mmtm) REVERT: B 824 ARG cc_start: 0.7298 (mtt-85) cc_final: 0.6585 (mtt90) REVERT: B 888 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.6626 (mtt) REVERT: B 933 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7002 (ttt90) REVERT: B 949 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6605 (mm) REVERT: B 999 THR cc_start: 0.6678 (t) cc_final: 0.6084 (p) outliers start: 40 outliers final: 20 residues processed: 277 average time/residue: 0.7918 time to fit residues: 239.2821 Evaluate side-chains 277 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 933 ARG Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 965 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 46 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 HIS A 627 ASN A 780 GLN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.162037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.129625 restraints weight = 17014.881| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.74 r_work: 0.3372 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17012 Z= 0.126 Angle : 0.515 9.180 23068 Z= 0.259 Chirality : 0.040 0.131 2467 Planarity : 0.004 0.048 2987 Dihedral : 7.057 89.446 2374 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.27 % Allowed : 13.15 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 2042 helix: 1.42 (0.17), residues: 939 sheet: -0.58 (0.31), residues: 280 loop : -0.01 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 112 TYR 0.015 0.001 TYR B 817 PHE 0.018 0.001 PHE B 160 TRP 0.021 0.001 TRP A 98 HIS 0.004 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (17010) covalent geometry : angle 0.51517 / 0.26 (23068) hydrogen bonds : bond 0.03949 / 2.61 ( 796) hydrogen bonds : angle 4.62841 / 3.37 ( 2337) Misc. bond : bond 0.00659 / 0.34 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7338 (m-30) cc_final: 0.6908 (t0) REVERT: A 45 GLN cc_start: 0.7318 (mt0) cc_final: 0.6891 (mm-40) REVERT: A 50 SER cc_start: 0.7368 (t) cc_final: 0.6991 (p) REVERT: A 58 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6522 (pm20) REVERT: A 133 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.7062 (mm) REVERT: A 187 MET cc_start: 0.7955 (ttp) cc_final: 0.6858 (mmm) REVERT: A 194 ASP cc_start: 0.7825 (m-30) cc_final: 0.7558 (m-30) REVERT: A 196 GLN cc_start: 0.6435 (mt0) cc_final: 0.6135 (tt0) REVERT: A 217 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8084 (tm) REVERT: A 224 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6328 (tp30) REVERT: A 250 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6684 (pt0) REVERT: A 270 GLU cc_start: 0.7385 (tt0) cc_final: 0.7179 (mm-30) REVERT: A 295 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6151 (mt-10) REVERT: A 343 ILE cc_start: 0.7012 (mm) cc_final: 0.6566 (pp) REVERT: A 352 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7249 (tttp) REVERT: A 373 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6311 (mm-30) REVERT: A 388 LYS cc_start: 0.7290 (mttp) cc_final: 0.6991 (mtmm) REVERT: A 423 ARG cc_start: 0.6678 (mmm160) cc_final: 0.6466 (tpt90) REVERT: A 485 GLU cc_start: 0.7731 (tt0) cc_final: 0.6671 (mm-30) REVERT: A 573 LYS cc_start: 0.8258 (tttt) cc_final: 0.7854 (ttmm) REVERT: A 604 GLU cc_start: 0.7296 (pt0) cc_final: 0.6740 (pp20) REVERT: A 612 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6816 (pm20) REVERT: A 644 ARG cc_start: 0.8114 (mmt90) cc_final: 0.7126 (mmp-170) REVERT: A 779 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7030 (tp30) REVERT: A 783 LYS cc_start: 0.8262 (tmmt) cc_final: 0.7552 (tppt) REVERT: A 799 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7515 (mt-10) REVERT: A 804 ARG cc_start: 0.7778 (tpt-90) cc_final: 0.6297 (mmt180) REVERT: A 860 LYS cc_start: 0.7539 (mttt) cc_final: 0.6980 (mmtm) REVERT: A 867 MET cc_start: 0.9139 (pp-130) cc_final: 0.8742 (ppp) REVERT: A 910 GLN cc_start: 0.7458 (mm110) cc_final: 0.7022 (mm-40) REVERT: A 934 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7474 (mmtt) REVERT: A 990 SER cc_start: 0.8032 (p) cc_final: 0.7735 (m) REVERT: A 1012 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5492 (mm-30) REVERT: A 1027 GLN cc_start: 0.8478 (tt0) cc_final: 0.8164 (tt0) REVERT: B 23 ASP cc_start: 0.7693 (t70) cc_final: 0.6787 (t0) REVERT: B 24 LYS cc_start: 0.7568 (pttm) cc_final: 0.6778 (mttp) REVERT: B 61 LYS cc_start: 0.7422 (ttmt) cc_final: 0.7132 (ttpp) REVERT: B 120 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7712 (mtt) REVERT: B 187 MET cc_start: 0.7982 (ttp) cc_final: 0.6872 (tpp) REVERT: B 198 LYS cc_start: 0.7800 (mttt) cc_final: 0.7200 (pptt) REVERT: B 288 ASP cc_start: 0.6505 (OUTLIER) cc_final: 0.6116 (p0) REVERT: B 295 GLU cc_start: 0.6788 (tt0) cc_final: 0.6019 (mt-10) REVERT: B 309 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.5871 (ttpp) REVERT: B 315 LYS cc_start: 0.7463 (mmtp) cc_final: 0.6592 (mtpt) REVERT: B 354 GLN cc_start: 0.7771 (mt0) cc_final: 0.7213 (mm110) REVERT: B 434 GLN cc_start: 0.6722 (OUTLIER) cc_final: 0.5924 (mp10) REVERT: B 444 LYS cc_start: 0.8371 (pttt) cc_final: 0.7732 (ptpp) REVERT: B 454 PRO cc_start: 0.7906 (Cg_exo) cc_final: 0.7584 (Cg_endo) REVERT: B 485 GLU cc_start: 0.8006 (tt0) cc_final: 0.7314 (tp30) REVERT: B 512 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7234 (tp30) REVERT: B 525 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8056 (mttm) REVERT: B 573 LYS cc_start: 0.8178 (tttt) cc_final: 0.7887 (ttpp) REVERT: B 588 GLU cc_start: 0.8355 (pt0) cc_final: 0.8050 (mt-10) REVERT: B 597 GLU cc_start: 0.7649 (tt0) cc_final: 0.6645 (tp30) REVERT: B 627 ASN cc_start: 0.7832 (m-40) cc_final: 0.7531 (m-40) REVERT: B 652 LYS cc_start: 0.8284 (tttt) cc_final: 0.7829 (ttmm) REVERT: B 666 ARG cc_start: 0.7033 (mmt180) cc_final: 0.6345 (mmm-85) REVERT: B 734 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7340 (ttm110) REVERT: B 744 GLN cc_start: 0.8248 (mt0) cc_final: 0.7923 (mt0) REVERT: B 780 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6231 (mp10) REVERT: B 783 LYS cc_start: 0.7900 (mttm) cc_final: 0.7276 (tttp) REVERT: B 813 LYS cc_start: 0.8569 (mtmp) cc_final: 0.7945 (mmtm) REVERT: B 824 ARG cc_start: 0.7289 (mtt-85) cc_final: 0.6625 (mtt90) REVERT: B 828 GLU cc_start: 0.7183 (mp0) cc_final: 0.6611 (mm-30) REVERT: B 888 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6691 (mtt) REVERT: B 933 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7150 (ttt90) REVERT: B 949 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6575 (mm) REVERT: B 999 THR cc_start: 0.6792 (t) cc_final: 0.6230 (p) outliers start: 40 outliers final: 20 residues processed: 273 average time/residue: 0.8021 time to fit residues: 239.2300 Evaluate side-chains 280 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 933 ARG Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 965 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 62 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 198 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 HIS ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN A 780 GLN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1008 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130593 restraints weight = 17091.151| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.75 r_work: 0.3384 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17012 Z= 0.114 Angle : 0.503 9.534 23068 Z= 0.253 Chirality : 0.039 0.128 2467 Planarity : 0.004 0.049 2987 Dihedral : 7.024 89.807 2374 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.21 % Allowed : 13.44 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 2042 helix: 1.45 (0.17), residues: 945 sheet: -0.57 (0.31), residues: 280 loop : 0.00 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 112 TYR 0.014 0.001 TYR B 817 PHE 0.017 0.001 PHE B 160 TRP 0.021 0.001 TRP A 98 HIS 0.005 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (17010) covalent geometry : angle 0.50262 / 0.25 (23068) hydrogen bonds : bond 0.03800 / 2.51 ( 796) hydrogen bonds : angle 4.56367 / 3.32 ( 2337) Misc. bond : bond 0.00494 / 0.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7334 (m-30) cc_final: 0.6904 (t0) REVERT: A 45 GLN cc_start: 0.7320 (mt0) cc_final: 0.6899 (mm-40) REVERT: A 50 SER cc_start: 0.7362 (t) cc_final: 0.6990 (p) REVERT: A 58 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6425 (pm20) REVERT: A 133 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.7042 (mm) REVERT: A 187 MET cc_start: 0.7920 (ttp) cc_final: 0.6831 (mmm) REVERT: A 194 ASP cc_start: 0.7820 (m-30) cc_final: 0.7559 (m-30) REVERT: A 196 GLN cc_start: 0.6450 (mt0) cc_final: 0.6152 (tt0) REVERT: A 217 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8048 (tm) REVERT: A 224 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6319 (tp30) REVERT: A 250 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6671 (pt0) REVERT: A 295 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6169 (mt-10) REVERT: A 343 ILE cc_start: 0.7052 (mm) cc_final: 0.6583 (pp) REVERT: A 352 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7244 (tttp) REVERT: A 373 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6334 (mm-30) REVERT: A 388 LYS cc_start: 0.7258 (mttp) cc_final: 0.6974 (mtmm) REVERT: A 423 ARG cc_start: 0.6683 (mmm160) cc_final: 0.6470 (tpt90) REVERT: A 485 GLU cc_start: 0.7707 (tt0) cc_final: 0.6661 (mm-30) REVERT: A 573 LYS cc_start: 0.8259 (tttt) cc_final: 0.7854 (ttmm) REVERT: A 604 GLU cc_start: 0.7291 (pt0) cc_final: 0.6734 (pp20) REVERT: A 612 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6794 (pm20) REVERT: A 644 ARG cc_start: 0.8110 (mmt90) cc_final: 0.7111 (mmp-170) REVERT: A 783 LYS cc_start: 0.8267 (tmmt) cc_final: 0.7531 (tppt) REVERT: A 799 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7482 (mt-10) REVERT: A 804 ARG cc_start: 0.7768 (tpt-90) cc_final: 0.6300 (mmt180) REVERT: A 860 LYS cc_start: 0.7523 (mttt) cc_final: 0.6981 (mmtm) REVERT: A 867 MET cc_start: 0.9140 (pp-130) cc_final: 0.8737 (ppp) REVERT: A 910 GLN cc_start: 0.7417 (mm110) cc_final: 0.6973 (mm-40) REVERT: A 925 ARG cc_start: 0.7057 (mtm-85) cc_final: 0.6650 (mtp180) REVERT: A 934 LYS cc_start: 0.7716 (mmtt) cc_final: 0.7466 (mmtt) REVERT: A 990 SER cc_start: 0.7994 (p) cc_final: 0.7693 (m) REVERT: A 1008 HIS cc_start: 0.7587 (OUTLIER) cc_final: 0.7366 (m170) REVERT: A 1012 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5342 (mm-30) REVERT: A 1027 GLN cc_start: 0.8474 (tt0) cc_final: 0.8169 (tt0) REVERT: B 23 ASP cc_start: 0.7681 (t70) cc_final: 0.6847 (t0) REVERT: B 24 LYS cc_start: 0.7588 (pttm) cc_final: 0.6826 (mttp) REVERT: B 61 LYS cc_start: 0.7406 (ttmt) cc_final: 0.7117 (ttpp) REVERT: B 120 MET cc_start: 0.7939 (mtt) cc_final: 0.7729 (mtt) REVERT: B 187 MET cc_start: 0.8059 (ttp) cc_final: 0.6875 (tpp) REVERT: B 198 LYS cc_start: 0.7797 (mttt) cc_final: 0.7198 (pptt) REVERT: B 288 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.6105 (p0) REVERT: B 295 GLU cc_start: 0.6773 (tt0) cc_final: 0.6004 (mt-10) REVERT: B 309 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.5990 (ttpp) REVERT: B 315 LYS cc_start: 0.7454 (mmtp) cc_final: 0.6593 (mtpt) REVERT: B 354 GLN cc_start: 0.7733 (mt0) cc_final: 0.7247 (tm-30) REVERT: B 434 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.5875 (mp10) REVERT: B 444 LYS cc_start: 0.8359 (pttt) cc_final: 0.7721 (ptpp) REVERT: B 454 PRO cc_start: 0.7890 (Cg_exo) cc_final: 0.7561 (Cg_endo) REVERT: B 485 GLU cc_start: 0.7992 (tt0) cc_final: 0.7282 (tp30) REVERT: B 512 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7232 (tp30) REVERT: B 525 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8036 (mttm) REVERT: B 573 LYS cc_start: 0.8214 (tttt) cc_final: 0.7940 (ttpp) REVERT: B 588 GLU cc_start: 0.8351 (pt0) cc_final: 0.8087 (mt-10) REVERT: B 597 GLU cc_start: 0.7588 (tt0) cc_final: 0.6664 (tp30) REVERT: B 627 ASN cc_start: 0.7795 (m-40) cc_final: 0.7508 (m-40) REVERT: B 652 LYS cc_start: 0.8278 (tttt) cc_final: 0.7818 (ttmm) REVERT: B 666 ARG cc_start: 0.7040 (mmt180) cc_final: 0.6346 (mmm-85) REVERT: B 734 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7332 (ttm110) REVERT: B 744 GLN cc_start: 0.8239 (mt0) cc_final: 0.7911 (mt0) REVERT: B 783 LYS cc_start: 0.7893 (mttm) cc_final: 0.7287 (tttp) REVERT: B 813 LYS cc_start: 0.8558 (mtmp) cc_final: 0.7925 (mmtm) REVERT: B 824 ARG cc_start: 0.7279 (mtt-85) cc_final: 0.6618 (mtt90) REVERT: B 828 GLU cc_start: 0.7118 (mp0) cc_final: 0.6564 (mm-30) REVERT: B 888 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6608 (mtt) REVERT: B 933 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7062 (ttt90) REVERT: B 949 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6584 (mm) REVERT: B 999 THR cc_start: 0.6712 (t) cc_final: 0.6232 (p) outliers start: 39 outliers final: 19 residues processed: 272 average time/residue: 0.7771 time to fit residues: 230.7132 Evaluate side-chains 274 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 1008 HIS Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 933 ARG Chi-restraints excluded: chain B residue 949 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 120 optimal weight: 2.9990 chunk 118 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.0117 > 50:) chunk 141 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 HIS A 627 ASN A 780 GLN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131003 restraints weight = 17018.230| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.74 r_work: 0.3397 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17012 Z= 0.110 Angle : 0.502 9.510 23068 Z= 0.252 Chirality : 0.039 0.129 2467 Planarity : 0.004 0.050 2987 Dihedral : 7.003 89.812 2374 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.10 % Allowed : 13.66 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 2042 helix: 1.48 (0.17), residues: 946 sheet: -0.55 (0.31), residues: 280 loop : -0.01 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 112 TYR 0.013 0.001 TYR B 817 PHE 0.016 0.001 PHE B 160 TRP 0.024 0.001 TRP A 371 HIS 0.005 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (17010) covalent geometry : angle 0.50198 / 0.25 (23068) hydrogen bonds : bond 0.03739 / 2.47 ( 796) hydrogen bonds : angle 4.53748 / 3.30 ( 2337) Misc. bond : bond 0.00455 / 0.23 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 243 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7333 (m-30) cc_final: 0.6905 (t0) REVERT: A 45 GLN cc_start: 0.7332 (mt0) cc_final: 0.6931 (mm-40) REVERT: A 50 SER cc_start: 0.7364 (t) cc_final: 0.6994 (p) REVERT: A 58 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6443 (pm20) REVERT: A 187 MET cc_start: 0.7949 (ttp) cc_final: 0.6872 (mmm) REVERT: A 194 ASP cc_start: 0.7831 (m-30) cc_final: 0.7574 (m-30) REVERT: A 196 GLN cc_start: 0.6463 (mt0) cc_final: 0.6174 (tt0) REVERT: A 217 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8053 (tm) REVERT: A 224 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6339 (tp30) REVERT: A 250 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6637 (pt0) REVERT: A 295 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6194 (mt-10) REVERT: A 343 ILE cc_start: 0.7056 (mm) cc_final: 0.6581 (pp) REVERT: A 352 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7244 (tttp) REVERT: A 373 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6353 (mm-30) REVERT: A 388 LYS cc_start: 0.7246 (mttp) cc_final: 0.6970 (mtmm) REVERT: A 485 GLU cc_start: 0.7713 (tt0) cc_final: 0.6667 (mm-30) REVERT: A 573 LYS cc_start: 0.8279 (tttt) cc_final: 0.7881 (ttmm) REVERT: A 604 GLU cc_start: 0.7301 (pt0) cc_final: 0.6754 (pp20) REVERT: A 612 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6875 (pm20) REVERT: A 644 ARG cc_start: 0.8120 (mmt90) cc_final: 0.7126 (mmp-170) REVERT: A 783 LYS cc_start: 0.8278 (tmmt) cc_final: 0.7546 (tppt) REVERT: A 799 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 804 ARG cc_start: 0.7782 (tpt-90) cc_final: 0.6328 (mmt180) REVERT: A 860 LYS cc_start: 0.7535 (mttt) cc_final: 0.7006 (mmtm) REVERT: A 867 MET cc_start: 0.9144 (pp-130) cc_final: 0.8551 (ppp) REVERT: A 910 GLN cc_start: 0.7407 (mm110) cc_final: 0.6972 (mm-40) REVERT: A 925 ARG cc_start: 0.7072 (mtm-85) cc_final: 0.6673 (mtp180) REVERT: A 934 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7474 (mmtt) REVERT: A 990 SER cc_start: 0.8006 (p) cc_final: 0.7731 (m) REVERT: A 1012 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5321 (mm-30) REVERT: A 1027 GLN cc_start: 0.8503 (tt0) cc_final: 0.8198 (tt0) REVERT: B 23 ASP cc_start: 0.7677 (t70) cc_final: 0.6802 (t0) REVERT: B 24 LYS cc_start: 0.7597 (pttm) cc_final: 0.6823 (mttp) REVERT: B 61 LYS cc_start: 0.7417 (ttmt) cc_final: 0.7132 (ttpp) REVERT: B 120 MET cc_start: 0.7892 (mtt) cc_final: 0.7689 (mtt) REVERT: B 187 MET cc_start: 0.8068 (ttp) cc_final: 0.6903 (tpp) REVERT: B 198 LYS cc_start: 0.7807 (mttt) cc_final: 0.7214 (pptt) REVERT: B 288 ASP cc_start: 0.6448 (OUTLIER) cc_final: 0.6080 (p0) REVERT: B 295 GLU cc_start: 0.6787 (tt0) cc_final: 0.5988 (mt-10) REVERT: B 315 LYS cc_start: 0.7500 (mmtp) cc_final: 0.6646 (mtpt) REVERT: B 354 GLN cc_start: 0.7733 (mt0) cc_final: 0.7276 (tm-30) REVERT: B 434 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.5887 (mp10) REVERT: B 444 LYS cc_start: 0.8362 (pttt) cc_final: 0.7709 (ptpp) REVERT: B 454 PRO cc_start: 0.7891 (Cg_exo) cc_final: 0.7564 (Cg_endo) REVERT: B 485 GLU cc_start: 0.8002 (tt0) cc_final: 0.7291 (tp30) REVERT: B 512 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7229 (tp30) REVERT: B 525 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8048 (mttm) REVERT: B 573 LYS cc_start: 0.8218 (tttt) cc_final: 0.7952 (ttpp) REVERT: B 588 GLU cc_start: 0.8344 (pt0) cc_final: 0.8111 (mt-10) REVERT: B 597 GLU cc_start: 0.7652 (tt0) cc_final: 0.6697 (tp30) REVERT: B 627 ASN cc_start: 0.7799 (m-40) cc_final: 0.7513 (m-40) REVERT: B 652 LYS cc_start: 0.8284 (tttt) cc_final: 0.7817 (ttmm) REVERT: B 666 ARG cc_start: 0.7049 (mmt180) cc_final: 0.6363 (mmm-85) REVERT: B 734 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7337 (ttm110) REVERT: B 744 GLN cc_start: 0.8232 (mt0) cc_final: 0.7896 (mt0) REVERT: B 783 LYS cc_start: 0.7904 (mttm) cc_final: 0.7282 (tttp) REVERT: B 813 LYS cc_start: 0.8559 (mtmp) cc_final: 0.7939 (mmtm) REVERT: B 824 ARG cc_start: 0.7288 (mtt-85) cc_final: 0.6617 (mtt90) REVERT: B 828 GLU cc_start: 0.7103 (mp0) cc_final: 0.6559 (mm-30) REVERT: B 888 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6614 (mtt) REVERT: B 933 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7271 (ttt90) REVERT: B 934 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6812 (tppp) REVERT: B 949 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6620 (mm) REVERT: B 999 THR cc_start: 0.6710 (t) cc_final: 0.6240 (p) outliers start: 37 outliers final: 19 residues processed: 270 average time/residue: 0.7356 time to fit residues: 217.4119 Evaluate side-chains 269 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 933 ARG Chi-restraints excluded: chain B residue 934 LYS Chi-restraints excluded: chain B residue 949 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 49 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 HIS A 627 ASN A 780 GLN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.160400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127815 restraints weight = 16980.203| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.74 r_work: 0.3350 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17012 Z= 0.161 Angle : 0.560 9.644 23068 Z= 0.281 Chirality : 0.041 0.136 2467 Planarity : 0.004 0.050 2987 Dihedral : 7.159 89.102 2374 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.93 % Allowed : 13.78 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.19), residues: 2042 helix: 1.29 (0.17), residues: 939 sheet: -0.50 (0.31), residues: 280 loop : -0.04 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 112 TYR 0.017 0.001 TYR B 817 PHE 0.020 0.002 PHE B 160 TRP 0.028 0.002 TRP A 371 HIS 0.005 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (17010) covalent geometry : angle 0.55977 / 0.28 (23068) hydrogen bonds : bond 0.04288 / 2.85 ( 796) hydrogen bonds : angle 4.74495 / 3.45 ( 2337) Misc. bond : bond 0.00943 / 0.49 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7362 (m-30) cc_final: 0.6911 (t0) REVERT: A 45 GLN cc_start: 0.7316 (mt0) cc_final: 0.6889 (mm-40) REVERT: A 50 SER cc_start: 0.7352 (t) cc_final: 0.6998 (p) REVERT: A 58 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6465 (pm20) REVERT: A 187 MET cc_start: 0.8040 (ttp) cc_final: 0.6939 (mmm) REVERT: A 194 ASP cc_start: 0.7860 (m-30) cc_final: 0.7579 (m-30) REVERT: A 196 GLN cc_start: 0.6522 (mt0) cc_final: 0.6204 (tt0) REVERT: A 217 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8084 (tm) REVERT: A 224 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6248 (tp30) REVERT: A 250 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6683 (pt0) REVERT: A 295 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6157 (mt-10) REVERT: A 343 ILE cc_start: 0.7071 (mm) cc_final: 0.6609 (pp) REVERT: A 352 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7287 (tttp) REVERT: A 373 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6436 (mm-30) REVERT: A 388 LYS cc_start: 0.7211 (mttp) cc_final: 0.6906 (mtmm) REVERT: A 485 GLU cc_start: 0.7757 (tt0) cc_final: 0.6676 (mm-30) REVERT: A 573 LYS cc_start: 0.8323 (tttt) cc_final: 0.7944 (ttmm) REVERT: A 604 GLU cc_start: 0.7325 (pt0) cc_final: 0.6771 (pp20) REVERT: A 612 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6826 (pm20) REVERT: A 627 ASN cc_start: 0.8336 (m-40) cc_final: 0.8069 (m110) REVERT: A 644 ARG cc_start: 0.8128 (mmt90) cc_final: 0.7504 (mpp-170) REVERT: A 774 GLU cc_start: 0.7082 (tp30) cc_final: 0.6744 (tt0) REVERT: A 783 LYS cc_start: 0.8250 (tmmt) cc_final: 0.7513 (tppt) REVERT: A 799 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 804 ARG cc_start: 0.7802 (tpt-90) cc_final: 0.6319 (mmt180) REVERT: A 860 LYS cc_start: 0.7537 (mttt) cc_final: 0.6987 (mmtm) REVERT: A 867 MET cc_start: 0.9135 (pp-130) cc_final: 0.8580 (ppp) REVERT: A 910 GLN cc_start: 0.7468 (mm110) cc_final: 0.7113 (mm-40) REVERT: A 934 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7487 (mmtt) REVERT: A 990 SER cc_start: 0.8105 (p) cc_final: 0.7844 (m) REVERT: A 1012 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5387 (mm-30) REVERT: A 1027 GLN cc_start: 0.8500 (tt0) cc_final: 0.8138 (tt0) REVERT: B 23 ASP cc_start: 0.7689 (t70) cc_final: 0.6782 (t0) REVERT: B 24 LYS cc_start: 0.7562 (pttm) cc_final: 0.6775 (mttp) REVERT: B 61 LYS cc_start: 0.7379 (ttmt) cc_final: 0.7062 (tttm) REVERT: B 62 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: B 187 MET cc_start: 0.8043 (ttp) cc_final: 0.6956 (tpp) REVERT: B 198 LYS cc_start: 0.7723 (mttt) cc_final: 0.7213 (pttt) REVERT: B 288 ASP cc_start: 0.6515 (OUTLIER) cc_final: 0.6122 (p0) REVERT: B 295 GLU cc_start: 0.6839 (tt0) cc_final: 0.6074 (mt-10) REVERT: B 315 LYS cc_start: 0.7481 (mmtp) cc_final: 0.6598 (mtpt) REVERT: B 354 GLN cc_start: 0.7744 (mt0) cc_final: 0.7326 (tm-30) REVERT: B 434 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6022 (mp10) REVERT: B 444 LYS cc_start: 0.8371 (pttt) cc_final: 0.7729 (ptpp) REVERT: B 454 PRO cc_start: 0.8020 (Cg_exo) cc_final: 0.7730 (Cg_endo) REVERT: B 485 GLU cc_start: 0.7997 (tt0) cc_final: 0.7304 (tp30) REVERT: B 512 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7212 (tp30) REVERT: B 573 LYS cc_start: 0.8221 (tttt) cc_final: 0.7926 (ttpp) REVERT: B 588 GLU cc_start: 0.8419 (pt0) cc_final: 0.8139 (mt-10) REVERT: B 597 GLU cc_start: 0.7626 (tt0) cc_final: 0.6652 (tp30) REVERT: B 627 ASN cc_start: 0.7915 (m-40) cc_final: 0.7621 (m-40) REVERT: B 652 LYS cc_start: 0.8267 (tttt) cc_final: 0.7813 (ttmm) REVERT: B 666 ARG cc_start: 0.7090 (mmt180) cc_final: 0.6381 (mmm-85) REVERT: B 734 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7352 (ttp-110) REVERT: B 744 GLN cc_start: 0.8271 (mt0) cc_final: 0.8013 (mt0) REVERT: B 783 LYS cc_start: 0.7971 (mttm) cc_final: 0.7336 (tttp) REVERT: B 804 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6438 (tpp-160) REVERT: B 813 LYS cc_start: 0.8650 (mtmp) cc_final: 0.7995 (mmtm) REVERT: B 824 ARG cc_start: 0.7299 (mtt-85) cc_final: 0.6643 (mtt90) REVERT: B 828 GLU cc_start: 0.7111 (mp0) cc_final: 0.6558 (mm-30) REVERT: B 888 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6717 (mtt) REVERT: B 933 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7065 (ttt90) REVERT: B 934 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6884 (tppp) REVERT: B 949 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6591 (mm) REVERT: B 999 THR cc_start: 0.6757 (t) cc_final: 0.6298 (p) outliers start: 34 outliers final: 16 residues processed: 269 average time/residue: 0.7127 time to fit residues: 209.3975 Evaluate side-chains 268 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 804 ARG Chi-restraints excluded: chain B residue 827 SER Chi-restraints excluded: chain B residue 888 MET Chi-restraints excluded: chain B residue 933 ARG Chi-restraints excluded: chain B residue 934 LYS Chi-restraints excluded: chain B residue 949 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 198 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 HIS A 780 GLN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 HIS ** 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 = 0.3807 r_free = 0.3807 target = 0.157845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125038 restraints weight = 16874.352| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.73 r_work: 0.3314 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17012 Z= 0.234 Angle : 0.640 9.741 23068 Z= 0.323 Chirality : 0.045 0.145 2467 Planarity : 0.005 0.055 2987 Dihedral : 7.518 88.656 2374 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.87 % Allowed : 13.95 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2042 helix: 0.95 (0.16), residues: 931 sheet: -0.57 (0.29), residues: 308 loop : -0.06 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 112 TYR 0.023 0.002 TYR B 817 PHE 0.026 0.002 PHE B 160 TRP 0.037 0.002 TRP A 371 HIS 0.008 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (17010) covalent geometry : angle 0.63990 / 0.32 (23068) hydrogen bonds : bond 0.04919 / 3.28 ( 796) hydrogen bonds : angle 5.02234 / 3.66 ( 2337) Misc. bond : bond 0.01760 / 0.91 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7226.92 seconds wall clock time: 123 minutes 42.05 seconds (7422.05 seconds total)