Starting phenix.real_space_refine on Sat Feb 7 07:50:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpr_26062/02_2026/7tpr_26062.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpr_26062/02_2026/7tpr_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_26062/02_2026/7tpr_26062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpr_26062/02_2026/7tpr_26062.map" model { file = "/net/cci-nas-00/data/ceres_data/7tpr_26062/02_2026/7tpr_26062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpr_26062/02_2026/7tpr_26062.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 11.94, per 1000 atoms: 0.38 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: 2.67 Conformation dependent library (CDL) restraints added in 2.3 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: 1.68 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: 8.85 Time building geometry restraints manager: 3.66 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: 0.04 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 38.900 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.940 ------------------------------------------------------------------------------- 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 : 8.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.007 0.001 ARG A1014 TYR 0.020 0.001 TYR B 265 PHE 0.029 0.001 PHE B 497 TRP 0.042 0.002 TRP C 64 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00412 (32516) covalent geometry : angle 0.60909 (44276) SS BOND : bond 0.00463 ( 50) SS BOND : angle 1.76434 ( 100) hydrogen bonds : bond 0.13620 ( 1298) hydrogen bonds : angle 7.44470 ( 3657) *********************** 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 : 1.293 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: 0.8053 (mm) REVERT: B 450 ASN cc_start: 0.8705 (m110) cc_final: 0.8443 (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: 0.7099 time to fit residues: 524.4551 Evaluate side-chains 556 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 554 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 197 optimal weight: 10.0000 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0050 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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 334 ASN A 394 ASN A 448 ASN A 498 GLN A 613 GLN A 901 GLN A 957 GLN A 969 ASN A1010 GLN A1054 GLN B 49 HIS B 137 ASN B 394 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 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.194809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.150277 restraints weight = 92569.161| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 3.06 r_work: 0.3716 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 32566 Z= 0.206 Angle : 0.687 11.503 44376 Z= 0.361 Chirality : 0.049 0.372 4912 Planarity : 0.005 0.073 5763 Dihedral : 5.436 75.993 4432 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.69 % Favored : 93.89 % Rotamer: Outliers : 1.14 % Allowed : 7.84 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 4070 helix: 1.38 (0.19), residues: 795 sheet: -0.02 (0.16), residues: 1016 loop : -1.69 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 319 TYR 0.036 0.002 TYR B 369 PHE 0.031 0.002 PHE H 68 TRP 0.030 0.002 TRP C 64 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00484 (32516) covalent geometry : angle 0.68209 (44276) SS BOND : bond 0.00518 ( 50) SS BOND : angle 1.90313 ( 100) hydrogen bonds : bond 0.04919 ( 1298) hydrogen bonds : angle 6.05289 ( 3657) *********************** 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 647 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 607 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8062 (p90) REVERT: A 498 GLN cc_start: 0.8282 (mm-40) cc_final: 0.8067 (mm110) REVERT: A 651 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8775 (mm) REVERT: B 58 PHE cc_start: 0.8186 (m-10) cc_final: 0.7863 (m-10) REVERT: B 164 ASN cc_start: 0.7694 (t0) cc_final: 0.7350 (t0) REVERT: B 165 ASN cc_start: 0.7160 (m-40) cc_final: 0.6714 (m110) REVERT: B 392 PHE cc_start: 0.8401 (m-80) cc_final: 0.8192 (m-80) REVERT: B 453 TYR cc_start: 0.7234 (p90) cc_final: 0.6622 (p90) REVERT: B 524 VAL cc_start: 0.7492 (OUTLIER) cc_final: 0.7277 (p) REVERT: B 703 ASN cc_start: 0.8174 (t0) cc_final: 0.7883 (t0) REVERT: B 854 LYS cc_start: 0.8612 (ptmm) cc_final: 0.8281 (ptmt) REVERT: B 950 ASP cc_start: 0.7652 (m-30) cc_final: 0.7300 (m-30) REVERT: B 1141 LEU cc_start: 0.8666 (tt) cc_final: 0.8249 (tm) REVERT: C 129 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7881 (ptmm) REVERT: C 278 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7875 (tptp) REVERT: C 319 ARG cc_start: 0.7928 (ttm110) cc_final: 0.7707 (mtm-85) REVERT: C 574 ASP cc_start: 0.7640 (t0) cc_final: 0.7381 (t0) REVERT: C 950 ASP cc_start: 0.7574 (m-30) cc_final: 0.7260 (m-30) REVERT: C 1084 ASP cc_start: 0.7968 (t70) cc_final: 0.7653 (t70) REVERT: G 83 MET cc_start: 0.2909 (tpt) cc_final: 0.2330 (tpt) REVERT: G 109 MET cc_start: -0.0925 (mmm) cc_final: -0.1508 (mmm) REVERT: H 31 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8631 (t) REVERT: H 53 ARG cc_start: 0.8558 (ptm-80) cc_final: 0.8348 (ptm-80) outliers start: 40 outliers final: 13 residues processed: 621 average time/residue: 0.6619 time to fit residues: 485.7511 Evaluate side-chains 600 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 583 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 430 THR 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 B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 524 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 588 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 162 optimal weight: 1.9990 chunk 359 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 261 optimal weight: 0.3980 chunk 234 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 369 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 969 ASN A1002 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 52 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 804 GLN C 969 ASN H 104 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.195234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.150088 restraints weight = 108979.063| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 3.39 r_work: 0.3691 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 32566 Z= 0.183 Angle : 0.651 10.201 44376 Z= 0.342 Chirality : 0.048 0.347 4912 Planarity : 0.005 0.059 5763 Dihedral : 5.244 74.587 4428 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.69 % Favored : 93.96 % Rotamer: Outliers : 1.37 % Allowed : 9.89 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 4070 helix: 1.52 (0.19), residues: 795 sheet: 0.06 (0.16), residues: 1019 loop : -1.67 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 995 TYR 0.030 0.002 TYR B 170 PHE 0.027 0.002 PHE B 497 TRP 0.042 0.002 TRP H 36 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00431 (32516) covalent geometry : angle 0.64624 (44276) SS BOND : bond 0.00449 ( 50) SS BOND : angle 1.82613 ( 100) hydrogen bonds : bond 0.04610 ( 1298) hydrogen bonds : angle 5.83417 ( 3657) *********************** 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 633 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 585 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8123 (p90) REVERT: A 675 GLN cc_start: 0.7335 (pp30) cc_final: 0.7110 (pp30) REVERT: B 58 PHE cc_start: 0.8221 (m-10) cc_final: 0.7905 (m-10) REVERT: B 164 ASN cc_start: 0.7672 (t0) cc_final: 0.7438 (t0) REVERT: B 297 SER cc_start: 0.7986 (m) cc_final: 0.7758 (p) REVERT: B 357 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7376 (ttm-80) REVERT: B 403 ARG cc_start: 0.7416 (mtp-110) cc_final: 0.7077 (mtp-110) REVERT: B 453 TYR cc_start: 0.7220 (p90) cc_final: 0.6887 (p90) REVERT: B 524 VAL cc_start: 0.7513 (OUTLIER) cc_final: 0.7312 (p) REVERT: B 773 GLU cc_start: 0.7791 (tt0) cc_final: 0.7576 (tt0) REVERT: B 854 LYS cc_start: 0.8723 (ptmm) cc_final: 0.8389 (ptmt) REVERT: B 936 ASP cc_start: 0.7361 (m-30) cc_final: 0.7143 (m-30) REVERT: B 950 ASP cc_start: 0.7710 (m-30) cc_final: 0.7325 (m-30) REVERT: B 1010 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: B 1141 LEU cc_start: 0.8594 (tt) cc_final: 0.8317 (tm) REVERT: C 129 LYS cc_start: 0.8375 (ttmt) cc_final: 0.8108 (ttmm) REVERT: C 574 ASP cc_start: 0.7653 (t0) cc_final: 0.7387 (t0) REVERT: C 651 ILE cc_start: 0.9008 (pt) cc_final: 0.8784 (mp) REVERT: C 950 ASP cc_start: 0.7591 (m-30) cc_final: 0.7271 (m-30) REVERT: C 1084 ASP cc_start: 0.8028 (t70) cc_final: 0.7681 (t70) REVERT: F 36 TRP cc_start: 0.7243 (m-90) cc_final: 0.7038 (m100) REVERT: F 83 MET cc_start: 0.7108 (mmm) cc_final: 0.6729 (mmm) REVERT: G 83 MET cc_start: 0.2785 (tpt) cc_final: 0.2285 (tpt) REVERT: H 36 TRP cc_start: 0.8157 (m100) cc_final: 0.7845 (m100) outliers start: 48 outliers final: 22 residues processed: 596 average time/residue: 0.6298 time to fit residues: 445.8609 Evaluate side-chains 602 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 577 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 238 PHE 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 921 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1045 LYS 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 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 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 304 LYS 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 54 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 330 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 246 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 391 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 969 ASN B 409 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 30 ASN C 81 ASN C 969 ASN D 123 GLN G 72 GLN H 3 GLN H 104 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.193864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.148286 restraints weight = 100257.573| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.26 r_work: 0.3668 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 32566 Z= 0.281 Angle : 0.693 18.106 44376 Z= 0.361 Chirality : 0.050 0.289 4912 Planarity : 0.005 0.074 5763 Dihedral : 5.320 73.164 4428 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.96 % Favored : 93.72 % Rotamer: Outliers : 1.60 % Allowed : 10.80 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 4070 helix: 1.31 (0.19), residues: 802 sheet: 0.02 (0.16), residues: 1019 loop : -1.71 (0.12), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 319 TYR 0.030 0.002 TYR B 265 PHE 0.028 0.002 PHE A 238 TRP 0.022 0.002 TRP A 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00665 (32516) covalent geometry : angle 0.68722 (44276) SS BOND : bond 0.00596 ( 50) SS BOND : angle 2.04696 ( 100) hydrogen bonds : bond 0.05059 ( 1298) hydrogen bonds : angle 5.85251 ( 3657) *********************** 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 641 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 585 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.8025 (p90) REVERT: A 651 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8750 (mm) REVERT: A 675 GLN cc_start: 0.7361 (pp30) cc_final: 0.7089 (pp30) REVERT: B 58 PHE cc_start: 0.8260 (m-10) cc_final: 0.7943 (m-10) REVERT: B 108 THR cc_start: 0.8354 (p) cc_final: 0.8119 (t) REVERT: B 164 ASN cc_start: 0.7773 (t0) cc_final: 0.7510 (t0) REVERT: B 202 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8287 (mttt) REVERT: B 297 SER cc_start: 0.8008 (m) cc_final: 0.7775 (p) REVERT: B 361 CYS cc_start: 0.6518 (p) cc_final: 0.6007 (p) REVERT: B 430 THR cc_start: 0.8789 (t) cc_final: 0.8569 (m) REVERT: B 453 TYR cc_start: 0.7246 (p90) cc_final: 0.6967 (p90) REVERT: B 524 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7401 (p) REVERT: B 859 THR cc_start: 0.8695 (m) cc_final: 0.8432 (p) REVERT: B 936 ASP cc_start: 0.7416 (m-30) cc_final: 0.7188 (m-30) REVERT: B 950 ASP cc_start: 0.7766 (m-30) cc_final: 0.7389 (m-30) REVERT: B 1010 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: B 1141 LEU cc_start: 0.8559 (tt) cc_final: 0.8266 (tm) REVERT: C 120 VAL cc_start: 0.8880 (t) cc_final: 0.8641 (m) REVERT: C 129 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8147 (ttpp) REVERT: C 574 ASP cc_start: 0.7706 (t0) cc_final: 0.7454 (t0) REVERT: C 950 ASP cc_start: 0.7700 (m-30) cc_final: 0.7382 (m-30) REVERT: C 1084 ASP cc_start: 0.8046 (t70) cc_final: 0.7694 (t70) REVERT: E 83 MET cc_start: 0.6806 (ppp) cc_final: 0.6101 (ppp) REVERT: G 83 MET cc_start: 0.2795 (tpt) cc_final: 0.2265 (tpt) REVERT: G 109 MET cc_start: -0.0980 (mmm) cc_final: -0.1485 (mmm) REVERT: H 36 TRP cc_start: 0.8301 (m100) cc_final: 0.7974 (m100) outliers start: 56 outliers final: 32 residues processed: 604 average time/residue: 0.7053 time to fit residues: 502.5726 Evaluate side-chains 611 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 574 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP 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 1045 LYS 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 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 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 934 ILE 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 H residue 23 VAL Chi-restraints excluded: chain H residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 300 optimal weight: 0.6980 chunk 387 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 386 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 316 optimal weight: 0.5980 chunk 276 optimal weight: 20.0000 chunk 247 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN B 30 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 901 GLN B 965 GLN B1005 GLN C 30 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 969 ASN D 123 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 = 0.4480 r_free = 0.4480 target = 0.195438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.150814 restraints weight = 99791.822| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 3.23 r_work: 0.3713 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32566 Z= 0.139 Angle : 0.626 15.860 44376 Z= 0.326 Chirality : 0.046 0.301 4912 Planarity : 0.004 0.057 5763 Dihedral : 5.098 71.776 4428 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.54 % Favored : 94.16 % Rotamer: Outliers : 1.42 % Allowed : 12.08 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 4070 helix: 1.57 (0.19), residues: 795 sheet: 0.13 (0.16), residues: 1022 loop : -1.63 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 357 TYR 0.030 0.001 TYR B 170 PHE 0.025 0.001 PHE A 238 TRP 0.027 0.001 TRP C 64 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00315 (32516) covalent geometry : angle 0.62154 (44276) SS BOND : bond 0.00387 ( 50) SS BOND : angle 1.61715 ( 100) hydrogen bonds : bond 0.04163 ( 1298) hydrogen bonds : angle 5.66524 ( 3657) *********************** 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 643 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 593 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8222 (ttp-110) cc_final: 0.8013 (ptp90) REVERT: A 675 GLN cc_start: 0.7251 (pp30) cc_final: 0.6630 (OUTLIER) REVERT: A 994 ASP cc_start: 0.7727 (t0) cc_final: 0.7453 (t0) REVERT: B 44 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7854 (mtt-85) REVERT: B 58 PHE cc_start: 0.8256 (m-10) cc_final: 0.7962 (m-10) REVERT: B 164 ASN cc_start: 0.7676 (t0) cc_final: 0.7473 (t0) REVERT: B 297 SER cc_start: 0.7928 (m) cc_final: 0.7671 (p) REVERT: B 331 ASN cc_start: 0.4989 (m-40) cc_final: 0.4412 (m110) REVERT: B 408 ARG cc_start: 0.8468 (mtp180) cc_final: 0.8222 (mtp180) REVERT: B 453 TYR cc_start: 0.7184 (p90) cc_final: 0.6867 (p90) REVERT: B 524 VAL cc_start: 0.7477 (OUTLIER) cc_final: 0.7245 (p) REVERT: B 773 GLU cc_start: 0.7925 (tt0) cc_final: 0.7711 (tt0) REVERT: B 854 LYS cc_start: 0.8726 (ptmm) cc_final: 0.8411 (ptmt) REVERT: B 859 THR cc_start: 0.8667 (m) cc_final: 0.8409 (p) REVERT: B 936 ASP cc_start: 0.7312 (m-30) cc_final: 0.7091 (m-30) REVERT: B 950 ASP cc_start: 0.7699 (m-30) cc_final: 0.7283 (m-30) REVERT: B 1010 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: B 1141 LEU cc_start: 0.8530 (tt) cc_final: 0.8230 (tm) REVERT: C 120 VAL cc_start: 0.8811 (t) cc_final: 0.8542 (m) REVERT: C 129 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8111 (ttmm) REVERT: C 195 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8069 (ttpt) REVERT: C 574 ASP cc_start: 0.7617 (t0) cc_final: 0.7350 (t0) REVERT: C 950 ASP cc_start: 0.7558 (m-30) cc_final: 0.7235 (m-30) REVERT: E 83 MET cc_start: 0.6668 (ppp) cc_final: 0.6213 (ppp) REVERT: G 83 MET cc_start: 0.2891 (tpt) cc_final: 0.2361 (tpt) REVERT: H 36 TRP cc_start: 0.8206 (m100) cc_final: 0.8003 (m100) outliers start: 50 outliers final: 25 residues processed: 609 average time/residue: 0.7180 time to fit residues: 517.7220 Evaluate side-chains 598 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 571 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 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 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 745 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 554 GLU 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 248 optimal weight: 1.9990 chunk 340 optimal weight: 1.9990 chunk 168 optimal weight: 0.3980 chunk 101 optimal weight: 0.8980 chunk 263 optimal weight: 10.0000 chunk 351 optimal weight: 3.9990 chunk 289 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 228 optimal weight: 30.0000 chunk 329 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1005 GLN C 81 ASN C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN D 123 GLN H 3 GLN H 104 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.194057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.148939 restraints weight = 108835.524| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 3.36 r_work: 0.3654 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 32566 Z= 0.226 Angle : 0.664 14.789 44376 Z= 0.345 Chirality : 0.048 0.331 4912 Planarity : 0.005 0.060 5763 Dihedral : 5.131 67.877 4428 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.94 % Favored : 93.77 % Rotamer: Outliers : 1.77 % Allowed : 12.40 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 4070 helix: 1.55 (0.19), residues: 782 sheet: 0.12 (0.16), residues: 988 loop : -1.68 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 190 TYR 0.029 0.002 TYR B 170 PHE 0.026 0.002 PHE A 238 TRP 0.026 0.002 TRP C 64 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00537 (32516) covalent geometry : angle 0.65751 (44276) SS BOND : bond 0.00575 ( 50) SS BOND : angle 1.98647 ( 100) hydrogen bonds : bond 0.04644 ( 1298) hydrogen bonds : angle 5.70477 ( 3657) *********************** 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 644 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 582 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7951 (t80) REVERT: A 408 ARG cc_start: 0.8302 (ttp-110) cc_final: 0.8087 (ptp90) REVERT: A 651 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8734 (mm) REVERT: A 675 GLN cc_start: 0.7318 (pp30) cc_final: 0.7045 (pp30) REVERT: B 44 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7899 (mtt-85) REVERT: B 58 PHE cc_start: 0.8273 (m-10) cc_final: 0.7968 (m-10) REVERT: B 108 THR cc_start: 0.8342 (p) cc_final: 0.8089 (t) REVERT: B 164 ASN cc_start: 0.7751 (t0) cc_final: 0.7549 (t0) REVERT: B 202 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8183 (mttt) REVERT: B 297 SER cc_start: 0.7939 (m) cc_final: 0.7700 (p) REVERT: B 331 ASN cc_start: 0.5119 (m-40) cc_final: 0.4490 (m110) REVERT: B 393 THR cc_start: 0.8696 (p) cc_final: 0.8396 (t) REVERT: B 408 ARG cc_start: 0.8564 (mtp180) cc_final: 0.8325 (mtp180) REVERT: B 453 TYR cc_start: 0.7206 (p90) cc_final: 0.6944 (p90) REVERT: B 524 VAL cc_start: 0.7593 (OUTLIER) cc_final: 0.7339 (p) REVERT: B 859 THR cc_start: 0.8696 (m) cc_final: 0.8418 (p) REVERT: B 936 ASP cc_start: 0.7386 (m-30) cc_final: 0.7157 (m-30) REVERT: B 950 ASP cc_start: 0.7721 (m-30) cc_final: 0.7318 (m-30) REVERT: B 1010 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7503 (mp10) REVERT: B 1141 LEU cc_start: 0.8556 (tt) cc_final: 0.8210 (tm) REVERT: C 120 VAL cc_start: 0.8866 (t) cc_final: 0.8581 (m) REVERT: C 129 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8096 (ttmm) REVERT: C 195 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8157 (ttpt) REVERT: C 574 ASP cc_start: 0.7724 (t0) cc_final: 0.7439 (t0) REVERT: C 950 ASP cc_start: 0.7621 (m-30) cc_final: 0.7308 (m-30) REVERT: E 34 MET cc_start: 0.7564 (tmm) cc_final: 0.6863 (tmm) REVERT: E 83 MET cc_start: 0.6729 (ppp) cc_final: 0.6236 (ppp) REVERT: G 83 MET cc_start: 0.2917 (tpt) cc_final: 0.2382 (tpt) REVERT: H 36 TRP cc_start: 0.8294 (m100) cc_final: 0.8061 (m100) outliers start: 62 outliers final: 33 residues processed: 607 average time/residue: 0.6952 time to fit residues: 498.4961 Evaluate side-chains 615 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 576 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 345 THR Chi-restraints excluded: chain A residue 347 PHE 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 1045 LYS 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 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 1010 GLN Chi-restraints excluded: chain C residue 105 ILE 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 731 MET 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 1040 VAL 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 H residue 23 VAL Chi-restraints excluded: chain H residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 42 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 chunk 120 optimal weight: 0.0670 chunk 37 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 261 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 402 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 chunk 328 optimal weight: 0.9980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A 675 GLN A 853 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1005 GLN C 81 ASN C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 853 GLN C 969 ASN D 123 GLN F 72 GLN H 104 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.195920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.151641 restraints weight = 101349.112| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.23 r_work: 0.3735 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32566 Z= 0.122 Angle : 0.608 13.520 44376 Z= 0.317 Chirality : 0.045 0.332 4912 Planarity : 0.004 0.056 5763 Dihedral : 4.914 64.700 4428 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.45 % Favored : 94.31 % Rotamer: Outliers : 1.28 % Allowed : 13.62 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.13), residues: 4070 helix: 1.75 (0.19), residues: 789 sheet: 0.18 (0.16), residues: 1005 loop : -1.60 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 190 TYR 0.031 0.001 TYR B 170 PHE 0.024 0.001 PHE A 238 TRP 0.022 0.001 TRP C 64 HIS 0.005 0.000 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00272 (32516) covalent geometry : angle 0.60433 (44276) SS BOND : bond 0.00334 ( 50) SS BOND : angle 1.49149 ( 100) hydrogen bonds : bond 0.03867 ( 1298) hydrogen bonds : angle 5.52584 ( 3657) *********************** 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 628 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 583 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7929 (ptp-110) REVERT: A 651 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8724 (mm) REVERT: A 675 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6911 (pp30) REVERT: B 44 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7803 (mtt-85) REVERT: B 58 PHE cc_start: 0.8250 (m-10) cc_final: 0.7965 (m-10) REVERT: B 393 THR cc_start: 0.8679 (p) cc_final: 0.8405 (t) REVERT: B 403 ARG cc_start: 0.7413 (mtp180) cc_final: 0.7186 (mtp180) REVERT: B 408 ARG cc_start: 0.8456 (mtp180) cc_final: 0.8213 (mtp180) REVERT: B 440 ASN cc_start: 0.8492 (p0) cc_final: 0.8266 (p0) REVERT: B 453 TYR cc_start: 0.7138 (p90) cc_final: 0.6861 (p90) REVERT: B 524 VAL cc_start: 0.7399 (p) cc_final: 0.7145 (p) REVERT: B 854 LYS cc_start: 0.8679 (ptmm) cc_final: 0.8357 (ptmt) REVERT: B 859 THR cc_start: 0.8666 (m) cc_final: 0.8411 (p) REVERT: B 936 ASP cc_start: 0.7212 (m-30) cc_final: 0.6999 (m-30) REVERT: B 950 ASP cc_start: 0.7655 (m-30) cc_final: 0.7255 (m-30) REVERT: B 1141 LEU cc_start: 0.8595 (tt) cc_final: 0.8266 (tm) REVERT: B 1144 GLU cc_start: 0.7335 (pp20) cc_final: 0.7115 (pp20) REVERT: C 120 VAL cc_start: 0.8799 (t) cc_final: 0.8506 (m) REVERT: C 129 LYS cc_start: 0.8341 (ttmt) cc_final: 0.8044 (ttmm) REVERT: C 195 LYS cc_start: 0.8539 (ttpt) cc_final: 0.7974 (ttpt) REVERT: C 278 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7749 (tptm) REVERT: C 574 ASP cc_start: 0.7637 (t0) cc_final: 0.7353 (t0) REVERT: C 819 GLU cc_start: 0.7870 (mt-10) cc_final: 0.6994 (tt0) REVERT: C 950 ASP cc_start: 0.7480 (m-30) cc_final: 0.7172 (m-30) REVERT: D 18 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6042 (mt) REVERT: E 34 MET cc_start: 0.7431 (tmm) cc_final: 0.7041 (tmm) REVERT: E 83 MET cc_start: 0.6329 (ppp) cc_final: 0.6060 (ppp) REVERT: F 83 MET cc_start: 0.7132 (mmm) cc_final: 0.6704 (mmm) REVERT: G 83 MET cc_start: 0.2896 (tpt) cc_final: 0.2446 (tpt) REVERT: G 109 MET cc_start: 0.0000 (mmm) cc_final: -0.1013 (mmm) REVERT: H 36 TRP cc_start: 0.8197 (m100) cc_final: 0.7942 (m100) outliers start: 45 outliers final: 30 residues processed: 598 average time/residue: 0.6544 time to fit residues: 463.9018 Evaluate side-chains 608 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 574 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 675 GLN 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 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 C residue 554 GLU 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 1092 GLU 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 E residue 12 VAL Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain H residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 388 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 143 optimal weight: 0.5980 chunk 372 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 330 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN B 99 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 901 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 784 GLN C 969 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.193862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147013 restraints weight = 100827.679| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.63 r_work: 0.3682 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 32566 Z= 0.247 Angle : 0.673 13.122 44376 Z= 0.351 Chirality : 0.049 0.364 4912 Planarity : 0.005 0.066 5763 Dihedral : 5.058 66.012 4428 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.99 % Favored : 93.77 % Rotamer: Outliers : 1.25 % Allowed : 14.22 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4070 helix: 1.56 (0.19), residues: 793 sheet: 0.21 (0.16), residues: 999 loop : -1.66 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 190 TYR 0.029 0.002 TYR B 170 PHE 0.024 0.002 PHE A 238 TRP 0.022 0.002 TRP C 64 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00590 (32516) covalent geometry : angle 0.66730 (44276) SS BOND : bond 0.00564 ( 50) SS BOND : angle 1.99385 ( 100) hydrogen bonds : bond 0.04754 ( 1298) hydrogen bonds : angle 5.64561 ( 3657) *********************** 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 627 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 583 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8699 (mm) REVERT: B 44 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7875 (mtt-85) REVERT: B 58 PHE cc_start: 0.8274 (m-10) cc_final: 0.7977 (m-10) REVERT: B 108 THR cc_start: 0.8369 (p) cc_final: 0.8163 (t) REVERT: B 393 THR cc_start: 0.8701 (p) cc_final: 0.8452 (t) REVERT: B 403 ARG cc_start: 0.7565 (mtp180) cc_final: 0.7285 (mtp180) REVERT: B 408 ARG cc_start: 0.8594 (mtp180) cc_final: 0.8357 (mtp180) REVERT: B 440 ASN cc_start: 0.8572 (p0) cc_final: 0.8369 (p0) REVERT: B 524 VAL cc_start: 0.7600 (OUTLIER) cc_final: 0.7349 (p) REVERT: B 859 THR cc_start: 0.8706 (m) cc_final: 0.8448 (p) REVERT: B 936 ASP cc_start: 0.7370 (m-30) cc_final: 0.7130 (m-30) REVERT: B 950 ASP cc_start: 0.7779 (m-30) cc_final: 0.7376 (m-30) REVERT: B 1010 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: B 1141 LEU cc_start: 0.8584 (tt) cc_final: 0.8209 (tm) REVERT: B 1144 GLU cc_start: 0.7409 (pp20) cc_final: 0.7191 (pp20) REVERT: C 120 VAL cc_start: 0.8872 (t) cc_final: 0.8601 (m) REVERT: C 195 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8140 (ttpt) REVERT: C 574 ASP cc_start: 0.7715 (t0) cc_final: 0.7436 (t0) REVERT: C 950 ASP cc_start: 0.7614 (m-30) cc_final: 0.7296 (m-30) REVERT: C 1031 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7807 (mt-10) REVERT: D 18 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6259 (mp) REVERT: E 34 MET cc_start: 0.7674 (tmm) cc_final: 0.7167 (tmm) REVERT: E 83 MET cc_start: 0.7161 (ppp) cc_final: 0.6659 (ppp) REVERT: G 83 MET cc_start: 0.2962 (tpt) cc_final: 0.2424 (tpt) REVERT: G 109 MET cc_start: -0.0061 (mmm) cc_final: -0.0913 (mmm) REVERT: H 36 TRP cc_start: 0.8336 (m100) cc_final: 0.8068 (m100) outliers start: 44 outliers final: 32 residues processed: 598 average time/residue: 0.6546 time to fit residues: 464.8669 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 : 1.104 ------------------------------------------------------------------------------- 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 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 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 189 LEU 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 392 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 571 ASP 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 C residue 105 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 729 VAL 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 18 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 234 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 259 optimal weight: 0.7980 chunk 260 optimal weight: 0.0170 chunk 319 optimal weight: 1.9990 chunk 385 optimal weight: 10.0000 chunk 382 optimal weight: 50.0000 chunk 334 optimal weight: 0.8980 chunk 283 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 256 optimal weight: 0.3980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 703 ASN B 901 GLN B1005 GLN C 30 ASN C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 804 GLN C 969 ASN C1074 ASN H 104 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.196112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.149973 restraints weight = 110937.871| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 3.59 r_work: 0.3719 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32566 Z= 0.119 Angle : 0.618 12.497 44376 Z= 0.322 Chirality : 0.045 0.372 4912 Planarity : 0.004 0.056 5763 Dihedral : 4.870 64.164 4428 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.50 % Favored : 94.26 % Rotamer: Outliers : 1.11 % Allowed : 14.82 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 4070 helix: 1.72 (0.19), residues: 796 sheet: 0.22 (0.16), residues: 1004 loop : -1.58 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 357 TYR 0.031 0.001 TYR B 170 PHE 0.023 0.001 PHE A 238 TRP 0.024 0.001 TRP C 64 HIS 0.005 0.000 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00265 (32516) covalent geometry : angle 0.61516 (44276) SS BOND : bond 0.00327 ( 50) SS BOND : angle 1.45876 ( 100) hydrogen bonds : bond 0.03816 ( 1298) hydrogen bonds : angle 5.46508 ( 3657) *********************** 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 610 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 571 time to evaluate : 1.285 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 240 THR cc_start: 0.7953 (t) cc_final: 0.7021 (p) REVERT: A 317 ASN cc_start: 0.8049 (m-40) cc_final: 0.7832 (m-40) REVERT: A 651 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8723 (mm) REVERT: B 44 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7824 (mtt-85) REVERT: B 58 PHE cc_start: 0.8262 (m-10) cc_final: 0.7970 (m-10) REVERT: B 138 ASP cc_start: 0.7723 (t0) cc_final: 0.7151 (t0) REVERT: B 393 THR cc_start: 0.8675 (p) cc_final: 0.8436 (t) REVERT: B 402 ILE cc_start: 0.8218 (mm) cc_final: 0.7993 (tp) REVERT: B 403 ARG cc_start: 0.7536 (mtp180) cc_final: 0.7250 (mtp180) REVERT: B 440 ASN cc_start: 0.8457 (p0) cc_final: 0.8214 (p0) REVERT: B 524 VAL cc_start: 0.7381 (OUTLIER) cc_final: 0.7127 (p) REVERT: B 773 GLU cc_start: 0.7710 (tt0) cc_final: 0.7445 (tt0) REVERT: B 854 LYS cc_start: 0.8659 (ptmm) cc_final: 0.8338 (ptmt) REVERT: B 859 THR cc_start: 0.8670 (m) cc_final: 0.8416 (p) REVERT: B 936 ASP cc_start: 0.7221 (m-30) cc_final: 0.6993 (m-30) REVERT: B 950 ASP cc_start: 0.7673 (m-30) cc_final: 0.7259 (m-30) REVERT: B 1010 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: B 1141 LEU cc_start: 0.8555 (tt) cc_final: 0.8005 (tm) REVERT: B 1144 GLU cc_start: 0.7319 (pp20) cc_final: 0.6988 (pp20) REVERT: C 129 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8180 (ttmm) REVERT: C 195 LYS cc_start: 0.8526 (ttpt) cc_final: 0.7912 (ttpt) REVERT: C 574 ASP cc_start: 0.7635 (t0) cc_final: 0.7359 (t0) REVERT: C 950 ASP cc_start: 0.7556 (m-30) cc_final: 0.7301 (m-30) REVERT: C 1031 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7871 (mt-10) REVERT: D 18 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6319 (mp) REVERT: E 34 MET cc_start: 0.7456 (tmm) cc_final: 0.7097 (tmm) REVERT: E 83 MET cc_start: 0.6581 (ppp) cc_final: 0.6218 (ppp) REVERT: G 83 MET cc_start: 0.2939 (tpt) cc_final: 0.2439 (tpt) REVERT: G 109 MET cc_start: -0.0178 (mmm) cc_final: -0.0594 (mmm) REVERT: H 36 TRP cc_start: 0.8186 (m100) cc_final: 0.7554 (m100) outliers start: 39 outliers final: 29 residues processed: 583 average time/residue: 0.7141 time to fit residues: 492.4994 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 : 1.195 ------------------------------------------------------------------------------- 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 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 188 ASN 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 571 ASP 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 C residue 235 ILE 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 1092 GLU 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 E residue 12 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 26 optimal weight: 0.0980 chunk 202 optimal weight: 0.2980 chunk 320 optimal weight: 0.8980 chunk 339 optimal weight: 0.1980 chunk 329 optimal weight: 1.9990 chunk 273 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN B 188 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 613 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.196271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149352 restraints weight = 118588.773| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 4.05 r_work: 0.3712 rms_B_bonded: 4.05 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 = 0.30 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 32566 Z= 0.187 Angle : 0.725 58.665 44376 Z= 0.399 Chirality : 0.046 0.402 4912 Planarity : 0.004 0.056 5763 Dihedral : 4.865 64.148 4428 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.35 % Favored : 94.38 % Rotamer: Outliers : 1.05 % Allowed : 15.02 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 4070 helix: 1.73 (0.19), residues: 796 sheet: 0.22 (0.16), residues: 1004 loop : -1.57 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 357 TYR 0.029 0.001 TYR B 170 PHE 0.023 0.001 PHE C 32 TRP 0.038 0.001 TRP H 36 HIS 0.005 0.000 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00366 (32516) covalent geometry : angle 0.71971 (44276) SS BOND : bond 0.00331 ( 50) SS BOND : angle 2.03693 ( 100) hydrogen bonds : bond 0.03812 ( 1298) hydrogen bonds : angle 5.46348 ( 3657) ********************** 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 597 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 560 time to evaluate : 1.136 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 240 THR cc_start: 0.7975 (t) cc_final: 0.7042 (p) REVERT: A 317 ASN cc_start: 0.8063 (m-40) cc_final: 0.7851 (m-40) REVERT: A 651 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8723 (mm) REVERT: B 44 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7791 (mtt-85) REVERT: B 58 PHE cc_start: 0.8265 (m-10) cc_final: 0.7941 (m-10) REVERT: B 138 ASP cc_start: 0.7796 (t0) cc_final: 0.7231 (t0) REVERT: B 188 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.7303 (p0) REVERT: B 189 LEU cc_start: 0.8309 (tm) cc_final: 0.8109 (tp) REVERT: B 393 THR cc_start: 0.8682 (p) cc_final: 0.8428 (t) REVERT: B 402 ILE cc_start: 0.8230 (mm) cc_final: 0.8002 (tp) REVERT: B 403 ARG cc_start: 0.7510 (mtp180) cc_final: 0.7225 (mtp180) REVERT: B 440 ASN cc_start: 0.8451 (p0) cc_final: 0.8204 (p0) REVERT: B 524 VAL cc_start: 0.7404 (OUTLIER) cc_final: 0.7152 (p) REVERT: B 854 LYS cc_start: 0.8649 (ptmm) cc_final: 0.8323 (ptmt) REVERT: B 859 THR cc_start: 0.8685 (m) cc_final: 0.8418 (p) REVERT: B 936 ASP cc_start: 0.7243 (m-30) cc_final: 0.7016 (m-30) REVERT: B 950 ASP cc_start: 0.7681 (m-30) cc_final: 0.7285 (m-30) REVERT: B 1010 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7592 (mp10) REVERT: B 1141 LEU cc_start: 0.8584 (tt) cc_final: 0.8255 (tm) REVERT: B 1144 GLU cc_start: 0.7382 (pp20) cc_final: 0.7178 (pp20) REVERT: C 129 LYS cc_start: 0.8370 (ttmt) cc_final: 0.8132 (ttmm) REVERT: C 195 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8092 (ttpt) REVERT: C 284 THR cc_start: 0.7127 (OUTLIER) cc_final: 0.6913 (p) REVERT: C 574 ASP cc_start: 0.7706 (t0) cc_final: 0.7416 (t0) REVERT: C 950 ASP cc_start: 0.7531 (m-30) cc_final: 0.7282 (m-30) REVERT: C 1031 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7909 (mt-10) REVERT: D 18 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6274 (mp) REVERT: E 34 MET cc_start: 0.7553 (tmm) cc_final: 0.7127 (tmm) REVERT: E 83 MET cc_start: 0.6887 (ppp) cc_final: 0.6434 (ppp) REVERT: G 83 MET cc_start: 0.2947 (tpt) cc_final: 0.2442 (tpt) REVERT: G 109 MET cc_start: -0.0187 (mmm) cc_final: -0.0577 (mmm) REVERT: H 36 TRP cc_start: 0.8118 (m100) cc_final: 0.7716 (m100) outliers start: 37 outliers final: 27 residues processed: 574 average time/residue: 0.7149 time to fit residues: 486.8239 Evaluate side-chains 592 residues out of total 3497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 558 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 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 A residue 1094 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 188 ASN 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 571 ASP 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 C residue 284 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 1092 GLU 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 E residue 12 VAL 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 76 optimal weight: 0.0000 chunk 258 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 164 optimal weight: 0.0370 chunk 388 optimal weight: 30.0000 chunk 377 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 371 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1005 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 969 ASN C1142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.195595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.151431 restraints weight = 94970.219| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 3.12 r_work: 0.3715 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2395 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= 0.179 Angle : 0.646 14.264 44376 Z= 0.335 Chirality : 0.047 0.393 4912 Planarity : 0.004 0.065 5763 Dihedral : 4.893 65.298 4428 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.67 % Favored : 94.06 % Rotamer: Outliers : 1.03 % Allowed : 15.13 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 4070 helix: 1.73 (0.19), residues: 791 sheet: 0.20 (0.16), residues: 1017 loop : -1.58 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 190 TYR 0.032 0.001 TYR B 170 PHE 0.023 0.002 PHE C 32 TRP 0.024 0.002 TRP C 64 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00425 (32516) covalent geometry : angle 0.64133 (44276) SS BOND : bond 0.00430 ( 50) SS BOND : angle 1.72235 ( 100) hydrogen bonds : bond 0.04222 ( 1298) hydrogen bonds : angle 5.49143 ( 3657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18155.74 seconds wall clock time: 308 minutes 6.94 seconds (18486.94 seconds total)