Starting phenix.real_space_refine on Fri Jun 27 11:57:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpr_26062/06_2025/7tpr_26062.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpr_26062/06_2025/7tpr_26062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tpr_26062/06_2025/7tpr_26062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpr_26062/06_2025/7tpr_26062.map" model { file = "/net/cci-nas-00/data/ceres_data/7tpr_26062/06_2025/7tpr_26062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpr_26062/06_2025/7tpr_26062.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 20167 2.51 5 N 5314 2.21 5 O 6107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31738 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8957 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1145, 8934 Classifications: {'peptide': 1145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 60, 'TRANS': 1084} Conformer: "B" Number of residues, atoms: 1145, 8934 Classifications: {'peptide': 1145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 60, 'TRANS': 1084} bond proxies already assigned to first conformer: 9121 Chain: "B" Number of atoms: 8957 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1145, 8934 Classifications: {'peptide': 1145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 60, 'TRANS': 1084} Conformer: "B" Number of residues, atoms: 1145, 8934 Classifications: {'peptide': 1145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 60, 'TRANS': 1084} bond proxies already assigned to first conformer: 9121 Chain: "C" Number of atoms: 8957 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1145, 8934 Classifications: {'peptide': 1145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 60, 'TRANS': 1084} Conformer: "B" Number of residues, atoms: 1145, 8934 Classifications: {'peptide': 1145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 60, 'TRANS': 1084} bond proxies already assigned to first conformer: 9121 Chain: "D" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 983 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "E" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 983 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "F" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATRP A 886 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 886 " occ=0.50 residue: pdb=" N ATRP B 886 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP B 886 " occ=0.50 residue: pdb=" N ATRP C 886 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP C 886 " occ=0.50 Time building chain proxies: 27.66, per 1000 atoms: 0.87 Number of scatterers: 31738 At special positions: 0 Unit cell: (157.508, 159.372, 215.292, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 6107 8.00 N 5314 7.00 C 20167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.07 Conformation dependent library (CDL) restraints added in 6.7 seconds 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7532 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 60 sheets defined 24.3% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.314A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.547A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.236A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.939A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.862A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.599A pdb=" N LEU A 629 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 679 through 685 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.570A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.752A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1159 removed outlier: 3.839A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A1151 " --> pdb=" O SER A1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 4.133A pdb=" N ASN B 149 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 150 " --> pdb=" O LYS B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 150' Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.807A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.546A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 679 through 685 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.592A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.592A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 831 removed outlier: 3.705A pdb=" N ASP B 830 " --> pdb=" O THR B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 846 through 855 removed outlier: 3.808A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.957A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1159 removed outlier: 4.105A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B1151 " --> pdb=" O SER B1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.739A pdb=" N VAL C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 159' Processing helix chain 'C' and resid 175 through 179 removed outlier: 3.948A pdb=" N ASP C 178 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 179 " --> pdb=" O LEU C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 175 through 179' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.640A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.350A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.601A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.314A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 620 through 624 removed outlier: 3.624A pdb=" N ILE C 624 " --> pdb=" O PRO C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.727A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 685 removed outlier: 3.796A pdb=" N SER C 683 " --> pdb=" O ASN C 679 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA C 684 " --> pdb=" O SER C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 690 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.758A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.643A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.752A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.547A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 843 Processing helix chain 'C' and resid 850 through 854 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.554A pdb=" N GLY C 889 " --> pdb=" O ATRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.256A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 964 Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.424A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1159 removed outlier: 3.747A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.517A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 4.073A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 4.073A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.582A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.124A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.834A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.223A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.545A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.984A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N MET F 109 " --> pdb=" O SER F 100 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N SER F 100 " --> pdb=" O MET F 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.984A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N MET F 109 " --> pdb=" O SER F 100 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N SER F 100 " --> pdb=" O MET F 109 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG F 32 " --> pdb=" O LYS F 52 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS F 52 " --> pdb=" O ARG F 32 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY F 50 " --> pdb=" O TYR F 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.598A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.530A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.394A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.531A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.418A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.953A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.058A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.808A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 245 through 246 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.447A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.301A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.056A pdb=" N TYR H 107 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N TYR H 102 " --> pdb=" O TYR H 107 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET H 109 " --> pdb=" O SER H 100 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N SER H 100 " --> pdb=" O MET H 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.056A pdb=" N TYR H 107 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N TYR H 102 " --> pdb=" O TYR H 107 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET H 109 " --> pdb=" O SER H 100 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N SER H 100 " --> pdb=" O MET H 109 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD7, first strand: chain 'B' and resid 714 through 728 removed outlier: 6.077A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.307A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1076 through 1078 removed outlier: 3.791A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 28 removed outlier: 4.148A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP C 64 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.408A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.208A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.910A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 5.771A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.481A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.491A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.577A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.577A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.269A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.874A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'D' and resid 11 through 13 Processing sheet with id=AG1, first strand: chain 'D' and resid 45 through 51 removed outlier: 5.416A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.734A pdb=" N SER E 127 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 33 " --> pdb=" O HIS E 99 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AG6, first strand: chain 'H' and resid 3 through 7 1380 hydrogen bonds defined for protein. 3657 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: 15.94 Time building geometry restraints manager: 8.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10300 1.35 - 1.47: 8577 1.47 - 1.60: 13443 1.60 - 1.73: 0 1.73 - 1.86: 196 Bond restraints: 32516 Sorted by residual: bond pdb=" N VAL B 620 " pdb=" CA VAL B 620 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.60e+00 bond pdb=" N ILE C1018 " pdb=" CA ILE C1018 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 7.04e+00 bond pdb=" N VAL B 615 " pdb=" CA VAL B 615 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 7.04e+00 bond pdb=" N GLU B 619 " pdb=" CA GLU B 619 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.90e+00 bond pdb=" N CYS B 617 " pdb=" CA CYS B 617 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.03e+00 ... (remaining 32511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 43674 2.19 - 4.39: 565 4.39 - 6.58: 33 6.58 - 8.77: 2 8.77 - 10.96: 2 Bond angle restraints: 44276 Sorted by residual: angle pdb=" CA CYS B 166 " pdb=" CB CYS B 166 " pdb=" SG CYS B 166 " ideal model delta sigma weight residual 114.40 125.36 -10.96 2.30e+00 1.89e-01 2.27e+01 angle pdb=" C LYS D 65 " pdb=" CA LYS D 65 " pdb=" CB LYS D 65 " ideal model delta sigma weight residual 116.63 111.10 5.53 1.16e+00 7.43e-01 2.27e+01 angle pdb=" C ASN B 709 " pdb=" N ASN B 710 " pdb=" CA ASN B 710 " ideal model delta sigma weight residual 121.54 130.55 -9.01 1.91e+00 2.74e-01 2.23e+01 angle pdb=" N GLN B 804 " pdb=" CA GLN B 804 " pdb=" C GLN B 804 " ideal model delta sigma weight residual 114.75 109.04 5.71 1.26e+00 6.30e-01 2.05e+01 angle pdb=" C VAL A 620 " pdb=" CA VAL A 620 " pdb=" CB VAL A 620 " ideal model delta sigma weight residual 114.35 110.16 4.19 1.06e+00 8.90e-01 1.56e+01 ... (remaining 44271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 17937 17.91 - 35.81: 1086 35.81 - 53.72: 177 53.72 - 71.62: 52 71.62 - 89.53: 30 Dihedral angle restraints: 19282 sinusoidal: 7467 harmonic: 11815 Sorted by residual: dihedral pdb=" CA ASN A 616 " pdb=" C ASN A 616 " pdb=" N CYS A 617 " pdb=" CA CYS A 617 " ideal model delta harmonic sigma weight residual 180.00 102.78 77.22 0 5.00e+00 4.00e-02 2.39e+02 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -169.36 83.36 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 14.00 79.00 1 1.00e+01 1.00e-02 7.77e+01 ... (remaining 19279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3625 0.043 - 0.086: 885 0.086 - 0.129: 361 0.129 - 0.172: 38 0.172 - 0.215: 3 Chirality restraints: 4912 Sorted by residual: chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA CYS B 166 " pdb=" N CYS B 166 " pdb=" C CYS B 166 " pdb=" CB CYS B 166 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA TYR C 266 " pdb=" N TYR C 266 " pdb=" C TYR C 266 " pdb=" CB TYR C 266 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 4909 not shown) Planarity restraints: 5763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 64 " 0.020 2.00e-02 2.50e+03 1.56e-02 6.12e+00 pdb=" CG TRP C 64 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP C 64 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 64 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 64 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 64 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 64 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 64 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 614 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C ASP B 614 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP B 614 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 615 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 38 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO B 39 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.027 5.00e-02 4.00e+02 ... (remaining 5760 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 589 2.66 - 3.22: 30783 3.22 - 3.78: 47467 3.78 - 4.34: 68109 4.34 - 4.90: 112786 Nonbonded interactions: 259734 Sorted by model distance: nonbonded pdb=" OG SER C 112 " pdb=" OE1 GLN C 134 " model vdw 2.103 3.040 nonbonded pdb=" O THR H 28 " pdb=" OG SER H 29 " model vdw 2.108 3.040 nonbonded pdb=" OG SER A 443 " pdb=" O PHE A 497 " model vdw 2.113 3.040 nonbonded pdb=" O LEU A 293 " pdb=" OG1 THR A 632 " model vdw 2.132 3.040 nonbonded pdb=" O ASN B 709 " pdb=" OD1 ASN B 710 " model vdw 2.155 3.040 ... (remaining 259729 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 885 or resid 887 through 1137 or resid 1139 thr \ ough 1159)) selection = (chain 'B' and (resid 15 through 885 or resid 887 through 1137 or resid 1139 thr \ ough 1159)) selection = (chain 'C' and (resid 15 through 885 or resid 887 through 1137 or resid 1139 thr \ ough 1159)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.050 Extract box with map and model: 1.410 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 87.340 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32566 Z= 0.189 Angle : 0.614 10.965 44376 Z= 0.345 Chirality : 0.045 0.215 4912 Planarity : 0.004 0.048 5763 Dihedral : 12.508 89.526 11600 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.46 % Favored : 93.08 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4070 helix: 0.78 (0.19), residues: 804 sheet: -0.18 (0.16), residues: 1014 loop : -1.76 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 64 HIS 0.004 0.001 HIS A1064 PHE 0.029 0.001 PHE B 497 TYR 0.020 0.001 TYR B 265 ARG 0.007 0.001 ARG A1014 Details of bonding type rmsd hydrogen bonds : bond 0.13620 ( 1298) hydrogen bonds : angle 7.44470 ( 3657) SS BOND : bond 0.00463 ( 50) SS BOND : angle 1.76434 ( 100) covalent geometry : bond 0.00412 (32516) covalent geometry : angle 0.60909 (44276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 625 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7385 (mtpp) cc_final: 0.7105 (mtpm) REVERT: A 773 GLU cc_start: 0.7032 (tt0) cc_final: 0.6818 (tt0) REVERT: B 49 HIS cc_start: 0.7905 (t70) cc_final: 0.7527 (t70) REVERT: B 386 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7607 (mtpp) REVERT: B 402 ILE cc_start: 0.8272 (pt) cc_final: 0.8054 (mm) REVERT: B 450 ASN cc_start: 0.8705 (m110) cc_final: 0.8442 (m-40) REVERT: B 1141 LEU cc_start: 0.8485 (tt) cc_final: 0.8093 (tm) REVERT: C 129 LYS cc_start: 0.7558 (ttmt) cc_final: 0.7209 (ptmm) REVERT: C 228 ASP cc_start: 0.6627 (p0) cc_final: 0.6380 (p0) REVERT: C 239 GLN cc_start: 0.7882 (pp30) cc_final: 0.7668 (pp30) REVERT: C 555 SER cc_start: 0.7734 (t) cc_final: 0.7272 (m) REVERT: C 574 ASP cc_start: 0.6982 (t0) cc_final: 0.6749 (t0) REVERT: C 642 VAL cc_start: 0.8638 (t) cc_final: 0.8383 (p) REVERT: C 835 LYS cc_start: 0.8004 (tttp) cc_final: 0.7487 (tttp) REVERT: C 839 ASP cc_start: 0.7182 (m-30) cc_final: 0.6793 (m-30) REVERT: C 950 ASP cc_start: 0.6974 (m-30) cc_final: 0.6587 (m-30) REVERT: G 109 MET cc_start: -0.0992 (mmm) cc_final: -0.1720 (mmm) outliers start: 5 outliers final: 2 residues processed: 627 average time/residue: 1.4061 time to fit residues: 1043.3665 Evaluate side-chains 558 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 556 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain B residue 439 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 5.9990 chunk 306 optimal weight: 1.9990 chunk 169 optimal weight: 0.0870 chunk 104 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 316 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 192 optimal weight: 0.5980 chunk 235 optimal weight: 0.9990 chunk 366 optimal weight: 30.0000 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 137 ASN A 234 ASN A 394 ASN A 448 ASN A 498 GLN A 564 GLN A 613 GLN A 957 GLN A 969 ASN A1010 GLN A1054 GLN B 49 HIS B 137 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 439 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B 755 GLN B 804 GLN C 30 ASN C 52 GLN C 440 ASN C 580 GLN C 751 ASN C 907 ASN C1074 ASN D 123 GLN G 57 ASN H 104 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.195810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.151297 restraints weight = 98363.524| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 3.19 r_work: 0.3730 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32566 Z= 0.151 Angle : 0.655 10.854 44376 Z= 0.345 Chirality : 0.048 0.336 4912 Planarity : 0.004 0.068 5763 Dihedral : 5.333 75.384 4432 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.45 % Favored : 94.14 % Rotamer: Outliers : 1.05 % Allowed : 7.87 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4070 helix: 1.53 (0.19), residues: 789 sheet: 0.00 (0.16), residues: 1001 loop : -1.63 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 64 HIS 0.005 0.001 HIS A 519 PHE 0.030 0.002 PHE H 68 TYR 0.033 0.002 TYR B 369 ARG 0.010 0.001 ARG C 319 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 1298) hydrogen bonds : angle 6.02561 ( 3657) SS BOND : bond 0.00436 ( 50) SS BOND : angle 1.69312 ( 100) covalent geometry : bond 0.00343 (32516) covalent geometry : angle 0.65102 (44276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 616 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8298 (tp) cc_final: 0.8030 (tm) REVERT: B 58 PHE cc_start: 0.8157 (m-10) cc_final: 0.7807 (m-10) REVERT: B 164 ASN cc_start: 0.7666 (t0) cc_final: 0.7289 (t0) REVERT: B 165 ASN cc_start: 0.7123 (m-40) cc_final: 0.6651 (m110) REVERT: B 453 TYR cc_start: 0.7215 (p90) cc_final: 0.6670 (p90) REVERT: B 854 LYS cc_start: 0.8592 (ptmm) cc_final: 0.8209 (ptmt) REVERT: B 950 ASP cc_start: 0.7602 (m-30) cc_final: 0.7245 (m-30) REVERT: B 1141 LEU cc_start: 0.8648 (tt) cc_final: 0.8149 (tm) REVERT: C 129 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7867 (ptmm) REVERT: C 278 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7877 (tptp) REVERT: C 319 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7664 (mtm-85) REVERT: C 555 SER cc_start: 0.7973 (t) cc_final: 0.7352 (m) REVERT: C 574 ASP cc_start: 0.7633 (t0) cc_final: 0.7363 (t0) REVERT: C 819 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7227 (tt0) REVERT: C 950 ASP cc_start: 0.7522 (m-30) cc_final: 0.7215 (m-30) REVERT: C 1031 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7959 (mt-10) REVERT: C 1084 ASP cc_start: 0.7939 (t70) cc_final: 0.7629 (t70) REVERT: C 1118 ASP cc_start: 0.7844 (t0) cc_final: 0.7632 (t0) REVERT: G 83 MET cc_start: 0.2878 (tpt) cc_final: 0.2334 (tpt) REVERT: G 109 MET cc_start: -0.0932 (mmm) cc_final: -0.1510 (mmm) REVERT: H 31 SER cc_start: 0.8859 (m) cc_final: 0.8642 (t) REVERT: H 36 TRP cc_start: 0.8158 (m100) cc_final: 0.7941 (m100) REVERT: H 53 ARG cc_start: 0.8497 (ptm-80) cc_final: 0.8282 (ptm-80) REVERT: H 93 MET cc_start: 0.6165 (tpt) cc_final: 0.5940 (tpt) outliers start: 37 outliers final: 11 residues processed: 629 average time/residue: 1.4236 time to fit residues: 1067.7158 Evaluate side-chains 589 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 578 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 360 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 304 optimal weight: 0.9990 chunk 338 optimal weight: 2.9990 chunk 327 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 307 optimal weight: 0.6980 chunk 267 optimal weight: 50.0000 chunk 261 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 498 GLN A 703 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 969 ASN A1002 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1005 GLN B1011 GLN B1101 HIS C 52 GLN C 804 GLN C 969 ASN H 104 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.194644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.150318 restraints weight = 93297.923| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.05 r_work: 0.3709 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 32566 Z= 0.215 Angle : 0.664 10.112 44376 Z= 0.349 Chirality : 0.049 0.362 4912 Planarity : 0.005 0.066 5763 Dihedral : 5.254 74.296 4428 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.06 % Favored : 93.59 % Rotamer: Outliers : 1.60 % Allowed : 9.55 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4070 helix: 1.50 (0.19), residues: 795 sheet: 0.08 (0.16), residues: 1007 loop : -1.66 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 64 HIS 0.005 0.001 HIS A1064 PHE 0.025 0.002 PHE A 238 TYR 0.031 0.002 TYR A 265 ARG 0.010 0.001 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 1298) hydrogen bonds : angle 5.86027 ( 3657) SS BOND : bond 0.00491 ( 50) SS BOND : angle 1.91727 ( 100) covalent geometry : bond 0.00510 (32516) covalent geometry : angle 0.65870 (44276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 593 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7985 (mm110) REVERT: A 651 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8721 (mm) REVERT: B 58 PHE cc_start: 0.8192 (m-10) cc_final: 0.7898 (m-10) REVERT: B 164 ASN cc_start: 0.7658 (t0) cc_final: 0.7437 (t0) REVERT: B 297 SER cc_start: 0.7975 (m) cc_final: 0.7745 (p) REVERT: B 439 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7895 (t0) REVERT: B 453 TYR cc_start: 0.7192 (p90) cc_final: 0.6852 (p90) REVERT: B 524 VAL cc_start: 0.7537 (p) cc_final: 0.7334 (p) REVERT: B 702 GLU cc_start: 0.7582 (tp30) cc_final: 0.7350 (tp30) REVERT: B 703 ASN cc_start: 0.8217 (t0) cc_final: 0.7979 (t0) REVERT: B 773 GLU cc_start: 0.7748 (tt0) cc_final: 0.7516 (tt0) REVERT: B 854 LYS cc_start: 0.8729 (ptmm) cc_final: 0.8405 (ptmt) REVERT: B 859 THR cc_start: 0.8654 (m) cc_final: 0.8406 (p) REVERT: B 936 ASP cc_start: 0.7338 (m-30) cc_final: 0.7112 (m-30) REVERT: B 950 ASP cc_start: 0.7657 (m-30) cc_final: 0.7267 (m-30) REVERT: B 959 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8510 (mp) REVERT: C 129 LYS cc_start: 0.8312 (ttmt) cc_final: 0.8022 (ttmm) REVERT: C 190 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7143 (mtt90) REVERT: C 195 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8162 (ttpt) REVERT: C 574 ASP cc_start: 0.7635 (t0) cc_final: 0.7367 (t0) REVERT: C 651 ILE cc_start: 0.8978 (pt) cc_final: 0.8723 (mp) REVERT: C 950 ASP cc_start: 0.7515 (m-30) cc_final: 0.7215 (m-30) REVERT: C 1084 ASP cc_start: 0.7956 (t70) cc_final: 0.7609 (t70) REVERT: F 36 TRP cc_start: 0.7259 (m-90) cc_final: 0.7044 (m100) REVERT: G 83 MET cc_start: 0.2837 (tpt) cc_final: 0.2264 (tpt) REVERT: H 36 TRP cc_start: 0.8287 (m100) cc_final: 0.8014 (m100) REVERT: H 93 MET cc_start: 0.6225 (tpt) cc_final: 0.5928 (tpt) outliers start: 56 outliers final: 26 residues processed: 608 average time/residue: 1.4212 time to fit residues: 1031.0805 Evaluate side-chains 603 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 574 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 31 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 277 optimal weight: 6.9990 chunk 401 optimal weight: 3.9990 chunk 267 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 334 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 309 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN B 134 GLN B 440 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 901 GLN B 965 GLN B1101 HIS C 81 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN F 72 GLN G 72 GLN H 3 GLN H 104 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.195149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.149089 restraints weight = 116511.277| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.85 r_work: 0.3702 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32566 Z= 0.153 Angle : 0.631 17.457 44376 Z= 0.327 Chirality : 0.046 0.279 4912 Planarity : 0.004 0.055 5763 Dihedral : 5.102 71.590 4428 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.52 % Favored : 94.18 % Rotamer: Outliers : 1.28 % Allowed : 11.34 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4070 helix: 1.56 (0.19), residues: 802 sheet: 0.12 (0.15), residues: 1034 loop : -1.62 (0.12), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.003 0.001 HIS A1064 PHE 0.022 0.001 PHE A 238 TYR 0.029 0.001 TYR B 170 ARG 0.009 0.001 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 1298) hydrogen bonds : angle 5.69085 ( 3657) SS BOND : bond 0.00388 ( 50) SS BOND : angle 1.64227 ( 100) covalent geometry : bond 0.00354 (32516) covalent geometry : angle 0.62718 (44276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 584 time to evaluate : 4.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8303 (tp) cc_final: 0.8022 (tm) REVERT: A 498 GLN cc_start: 0.8216 (mm-40) cc_final: 0.8008 (mm110) REVERT: A 994 ASP cc_start: 0.7723 (t0) cc_final: 0.7420 (t0) REVERT: B 164 ASN cc_start: 0.7682 (t0) cc_final: 0.7455 (t0) REVERT: B 297 SER cc_start: 0.7946 (m) cc_final: 0.7706 (p) REVERT: B 331 ASN cc_start: 0.5051 (m-40) cc_final: 0.4437 (m110) REVERT: B 361 CYS cc_start: 0.6504 (p) cc_final: 0.5956 (p) REVERT: B 430 THR cc_start: 0.8782 (t) cc_final: 0.8557 (m) REVERT: B 453 TYR cc_start: 0.7088 (p90) cc_final: 0.6850 (p90) REVERT: B 524 VAL cc_start: 0.7521 (OUTLIER) cc_final: 0.7291 (p) REVERT: B 702 GLU cc_start: 0.7653 (tp30) cc_final: 0.7414 (tp30) REVERT: B 703 ASN cc_start: 0.8242 (t0) cc_final: 0.7996 (t0) REVERT: B 854 LYS cc_start: 0.8717 (ptmm) cc_final: 0.8363 (ptmt) REVERT: B 859 THR cc_start: 0.8676 (m) cc_final: 0.8426 (p) REVERT: B 936 ASP cc_start: 0.7374 (m-30) cc_final: 0.7135 (m-30) REVERT: B 950 ASP cc_start: 0.7736 (m-30) cc_final: 0.7329 (m-30) REVERT: B 1010 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: C 120 VAL cc_start: 0.8822 (t) cc_final: 0.8556 (m) REVERT: C 129 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8130 (ttmm) REVERT: C 195 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8048 (ttpt) REVERT: C 574 ASP cc_start: 0.7661 (t0) cc_final: 0.7386 (t0) REVERT: C 651 ILE cc_start: 0.8960 (pt) cc_final: 0.8705 (mp) REVERT: C 950 ASP cc_start: 0.7593 (m-30) cc_final: 0.7269 (m-30) REVERT: C 1084 ASP cc_start: 0.8053 (t70) cc_final: 0.7714 (t70) REVERT: E 83 MET cc_start: 0.7270 (ppp) cc_final: 0.6585 (ppp) REVERT: G 83 MET cc_start: 0.2859 (tpt) cc_final: 0.2344 (tpt) REVERT: G 109 MET cc_start: -0.0593 (mmm) cc_final: -0.1408 (mmm) REVERT: H 36 TRP cc_start: 0.8330 (m100) cc_final: 0.8038 (m100) REVERT: H 93 MET cc_start: 0.6267 (tpt) cc_final: 0.5924 (tpt) outliers start: 45 outliers final: 22 residues processed: 599 average time/residue: 2.0000 time to fit residues: 1450.5394 Evaluate side-chains 598 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 574 time to evaluate : 6.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 282 optimal weight: 2.9990 chunk 347 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 370 optimal weight: 9.9990 chunk 285 optimal weight: 0.7980 chunk 286 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 969 ASN B 409 GLN B 437 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 804 GLN B1101 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN H 3 GLN H 104 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.196187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151124 restraints weight = 100745.193| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.29 r_work: 0.3702 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32566 Z= 0.136 Angle : 0.617 15.141 44376 Z= 0.320 Chirality : 0.046 0.300 4912 Planarity : 0.004 0.060 5763 Dihedral : 4.972 70.681 4428 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.74 % Favored : 93.99 % Rotamer: Outliers : 1.51 % Allowed : 12.03 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4070 helix: 1.67 (0.19), residues: 794 sheet: 0.19 (0.16), residues: 1014 loop : -1.59 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 64 HIS 0.003 0.000 HIS A 519 PHE 0.020 0.001 PHE A 238 TYR 0.030 0.001 TYR B 170 ARG 0.010 0.001 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 1298) hydrogen bonds : angle 5.55237 ( 3657) SS BOND : bond 0.00370 ( 50) SS BOND : angle 1.51266 ( 100) covalent geometry : bond 0.00310 (32516) covalent geometry : angle 0.61335 (44276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 582 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8302 (tp) cc_final: 0.8035 (tm) REVERT: A 498 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7941 (mm110) REVERT: A 651 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8721 (mm) REVERT: B 297 SER cc_start: 0.7887 (m) cc_final: 0.7654 (p) REVERT: B 331 ASN cc_start: 0.5293 (m-40) cc_final: 0.4925 (m110) REVERT: B 361 CYS cc_start: 0.6404 (p) cc_final: 0.5866 (p) REVERT: B 453 TYR cc_start: 0.7168 (p90) cc_final: 0.6813 (p90) REVERT: B 465 GLU cc_start: 0.7113 (pm20) cc_final: 0.6890 (pm20) REVERT: B 524 VAL cc_start: 0.7395 (OUTLIER) cc_final: 0.7159 (p) REVERT: B 702 GLU cc_start: 0.7582 (tp30) cc_final: 0.7381 (tp30) REVERT: B 703 ASN cc_start: 0.8205 (t0) cc_final: 0.7998 (t0) REVERT: B 773 GLU cc_start: 0.7889 (tt0) cc_final: 0.7664 (tt0) REVERT: B 825 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8273 (mtmm) REVERT: B 854 LYS cc_start: 0.8682 (ptmm) cc_final: 0.8364 (ptmt) REVERT: B 859 THR cc_start: 0.8663 (m) cc_final: 0.8405 (p) REVERT: B 936 ASP cc_start: 0.7325 (m-30) cc_final: 0.7085 (m-30) REVERT: B 950 ASP cc_start: 0.7682 (m-30) cc_final: 0.7281 (m-30) REVERT: B 1010 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: C 120 VAL cc_start: 0.8809 (t) cc_final: 0.8523 (m) REVERT: C 129 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8101 (ttmm) REVERT: C 195 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8004 (ttpt) REVERT: C 574 ASP cc_start: 0.7613 (t0) cc_final: 0.7317 (t0) REVERT: C 651 ILE cc_start: 0.8908 (pt) cc_final: 0.8672 (mp) REVERT: C 819 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7132 (tt0) REVERT: C 950 ASP cc_start: 0.7573 (m-30) cc_final: 0.7254 (m-30) REVERT: C 1084 ASP cc_start: 0.7982 (t70) cc_final: 0.7647 (t70) REVERT: E 83 MET cc_start: 0.6405 (ppp) cc_final: 0.5960 (ppp) REVERT: G 83 MET cc_start: 0.2832 (tpt) cc_final: 0.2335 (tpt) REVERT: H 36 TRP cc_start: 0.8263 (m100) cc_final: 0.8015 (m100) REVERT: H 93 MET cc_start: 0.6297 (tpt) cc_final: 0.6094 (tpt) outliers start: 53 outliers final: 30 residues processed: 597 average time/residue: 1.4598 time to fit residues: 1050.5054 Evaluate side-chains 611 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 578 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 126 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 302 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 255 optimal weight: 0.0030 chunk 31 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 64 optimal weight: 0.0870 chunk 171 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.5972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 613 GLN B1005 GLN B1101 HIS C 81 ASN C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN H 3 GLN H 104 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.196317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.150185 restraints weight = 93492.513| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 3.58 r_work: 0.3735 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32566 Z= 0.127 Angle : 0.608 14.144 44376 Z= 0.315 Chirality : 0.045 0.309 4912 Planarity : 0.004 0.071 5763 Dihedral : 4.845 65.497 4428 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.52 % Favored : 94.23 % Rotamer: Outliers : 1.40 % Allowed : 12.82 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4070 helix: 1.78 (0.19), residues: 790 sheet: 0.24 (0.16), residues: 1017 loop : -1.57 (0.12), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 64 HIS 0.007 0.001 HIS C 66 PHE 0.019 0.001 PHE A 238 TYR 0.029 0.001 TYR B 170 ARG 0.008 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 1298) hydrogen bonds : angle 5.46810 ( 3657) SS BOND : bond 0.00325 ( 50) SS BOND : angle 1.58187 ( 100) covalent geometry : bond 0.00290 (32516) covalent geometry : angle 0.60445 (44276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 580 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8263 (tp) cc_final: 0.7982 (tm) REVERT: A 347 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7878 (t80) REVERT: A 498 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7968 (mm110) REVERT: A 651 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8706 (mm) REVERT: A 994 ASP cc_start: 0.7448 (t0) cc_final: 0.7021 (t0) REVERT: A 1141 LEU cc_start: 0.8602 (tp) cc_final: 0.8389 (tm) REVERT: B 58 PHE cc_start: 0.8151 (m-10) cc_final: 0.7865 (m-10) REVERT: B 202 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8246 (mmtt) REVERT: B 453 TYR cc_start: 0.6981 (p90) cc_final: 0.6722 (p90) REVERT: B 702 GLU cc_start: 0.7647 (tp30) cc_final: 0.7439 (tp30) REVERT: B 703 ASN cc_start: 0.8202 (t0) cc_final: 0.7992 (t0) REVERT: B 854 LYS cc_start: 0.8662 (ptmm) cc_final: 0.8364 (ptmt) REVERT: B 859 THR cc_start: 0.8671 (m) cc_final: 0.8419 (p) REVERT: B 936 ASP cc_start: 0.7249 (m-30) cc_final: 0.7012 (m-30) REVERT: B 950 ASP cc_start: 0.7610 (m-30) cc_final: 0.7201 (m-30) REVERT: B 995 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7791 (mtm-85) REVERT: B 1010 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: C 129 LYS cc_start: 0.8406 (ttmt) cc_final: 0.8109 (ttmm) REVERT: C 195 LYS cc_start: 0.8511 (ttpt) cc_final: 0.7909 (ttpt) REVERT: C 553 THR cc_start: 0.8305 (m) cc_final: 0.8064 (p) REVERT: C 574 ASP cc_start: 0.7583 (t0) cc_final: 0.7293 (t0) REVERT: C 651 ILE cc_start: 0.8902 (pt) cc_final: 0.8668 (mp) REVERT: C 950 ASP cc_start: 0.7436 (m-30) cc_final: 0.7123 (m-30) REVERT: C 1084 ASP cc_start: 0.7983 (t70) cc_final: 0.7687 (t70) REVERT: E 34 MET cc_start: 0.7662 (tmm) cc_final: 0.6921 (tmm) REVERT: E 83 MET cc_start: 0.7122 (ppp) cc_final: 0.6595 (ppp) REVERT: G 83 MET cc_start: 0.2878 (tpt) cc_final: 0.2377 (tpt) REVERT: H 36 TRP cc_start: 0.8325 (m100) cc_final: 0.8088 (m100) REVERT: H 93 MET cc_start: 0.6178 (tpt) cc_final: 0.5975 (tpt) outliers start: 49 outliers final: 29 residues processed: 599 average time/residue: 1.6206 time to fit residues: 1165.8287 Evaluate side-chains 603 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 569 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 61 optimal weight: 10.0000 chunk 379 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 241 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 398 optimal weight: 1.9990 chunk 149 optimal weight: 0.0470 chunk 184 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 397 optimal weight: 4.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1101 HIS C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 969 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.195578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.148972 restraints weight = 110971.205| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 3.70 r_work: 0.3702 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32566 Z= 0.176 Angle : 0.633 12.975 44376 Z= 0.328 Chirality : 0.047 0.346 4912 Planarity : 0.004 0.101 5763 Dihedral : 4.887 64.812 4428 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.69 % Favored : 94.06 % Rotamer: Outliers : 1.23 % Allowed : 13.42 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4070 helix: 1.69 (0.19), residues: 792 sheet: 0.25 (0.16), residues: 1013 loop : -1.58 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 64 HIS 0.006 0.001 HIS C 66 PHE 0.020 0.002 PHE B 497 TYR 0.030 0.001 TYR B 170 ARG 0.011 0.001 ARG C 995 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 1298) hydrogen bonds : angle 5.51222 ( 3657) SS BOND : bond 0.00442 ( 50) SS BOND : angle 1.75691 ( 100) covalent geometry : bond 0.00419 (32516) covalent geometry : angle 0.62775 (44276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 576 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7939 (t80) REVERT: A 408 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7861 (ptp-110) REVERT: A 617 CYS cc_start: 0.2664 (OUTLIER) cc_final: 0.2346 (m) REVERT: A 651 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8716 (mm) REVERT: B 58 PHE cc_start: 0.8185 (m-10) cc_final: 0.7868 (m-10) REVERT: B 108 THR cc_start: 0.8345 (p) cc_final: 0.8123 (t) REVERT: B 177 MET cc_start: -0.1367 (mpt) cc_final: -0.1821 (mpt) REVERT: B 202 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8261 (mmtt) REVERT: B 393 THR cc_start: 0.8776 (p) cc_final: 0.8438 (t) REVERT: B 453 TYR cc_start: 0.7052 (p90) cc_final: 0.6769 (p90) REVERT: B 773 GLU cc_start: 0.7921 (tt0) cc_final: 0.7665 (tt0) REVERT: B 854 LYS cc_start: 0.8687 (ptmm) cc_final: 0.8391 (ptmt) REVERT: B 859 THR cc_start: 0.8681 (m) cc_final: 0.8430 (p) REVERT: B 936 ASP cc_start: 0.7361 (m-30) cc_final: 0.7118 (m-30) REVERT: B 950 ASP cc_start: 0.7705 (m-30) cc_final: 0.7302 (m-30) REVERT: B 1010 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: C 32 PHE cc_start: 0.7434 (m-10) cc_final: 0.7227 (m-10) REVERT: C 106 PHE cc_start: 0.8366 (m-80) cc_final: 0.7778 (m-80) REVERT: C 120 VAL cc_start: 0.8844 (t) cc_final: 0.8562 (m) REVERT: C 129 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8153 (ttmm) REVERT: C 195 LYS cc_start: 0.8552 (ttpt) cc_final: 0.7960 (ttpt) REVERT: C 553 THR cc_start: 0.8314 (m) cc_final: 0.8097 (p) REVERT: C 574 ASP cc_start: 0.7672 (t0) cc_final: 0.7390 (t0) REVERT: C 651 ILE cc_start: 0.8944 (pt) cc_final: 0.8704 (mp) REVERT: C 950 ASP cc_start: 0.7563 (m-30) cc_final: 0.7252 (m-30) REVERT: C 1031 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7915 (mt-10) REVERT: C 1084 ASP cc_start: 0.8046 (t70) cc_final: 0.7762 (t70) REVERT: E 34 MET cc_start: 0.7726 (tmm) cc_final: 0.7104 (tmm) REVERT: E 83 MET cc_start: 0.7109 (ppp) cc_final: 0.6584 (ppp) REVERT: G 83 MET cc_start: 0.2955 (tpt) cc_final: 0.2425 (tpt) REVERT: G 109 MET cc_start: -0.0168 (mmm) cc_final: -0.0555 (mmm) REVERT: H 36 TRP cc_start: 0.8341 (m100) cc_final: 0.8091 (m100) REVERT: H 93 MET cc_start: 0.6233 (tpt) cc_final: 0.5974 (tpt) outliers start: 43 outliers final: 32 residues processed: 590 average time/residue: 1.4582 time to fit residues: 1026.4205 Evaluate side-chains 608 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 571 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain H residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 346 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 330 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 339 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 371 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 853 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 703 ASN B1005 GLN B1101 HIS C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 969 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.195788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.149037 restraints weight = 103050.108| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.58 r_work: 0.3711 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32566 Z= 0.150 Angle : 0.619 12.398 44376 Z= 0.321 Chirality : 0.046 0.351 4912 Planarity : 0.004 0.060 5763 Dihedral : 4.825 63.968 4428 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.40 % Favored : 94.36 % Rotamer: Outliers : 1.54 % Allowed : 13.48 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4070 helix: 1.76 (0.19), residues: 788 sheet: 0.26 (0.16), residues: 1007 loop : -1.58 (0.12), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 64 HIS 0.005 0.001 HIS C 66 PHE 0.019 0.001 PHE A 238 TYR 0.030 0.001 TYR B 170 ARG 0.009 0.001 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 1298) hydrogen bonds : angle 5.46061 ( 3657) SS BOND : bond 0.00396 ( 50) SS BOND : angle 1.58998 ( 100) covalent geometry : bond 0.00353 (32516) covalent geometry : angle 0.61467 (44276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 578 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8282 (tp) cc_final: 0.8019 (tm) REVERT: A 617 CYS cc_start: 0.2595 (OUTLIER) cc_final: 0.2311 (m) REVERT: A 651 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8710 (mm) REVERT: B 58 PHE cc_start: 0.8191 (m-10) cc_final: 0.7869 (m-10) REVERT: B 108 THR cc_start: 0.8323 (p) cc_final: 0.8099 (t) REVERT: B 177 MET cc_start: -0.1327 (mpt) cc_final: -0.1735 (mpt) REVERT: B 393 THR cc_start: 0.8775 (p) cc_final: 0.8483 (t) REVERT: B 453 TYR cc_start: 0.7051 (p90) cc_final: 0.6734 (p90) REVERT: B 854 LYS cc_start: 0.8612 (ptmm) cc_final: 0.8303 (ptmt) REVERT: B 859 THR cc_start: 0.8686 (m) cc_final: 0.8424 (p) REVERT: B 936 ASP cc_start: 0.7311 (m-30) cc_final: 0.7061 (m-30) REVERT: B 950 ASP cc_start: 0.7659 (m-30) cc_final: 0.7241 (m-30) REVERT: B 1010 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: C 106 PHE cc_start: 0.8376 (m-80) cc_final: 0.7794 (m-80) REVERT: C 120 VAL cc_start: 0.8850 (t) cc_final: 0.8568 (m) REVERT: C 129 LYS cc_start: 0.8389 (ttmt) cc_final: 0.8102 (ttmm) REVERT: C 195 LYS cc_start: 0.8566 (ttpt) cc_final: 0.7969 (ttpt) REVERT: C 553 THR cc_start: 0.8299 (m) cc_final: 0.8071 (p) REVERT: C 574 ASP cc_start: 0.7664 (t0) cc_final: 0.7375 (t0) REVERT: C 651 ILE cc_start: 0.8937 (pt) cc_final: 0.8693 (mp) REVERT: C 950 ASP cc_start: 0.7532 (m-30) cc_final: 0.7217 (m-30) REVERT: C 1031 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7934 (mt-10) REVERT: C 1084 ASP cc_start: 0.8033 (t70) cc_final: 0.7738 (t70) REVERT: D 18 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6235 (mp) REVERT: E 34 MET cc_start: 0.7613 (tmm) cc_final: 0.7132 (tmm) REVERT: E 83 MET cc_start: 0.6880 (ppp) cc_final: 0.6472 (ppp) REVERT: G 83 MET cc_start: 0.2828 (tpt) cc_final: 0.2346 (tpt) REVERT: G 109 MET cc_start: -0.0299 (mmm) cc_final: -0.0660 (mmm) REVERT: H 36 TRP cc_start: 0.8325 (m100) cc_final: 0.7690 (m100) REVERT: H 93 MET cc_start: 0.6227 (tpt) cc_final: 0.5966 (tpt) outliers start: 54 outliers final: 39 residues processed: 597 average time/residue: 1.3940 time to fit residues: 990.8112 Evaluate side-chains 622 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 579 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 356 optimal weight: 30.0000 chunk 66 optimal weight: 0.0870 chunk 219 optimal weight: 0.9990 chunk 226 optimal weight: 0.0040 chunk 11 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 331 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.4972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 501 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 703 ASN B1101 HIS C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.196855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.152060 restraints weight = 106753.163| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 3.36 r_work: 0.3712 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32566 Z= 0.123 Angle : 0.609 11.917 44376 Z= 0.316 Chirality : 0.045 0.364 4912 Planarity : 0.004 0.061 5763 Dihedral : 4.757 63.283 4428 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.54 % Favored : 94.21 % Rotamer: Outliers : 1.20 % Allowed : 14.08 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4070 helix: 1.79 (0.19), residues: 798 sheet: 0.23 (0.16), residues: 1023 loop : -1.55 (0.12), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 64 HIS 0.005 0.000 HIS C 66 PHE 0.019 0.001 PHE B 497 TYR 0.031 0.001 TYR B 170 ARG 0.009 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 1298) hydrogen bonds : angle 5.40696 ( 3657) SS BOND : bond 0.00360 ( 50) SS BOND : angle 1.43886 ( 100) covalent geometry : bond 0.00281 (32516) covalent geometry : angle 0.60633 (44276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 578 time to evaluate : 3.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8281 (tp) cc_final: 0.8041 (tm) REVERT: A 617 CYS cc_start: 0.2467 (OUTLIER) cc_final: 0.2186 (m) REVERT: B 58 PHE cc_start: 0.8197 (m-10) cc_final: 0.7907 (m-10) REVERT: B 177 MET cc_start: -0.1411 (mpt) cc_final: -0.1784 (mpt) REVERT: B 393 THR cc_start: 0.8749 (p) cc_final: 0.8468 (t) REVERT: B 453 TYR cc_start: 0.7062 (p90) cc_final: 0.6760 (p90) REVERT: B 854 LYS cc_start: 0.8596 (ptmm) cc_final: 0.8303 (ptmt) REVERT: B 859 THR cc_start: 0.8698 (m) cc_final: 0.8448 (p) REVERT: B 936 ASP cc_start: 0.7258 (m-30) cc_final: 0.7012 (m-30) REVERT: B 950 ASP cc_start: 0.7689 (m-30) cc_final: 0.7252 (m-30) REVERT: B 1010 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: C 120 VAL cc_start: 0.8825 (t) cc_final: 0.8553 (m) REVERT: C 129 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8124 (ttmm) REVERT: C 195 LYS cc_start: 0.8571 (ttpt) cc_final: 0.7952 (ttpt) REVERT: C 553 THR cc_start: 0.8293 (m) cc_final: 0.8074 (p) REVERT: C 574 ASP cc_start: 0.7663 (t0) cc_final: 0.7372 (t0) REVERT: C 651 ILE cc_start: 0.8907 (pt) cc_final: 0.8685 (mt) REVERT: C 819 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7112 (tt0) REVERT: C 950 ASP cc_start: 0.7531 (m-30) cc_final: 0.7214 (m-30) REVERT: C 1084 ASP cc_start: 0.8055 (t70) cc_final: 0.7754 (t70) REVERT: D 18 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6265 (mp) REVERT: E 34 MET cc_start: 0.7482 (tmm) cc_final: 0.7123 (tmm) REVERT: E 83 MET cc_start: 0.6525 (ppp) cc_final: 0.6227 (ppp) REVERT: F 83 MET cc_start: 0.7108 (mmm) cc_final: 0.6516 (mmm) REVERT: G 83 MET cc_start: 0.2834 (tpt) cc_final: 0.2368 (tpt) REVERT: G 109 MET cc_start: -0.0208 (mmm) cc_final: -0.0515 (mmm) REVERT: H 93 MET cc_start: 0.6295 (tpt) cc_final: 0.5959 (tpt) outliers start: 42 outliers final: 32 residues processed: 591 average time/residue: 2.0678 time to fit residues: 1472.0997 Evaluate side-chains 608 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 573 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 265 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 175 optimal weight: 0.0370 chunk 379 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 chunk 191 optimal weight: 0.0030 chunk 234 optimal weight: 6.9990 chunk 252 optimal weight: 50.0000 chunk 267 optimal weight: 50.0000 chunk 169 optimal weight: 2.9990 overall best weight: 0.4868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 777 ASN B1101 HIS C 87 ASN C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.197339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.152534 restraints weight = 111290.681| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 3.45 r_work: 0.3720 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32566 Z= 0.119 Angle : 0.603 12.151 44376 Z= 0.312 Chirality : 0.045 0.383 4912 Planarity : 0.004 0.060 5763 Dihedral : 4.679 62.008 4428 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.22 % Favored : 94.53 % Rotamer: Outliers : 1.14 % Allowed : 14.36 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4070 helix: 1.82 (0.19), residues: 803 sheet: 0.27 (0.16), residues: 1020 loop : -1.53 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP H 36 HIS 0.005 0.000 HIS C 66 PHE 0.024 0.001 PHE C 168 TYR 0.031 0.001 TYR B 170 ARG 0.009 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 1298) hydrogen bonds : angle 5.34424 ( 3657) SS BOND : bond 0.00362 ( 50) SS BOND : angle 1.37304 ( 100) covalent geometry : bond 0.00271 (32516) covalent geometry : angle 0.60052 (44276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8140 Ramachandran restraints generated. 4070 Oldfield, 0 Emsley, 4070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 571 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8271 (tp) cc_final: 0.8034 (tm) REVERT: A 617 CYS cc_start: 0.2290 (OUTLIER) cc_final: 0.2037 (m) REVERT: B 58 PHE cc_start: 0.8191 (m-10) cc_final: 0.7873 (m-10) REVERT: B 177 MET cc_start: -0.1391 (mpt) cc_final: -0.1991 (mpt) REVERT: B 393 THR cc_start: 0.8749 (p) cc_final: 0.8482 (t) REVERT: B 453 TYR cc_start: 0.7002 (p90) cc_final: 0.6699 (p90) REVERT: B 854 LYS cc_start: 0.8563 (ptmm) cc_final: 0.8265 (ptmt) REVERT: B 859 THR cc_start: 0.8700 (m) cc_final: 0.8441 (p) REVERT: B 936 ASP cc_start: 0.7246 (m-30) cc_final: 0.7024 (m-30) REVERT: B 950 ASP cc_start: 0.7664 (m-30) cc_final: 0.7315 (m-30) REVERT: B 1010 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: C 120 VAL cc_start: 0.8824 (t) cc_final: 0.8540 (m) REVERT: C 129 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8120 (ttmm) REVERT: C 195 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8128 (ttpt) REVERT: C 553 THR cc_start: 0.8267 (m) cc_final: 0.8048 (p) REVERT: C 574 ASP cc_start: 0.7669 (t0) cc_final: 0.7390 (t0) REVERT: C 651 ILE cc_start: 0.8905 (pt) cc_final: 0.8683 (mt) REVERT: C 950 ASP cc_start: 0.7526 (m-30) cc_final: 0.7271 (m-30) REVERT: C 1084 ASP cc_start: 0.8078 (t70) cc_final: 0.7766 (t70) REVERT: D 18 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6337 (mp) REVERT: E 34 MET cc_start: 0.7406 (tmm) cc_final: 0.7066 (tmm) REVERT: E 83 MET cc_start: 0.6553 (ppp) cc_final: 0.6273 (ppp) REVERT: G 83 MET cc_start: 0.2839 (tpt) cc_final: 0.2400 (tpt) REVERT: G 109 MET cc_start: -0.0247 (mmm) cc_final: -0.0534 (mmm) REVERT: H 93 MET cc_start: 0.6209 (tpt) cc_final: 0.5973 (tpt) outliers start: 40 outliers final: 31 residues processed: 583 average time/residue: 1.4319 time to fit residues: 997.5804 Evaluate side-chains 594 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 560 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 181 optimal weight: 0.3980 chunk 341 optimal weight: 0.2980 chunk 350 optimal weight: 8.9990 chunk 368 optimal weight: 6.9990 chunk 372 optimal weight: 10.0000 chunk 171 optimal weight: 0.5980 chunk 215 optimal weight: 0.9980 chunk 198 optimal weight: 0.0770 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 0.0670 chunk 58 optimal weight: 0.9980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 777 ASN B1101 HIS C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 282 ASN C 804 GLN C 853 GLN C 969 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.198061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.152365 restraints weight = 116531.657| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 3.47 r_work: 0.3753 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32566 Z= 0.110 Angle : 0.596 11.475 44376 Z= 0.309 Chirality : 0.044 0.193 4912 Planarity : 0.004 0.062 5763 Dihedral : 4.597 61.470 4428 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.13 % Favored : 94.63 % Rotamer: Outliers : 1.03 % Allowed : 14.88 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.13), residues: 4070 helix: 1.87 (0.19), residues: 801 sheet: 0.28 (0.16), residues: 1023 loop : -1.49 (0.12), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.002 TRP H 36 HIS 0.005 0.000 HIS C 66 PHE 0.023 0.001 PHE C 168 TYR 0.031 0.001 TYR B 170 ARG 0.010 0.001 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 1298) hydrogen bonds : angle 5.28387 ( 3657) SS BOND : bond 0.00318 ( 50) SS BOND : angle 1.23664 ( 100) covalent geometry : bond 0.00245 (32516) covalent geometry : angle 0.59371 (44276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39589.87 seconds wall clock time: 686 minutes 9.52 seconds (41169.52 seconds total)