Starting phenix.real_space_refine on Wed Mar 4 20:47:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xnz_22274/03_2026/6xnz_22274.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xnz_22274/03_2026/6xnz_22274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xnz_22274/03_2026/6xnz_22274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xnz_22274/03_2026/6xnz_22274.map" model { file = "/net/cci-nas-00/data/ceres_data/6xnz_22274/03_2026/6xnz_22274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xnz_22274/03_2026/6xnz_22274.cif" } resolution = 3.8 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 114 5.49 5 S 104 5.16 5 C 10112 2.51 5 N 2889 2.21 5 O 3323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16544 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4411 Classifications: {'peptide': 550} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 524} Chain: "B" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2680 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 322} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4402 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 523} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2677 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 635 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "J" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 636 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "x" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 301 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "M" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 311 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "y" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "L" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2082 SG CYS A 727 67.544 87.710 59.807 1.00 37.38 S ATOM 2103 SG CYS A 730 67.479 91.036 62.352 1.00 37.40 S ATOM 9173 SG CYS C 727 66.428 22.258 60.083 1.00 39.34 S ATOM 9194 SG CYS C 730 66.463 18.402 61.597 1.00 39.94 S Time building chain proxies: 3.55, per 1000 atoms: 0.21 Number of scatterers: 16544 At special positions: 0 Unit cell: (134.4, 111.3, 114.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 104 16.00 P 114 15.00 O 3323 8.00 N 2889 7.00 C 10112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 688.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 727 " Number of angles added : 4 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3338 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 23 sheets defined 33.6% alpha, 9.9% beta 52 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 4.333A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.551A pdb=" N SER A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASP A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 735 through 739 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'A' and resid 822 through 840 removed outlier: 3.612A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 868 Processing helix chain 'A' and resid 872 through 895 Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.734A pdb=" N GLU A 901 " --> pdb=" O CYS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 923 removed outlier: 4.418A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.895A pdb=" N HIS A 937 " --> pdb=" O THR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 4.272A pdb=" N LYS A 966 " --> pdb=" O GLU A 962 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 995 removed outlier: 4.841A pdb=" N MET A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLU A 985 " --> pdb=" O CYS A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1005 removed outlier: 4.598A pdb=" N PHE A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.918A pdb=" N SER B 314 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 473 Processing helix chain 'C' and resid 479 through 492 Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.816A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 580 removed outlier: 5.205A pdb=" N GLU C 572 " --> pdb=" O MET C 568 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP C 573 " --> pdb=" O ASP C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 652 Processing helix chain 'C' and resid 666 through 685 Proline residue: C 674 - end of helix removed outlier: 4.100A pdb=" N SER C 684 " --> pdb=" O GLU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 776 Processing helix chain 'C' and resid 792 through 813 Processing helix chain 'C' and resid 822 through 828 Processing helix chain 'C' and resid 830 through 840 Processing helix chain 'C' and resid 850 through 856 Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 872 through 894 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 923 removed outlier: 4.513A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N PHE C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 960 through 974 removed outlier: 3.844A pdb=" N LYS C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 995 Processing helix chain 'C' and resid 996 through 1004 removed outlier: 4.442A pdb=" N PHE C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1007 No H-bonds generated for 'chain 'C' and resid 1005 through 1007' Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.538A pdb=" N ILE D 15 " --> pdb=" O ILE D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 308 through 313 removed outlier: 4.103A pdb=" N LYS D 312 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 313' Processing sheet with id=AA1, first strand: chain 'A' and resid 592 through 597 removed outlier: 6.258A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 653 " --> pdb=" O PHE A 624 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 691 Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 49 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 77 removed outlier: 3.512A pdb=" N ARG B 73 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY B 95 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR B 77 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE B 93 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 110 removed outlier: 4.466A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 146 Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 215 through 219 removed outlier: 3.705A pdb=" N TYR B 234 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.812A pdb=" N THR B 264 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AB4, first strand: chain 'C' and resid 591 through 592 Processing sheet with id=AB5, first strand: chain 'C' and resid 594 through 603 removed outlier: 6.872A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 632 through 633 Processing sheet with id=AB7, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=AB8, first strand: chain 'D' and resid 20 through 24 removed outlier: 3.539A pdb=" N PHE D 31 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.693A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AC2, first strand: chain 'D' and resid 137 through 138 removed outlier: 3.560A pdb=" N SER D 160 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 142 through 144 Processing sheet with id=AC4, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.563A pdb=" N LEU D 219 " --> pdb=" O VAL D 208 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 272 through 273 481 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 264 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.45: 7975 1.45 - 1.72: 9020 1.72 - 1.99: 160 1.99 - 2.25: 0 2.25 - 2.52: 1 Bond restraints: 17156 Sorted by residual: bond pdb=" C LYS B 81 " pdb=" N HIS B 89 " ideal model delta sigma weight residual 1.330 2.522 -1.192 1.29e-02 6.01e+03 8.53e+03 bond pdb=" C TYR B 80 " pdb=" N LYS B 81 " ideal model delta sigma weight residual 1.332 1.231 0.101 1.40e-02 5.10e+03 5.24e+01 bond pdb=" C VAL A 759 " pdb=" O VAL A 759 " ideal model delta sigma weight residual 1.237 1.184 0.054 1.17e-02 7.31e+03 2.10e+01 bond pdb=" C GLU C 918 " pdb=" O GLU C 918 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.18e-02 7.18e+03 1.83e+01 bond pdb=" O3' DC J 26 " pdb=" P DC J 27 " ideal model delta sigma weight residual 1.607 1.662 -0.055 1.50e-02 4.44e+03 1.34e+01 ... (remaining 17151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.89: 23668 7.89 - 15.78: 10 15.78 - 23.67: 0 23.67 - 31.56: 1 31.56 - 39.46: 3 Bond angle restraints: 23682 Sorted by residual: angle pdb=" O LYS B 81 " pdb=" C LYS B 81 " pdb=" N HIS B 89 " ideal model delta sigma weight residual 122.59 83.13 39.46 1.33e+00 5.65e-01 8.80e+02 angle pdb=" C LYS B 81 " pdb=" N HIS B 89 " pdb=" CA HIS B 89 " ideal model delta sigma weight residual 122.46 160.88 -38.42 1.41e+00 5.03e-01 7.43e+02 angle pdb=" CA LYS B 81 " pdb=" C LYS B 81 " pdb=" N HIS B 89 " ideal model delta sigma weight residual 116.84 151.86 -35.02 1.71e+00 3.42e-01 4.19e+02 angle pdb=" C TYR B 80 " pdb=" CA TYR B 80 " pdb=" CB TYR B 80 " ideal model delta sigma weight residual 109.65 84.04 25.61 2.07e+00 2.33e-01 1.53e+02 angle pdb=" CA TYR B 80 " pdb=" CB TYR B 80 " pdb=" CG TYR B 80 " ideal model delta sigma weight residual 113.90 129.40 -15.50 1.80e+00 3.09e-01 7.41e+01 ... (remaining 23677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.83: 9178 31.83 - 63.66: 775 63.66 - 95.49: 32 95.49 - 127.32: 2 127.32 - 159.15: 6 Dihedral angle restraints: 9993 sinusoidal: 4808 harmonic: 5185 Sorted by residual: dihedral pdb=" C TYR B 80 " pdb=" N TYR B 80 " pdb=" CA TYR B 80 " pdb=" CB TYR B 80 " ideal model delta harmonic sigma weight residual -122.60 -87.64 -34.96 0 2.50e+00 1.60e-01 1.96e+02 dihedral pdb=" N TYR B 80 " pdb=" C TYR B 80 " pdb=" CA TYR B 80 " pdb=" CB TYR B 80 " ideal model delta harmonic sigma weight residual 122.80 98.87 23.93 0 2.50e+00 1.60e-01 9.17e+01 dihedral pdb=" CA LYS B 81 " pdb=" C LYS B 81 " pdb=" N HIS B 89 " pdb=" CA HIS B 89 " ideal model delta harmonic sigma weight residual -180.00 -134.92 -45.08 0 5.00e+00 4.00e-02 8.13e+01 ... (remaining 9990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2559 0.156 - 0.312: 25 0.312 - 0.469: 2 0.469 - 0.625: 1 0.625 - 0.781: 2 Chirality restraints: 2589 Sorted by residual: chirality pdb=" CA ASN B 101 " pdb=" N ASN B 101 " pdb=" C ASN B 101 " pdb=" CB ASN B 101 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CA TYR B 80 " pdb=" N TYR B 80 " pdb=" C TYR B 80 " pdb=" CB TYR B 80 " both_signs ideal model delta sigma weight residual False 2.51 3.15 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA ASP C 986 " pdb=" N ASP C 986 " pdb=" C ASP C 986 " pdb=" CB ASP C 986 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.59 2.00e-01 2.50e+01 8.57e+00 ... (remaining 2586 not shown) Planarity restraints: 2647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 81 " -0.087 2.00e-02 2.50e+03 1.03e-01 1.06e+02 pdb=" C LYS B 81 " 0.176 2.00e-02 2.50e+03 pdb=" O LYS B 81 " -0.044 2.00e-02 2.50e+03 pdb=" N HIS B 89 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 80 " -0.098 2.00e-02 2.50e+03 5.30e-02 5.61e+01 pdb=" CG TYR B 80 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 TYR B 80 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 80 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 80 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 80 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 80 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 80 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 80 " -0.034 2.00e-02 2.50e+03 6.41e-02 4.11e+01 pdb=" C TYR D 80 " 0.111 2.00e-02 2.50e+03 pdb=" O TYR D 80 " -0.040 2.00e-02 2.50e+03 pdb=" N LYS D 81 " -0.037 2.00e-02 2.50e+03 ... (remaining 2644 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 200 2.45 - 3.07: 12983 3.07 - 3.68: 29492 3.68 - 4.29: 43585 4.29 - 4.90: 66941 Nonbonded interactions: 153201 Sorted by model distance: nonbonded pdb=" O LEU C 729 " pdb="ZN ZN C1101 " model vdw 1.842 2.230 nonbonded pdb=" O GLN B 265 " pdb=" OG1 THR B 266 " model vdw 1.950 3.040 nonbonded pdb=" O ALA A 941 " pdb=" ND1 HIS A 942 " model vdw 2.138 3.120 nonbonded pdb=" OD1 ASP C 600 " pdb=" N4 DC I 17 " model vdw 2.198 3.120 nonbonded pdb=" ND2 ASN D 335 " pdb=" OH TYR D 344 " model vdw 2.198 3.120 ... (remaining 153196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 459 through 1006 or (resid 1007 and (name N or name CA or \ name C or name O or name CB )) or resid 1101)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 116 or (resid 117 through 118 and (name N or nam \ e CA or name C or name O or name CB )) or resid 119 through 338 or resid 340 thr \ ough 350)) selection = (chain 'D' and (resid 1 through 336 or (resid 337 through 338 and (name N or nam \ e CA or name C or name O or name CB )) or resid 340 through 350)) } ncs_group { reference = (chain 'I' and (resid 5 through 18 or resid 20 through 33)) selection = (chain 'J' and (resid 5 through 18 or resid 20 through 33)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.450 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 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 : 0.011 1.192 17164 Z= 0.771 Angle : 1.071 41.670 23686 Z= 0.605 Chirality : 0.055 0.781 2589 Planarity : 0.006 0.103 2647 Dihedral : 20.609 159.149 6655 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 27.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.34 % Favored : 85.54 % Rotamer: Outliers : 1.72 % Allowed : 4.73 % Favored : 93.55 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.04 (0.14), residues: 1771 helix: -3.55 (0.15), residues: 533 sheet: -4.58 (0.26), residues: 212 loop : -4.34 (0.14), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 159 TYR 0.103 0.003 TYR B 80 PHE 0.018 0.002 PHE D 206 TRP 0.022 0.002 TRP D 317 HIS 0.007 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.01083 (17156) covalent geometry : angle 0.96562 (23682) hydrogen bonds : bond 0.14783 ( 613) hydrogen bonds : angle 8.44440 ( 1617) metal coordination : bond 0.11909 ( 8) metal coordination : angle 35.64946 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 328 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6777 (ttt180) REVERT: A 916 PHE cc_start: 0.7639 (t80) cc_final: 0.7229 (t80) REVERT: A 926 TYR cc_start: 0.7492 (p90) cc_final: 0.4025 (p90) REVERT: A 970 ARG cc_start: 0.6383 (mtp85) cc_final: 0.5753 (mtp85) REVERT: B 102 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: B 172 TRP cc_start: 0.8207 (t-100) cc_final: 0.7688 (t-100) REVERT: B 321 ASN cc_start: 0.7537 (p0) cc_final: 0.7233 (p0) REVERT: C 859 THR cc_start: 0.7414 (OUTLIER) cc_final: 0.7197 (p) REVERT: D 159 ARG cc_start: 0.7414 (ptp-110) cc_final: 0.7050 (ptp-170) REVERT: D 206 PHE cc_start: 0.7462 (m-80) cc_final: 0.7257 (m-80) outliers start: 27 outliers final: 4 residues processed: 349 average time/residue: 0.1461 time to fit residues: 73.7280 Evaluate side-chains 219 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 212 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 773 ARG Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0170 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN A 609 HIS A 633 HIS A 647 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS A 965 ASN B 53 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN C 473 ASN C 520 GLN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.138575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.125092 restraints weight = 34903.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.127137 restraints weight = 22687.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.128550 restraints weight = 16413.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.129623 restraints weight = 12905.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.130300 restraints weight = 10743.034| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 17164 Z= 0.233 Angle : 0.811 18.062 23686 Z= 0.427 Chirality : 0.047 0.176 2589 Planarity : 0.006 0.067 2647 Dihedral : 23.023 157.756 3194 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 22.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.62 % Favored : 88.32 % Rotamer: Outliers : 1.85 % Allowed : 14.24 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.58 (0.16), residues: 1773 helix: -2.23 (0.18), residues: 546 sheet: -3.97 (0.28), residues: 230 loop : -3.39 (0.16), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 972 TYR 0.039 0.002 TYR B 80 PHE 0.030 0.003 PHE C 557 TRP 0.027 0.003 TRP D 317 HIS 0.011 0.002 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00532 (17156) covalent geometry : angle 0.80249 (23682) hydrogen bonds : bond 0.05512 ( 613) hydrogen bonds : angle 6.59003 ( 1617) metal coordination : bond 0.04366 ( 8) metal coordination : angle 9.25130 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 858 MET cc_start: 0.7516 (mmt) cc_final: 0.7013 (mmt) REVERT: A 886 TYR cc_start: 0.6901 (t80) cc_final: 0.6526 (t80) REVERT: A 916 PHE cc_start: 0.7456 (t80) cc_final: 0.7055 (t80) REVERT: A 926 TYR cc_start: 0.7769 (p90) cc_final: 0.5392 (p90) REVERT: A 972 ARG cc_start: 0.6174 (ttp80) cc_final: 0.5897 (ttp80) REVERT: A 974 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.6053 (ptm) REVERT: A 994 TYR cc_start: 0.8201 (t80) cc_final: 0.7522 (t80) REVERT: B 1 MET cc_start: 0.1847 (mpp) cc_final: 0.0668 (mmt) REVERT: B 321 ASN cc_start: 0.8000 (p0) cc_final: 0.7792 (p0) REVERT: C 568 MET cc_start: 0.7658 (mmm) cc_final: 0.7399 (mmm) REVERT: C 841 MET cc_start: 0.4035 (mmp) cc_final: 0.3668 (mmp) REVERT: D 16 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7538 (pt0) REVERT: D 46 PHE cc_start: 0.7855 (m-80) cc_final: 0.7624 (m-80) REVERT: D 299 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7577 (mp) outliers start: 29 outliers final: 13 residues processed: 283 average time/residue: 0.1321 time to fit residues: 56.4446 Evaluate side-chains 229 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 299 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 116 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 335 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 818 HIS ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.133939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.119361 restraints weight = 35451.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.121646 restraints weight = 22100.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.123273 restraints weight = 15636.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.124400 restraints weight = 12064.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.125229 restraints weight = 9887.323| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 17164 Z= 0.284 Angle : 0.802 19.661 23686 Z= 0.421 Chirality : 0.047 0.179 2589 Planarity : 0.006 0.061 2647 Dihedral : 23.048 158.596 3182 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 25.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 3.26 % Allowed : 18.33 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.17), residues: 1773 helix: -1.93 (0.18), residues: 559 sheet: -3.92 (0.27), residues: 240 loop : -3.10 (0.17), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 703 TYR 0.021 0.003 TYR A 725 PHE 0.024 0.003 PHE C 557 TRP 0.030 0.003 TRP C 829 HIS 0.008 0.002 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00644 (17156) covalent geometry : angle 0.79135 (23682) hydrogen bonds : bond 0.05609 ( 613) hydrogen bonds : angle 6.35711 ( 1617) metal coordination : bond 0.06151 ( 8) metal coordination : angle 10.04042 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 658 MET cc_start: 0.7917 (mpp) cc_final: 0.7014 (mtm) REVERT: A 858 MET cc_start: 0.7622 (mmt) cc_final: 0.6748 (mmt) REVERT: A 886 TYR cc_start: 0.6972 (t80) cc_final: 0.6747 (t80) REVERT: A 916 PHE cc_start: 0.7608 (t80) cc_final: 0.7342 (t80) REVERT: A 974 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6250 (ptp) REVERT: A 983 GLU cc_start: 0.6183 (pt0) cc_final: 0.5965 (tp30) REVERT: B 94 HIS cc_start: 0.6843 (t-90) cc_final: 0.6641 (t-170) REVERT: B 197 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7251 (mm) REVERT: B 232 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7488 (p0) REVERT: C 605 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8636 (p) REVERT: C 969 ARG cc_start: 0.8578 (ttm110) cc_final: 0.8342 (tpp80) REVERT: D 16 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8074 (pt0) REVERT: D 285 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5937 (mtm) outliers start: 51 outliers final: 26 residues processed: 280 average time/residue: 0.1255 time to fit residues: 53.4959 Evaluate side-chains 246 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 143 optimal weight: 0.0870 chunk 80 optimal weight: 8.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 GLN B 232 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.137573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.123746 restraints weight = 34988.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.125922 restraints weight = 22074.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.127489 restraints weight = 15694.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.128525 restraints weight = 12105.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.129189 restraints weight = 9972.520| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17164 Z= 0.182 Angle : 0.723 14.665 23686 Z= 0.380 Chirality : 0.044 0.179 2589 Planarity : 0.005 0.055 2647 Dihedral : 23.017 158.563 3180 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 3.26 % Allowed : 19.92 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.18), residues: 1773 helix: -1.57 (0.19), residues: 559 sheet: -3.66 (0.29), residues: 231 loop : -2.83 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 972 TYR 0.021 0.002 TYR A 725 PHE 0.018 0.002 PHE C 557 TRP 0.026 0.002 TRP C 829 HIS 0.008 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00413 (17156) covalent geometry : angle 0.71541 (23682) hydrogen bonds : bond 0.04732 ( 613) hydrogen bonds : angle 6.11243 ( 1617) metal coordination : bond 0.04672 ( 8) metal coordination : angle 7.92951 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 262 time to evaluate : 0.602 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 658 MET cc_start: 0.7996 (mpp) cc_final: 0.6935 (mtm) REVERT: A 711 LEU cc_start: 0.8535 (tt) cc_final: 0.8329 (tt) REVERT: A 858 MET cc_start: 0.7458 (mmt) cc_final: 0.6615 (mmt) REVERT: A 916 PHE cc_start: 0.7428 (t80) cc_final: 0.7215 (t80) REVERT: A 983 GLU cc_start: 0.6011 (pt0) cc_final: 0.5610 (tp30) REVERT: A 994 TYR cc_start: 0.8103 (t80) cc_final: 0.7735 (t80) REVERT: A 1000 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7737 (mm-40) REVERT: B 56 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6683 (tppt) REVERT: B 234 TYR cc_start: 0.7142 (m-80) cc_final: 0.6737 (m-80) REVERT: C 466 VAL cc_start: 0.8253 (t) cc_final: 0.7878 (p) REVERT: C 605 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8397 (p) REVERT: C 849 MET cc_start: 0.6481 (tpt) cc_final: 0.6197 (tpp) REVERT: C 915 ARG cc_start: 0.6506 (mtm-85) cc_final: 0.6182 (mtm-85) REVERT: D 16 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: D 73 ARG cc_start: 0.7080 (ptt-90) cc_final: 0.6775 (ptt-90) REVERT: D 99 PRO cc_start: 0.8845 (Cg_exo) cc_final: 0.8634 (Cg_endo) REVERT: D 299 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7603 (mp) outliers start: 51 outliers final: 25 residues processed: 299 average time/residue: 0.1234 time to fit residues: 56.7404 Evaluate side-chains 253 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 28 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 133 optimal weight: 0.1980 chunk 152 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.135733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.121701 restraints weight = 35244.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.123847 restraints weight = 22385.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.125316 restraints weight = 16011.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.126453 restraints weight = 12491.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.127254 restraints weight = 10232.927| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 17164 Z= 0.222 Angle : 0.749 14.056 23686 Z= 0.390 Chirality : 0.045 0.207 2589 Planarity : 0.006 0.073 2647 Dihedral : 23.094 158.475 3180 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 4.28 % Allowed : 20.24 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.18), residues: 1773 helix: -1.28 (0.20), residues: 561 sheet: -3.69 (0.28), residues: 238 loop : -2.76 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 703 TYR 0.019 0.002 TYR A 725 PHE 0.017 0.002 PHE D 48 TRP 0.028 0.002 TRP C 829 HIS 0.010 0.002 HIS C 942 Details of bonding type rmsd covalent geometry : bond 0.00507 (17156) covalent geometry : angle 0.74195 (23682) hydrogen bonds : bond 0.04970 ( 613) hydrogen bonds : angle 6.07179 ( 1617) metal coordination : bond 0.05494 ( 8) metal coordination : angle 7.94439 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 241 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 658 MET cc_start: 0.8031 (mpp) cc_final: 0.7260 (mpp) REVERT: A 956 TRP cc_start: 0.8539 (m100) cc_final: 0.8004 (m100) REVERT: A 974 MET cc_start: 0.6661 (ptp) cc_final: 0.6131 (ptm) REVERT: A 983 GLU cc_start: 0.6365 (pt0) cc_final: 0.5845 (tp30) REVERT: A 984 MET cc_start: 0.7165 (mmp) cc_final: 0.6906 (mmp) REVERT: A 994 TYR cc_start: 0.8147 (t80) cc_final: 0.7682 (t80) REVERT: A 1000 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7824 (mm110) REVERT: B 196 ILE cc_start: 0.6844 (tp) cc_final: 0.6576 (tp) REVERT: C 466 VAL cc_start: 0.8329 (t) cc_final: 0.7961 (p) REVERT: C 605 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8376 (p) REVERT: C 788 VAL cc_start: 0.7975 (t) cc_final: 0.6966 (t) REVERT: C 841 MET cc_start: 0.4812 (mmp) cc_final: 0.4404 (mmp) REVERT: C 842 ASN cc_start: 0.7997 (m-40) cc_final: 0.7732 (m-40) REVERT: C 847 MET cc_start: 0.6727 (tpp) cc_final: 0.6328 (tpp) REVERT: C 849 MET cc_start: 0.6689 (tpt) cc_final: 0.6393 (tpp) REVERT: D 16 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7907 (pt0) outliers start: 67 outliers final: 37 residues processed: 294 average time/residue: 0.1273 time to fit residues: 57.2557 Evaluate side-chains 251 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 473 ASN Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 ASN A 763 ASN B 16 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.139305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.125853 restraints weight = 34976.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.127951 restraints weight = 22424.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.129366 restraints weight = 16070.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.130478 restraints weight = 12561.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.131060 restraints weight = 10354.901| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17164 Z= 0.172 Angle : 0.725 12.026 23686 Z= 0.380 Chirality : 0.044 0.198 2589 Planarity : 0.005 0.054 2647 Dihedral : 23.064 158.595 3180 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 3.26 % Allowed : 21.84 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.18), residues: 1773 helix: -1.03 (0.20), residues: 558 sheet: -3.53 (0.28), residues: 239 loop : -2.62 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 972 TYR 0.031 0.002 TYR B 234 PHE 0.036 0.002 PHE A 916 TRP 0.024 0.002 TRP C 829 HIS 0.008 0.002 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00393 (17156) covalent geometry : angle 0.72086 (23682) hydrogen bonds : bond 0.04555 ( 613) hydrogen bonds : angle 5.98704 ( 1617) metal coordination : bond 0.03117 ( 8) metal coordination : angle 5.88132 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 545 VAL cc_start: 0.8654 (p) cc_final: 0.8424 (p) REVERT: A 658 MET cc_start: 0.8057 (mpp) cc_final: 0.7063 (mtm) REVERT: A 974 MET cc_start: 0.6447 (ptp) cc_final: 0.6067 (ptm) REVERT: A 983 GLU cc_start: 0.6035 (pt0) cc_final: 0.5804 (tp30) REVERT: A 994 TYR cc_start: 0.8053 (t80) cc_final: 0.7745 (t80) REVERT: B 196 ILE cc_start: 0.6517 (tp) cc_final: 0.6298 (tp) REVERT: C 466 VAL cc_start: 0.8130 (t) cc_final: 0.7733 (p) REVERT: C 605 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8154 (p) REVERT: C 842 ASN cc_start: 0.7707 (m-40) cc_final: 0.7402 (m-40) REVERT: C 847 MET cc_start: 0.6756 (tpp) cc_final: 0.5707 (tpp) REVERT: C 956 TRP cc_start: 0.7153 (m100) cc_final: 0.6805 (m-10) REVERT: D 16 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8254 (pt0) outliers start: 51 outliers final: 28 residues processed: 294 average time/residue: 0.1208 time to fit residues: 55.2438 Evaluate side-chains 253 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 144 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 766 HIS ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN D 101 ASN D 265 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.138502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.124624 restraints weight = 34994.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.126808 restraints weight = 22047.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.128368 restraints weight = 15632.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.129322 restraints weight = 12058.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.130176 restraints weight = 10058.711| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17164 Z= 0.191 Angle : 0.748 14.187 23686 Z= 0.389 Chirality : 0.045 0.275 2589 Planarity : 0.005 0.058 2647 Dihedral : 23.035 158.764 3180 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 3.70 % Allowed : 22.80 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.18), residues: 1773 helix: -0.96 (0.20), residues: 559 sheet: -3.43 (0.29), residues: 242 loop : -2.48 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 970 TYR 0.036 0.002 TYR B 234 PHE 0.034 0.002 PHE A 916 TRP 0.031 0.002 TRP A 956 HIS 0.011 0.002 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00437 (17156) covalent geometry : angle 0.74545 (23682) hydrogen bonds : bond 0.04628 ( 613) hydrogen bonds : angle 5.93752 ( 1617) metal coordination : bond 0.02899 ( 8) metal coordination : angle 4.69954 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 239 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 480 GLN cc_start: 0.6490 (mt0) cc_final: 0.6254 (mt0) REVERT: A 483 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7099 (ttpt) REVERT: A 545 VAL cc_start: 0.8681 (p) cc_final: 0.8478 (p) REVERT: A 658 MET cc_start: 0.8147 (mpp) cc_final: 0.7442 (mtm) REVERT: A 974 MET cc_start: 0.6616 (ptp) cc_final: 0.6090 (ptm) REVERT: A 983 GLU cc_start: 0.6206 (pt0) cc_final: 0.5805 (tp30) REVERT: A 994 TYR cc_start: 0.8245 (t80) cc_final: 0.7740 (t80) REVERT: C 466 VAL cc_start: 0.8163 (t) cc_final: 0.7902 (p) REVERT: C 605 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8171 (p) REVERT: C 785 ILE cc_start: 0.7991 (mp) cc_final: 0.7441 (mt) REVERT: C 841 MET cc_start: 0.4267 (mmp) cc_final: 0.4050 (mmp) REVERT: C 842 ASN cc_start: 0.7734 (m-40) cc_final: 0.7489 (m-40) REVERT: C 847 MET cc_start: 0.6896 (tpp) cc_final: 0.6420 (mpp) REVERT: D 99 PRO cc_start: 0.8919 (Cg_exo) cc_final: 0.8668 (Cg_endo) outliers start: 58 outliers final: 36 residues processed: 284 average time/residue: 0.1200 time to fit residues: 53.3790 Evaluate side-chains 248 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 473 ASN Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 46 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 158 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.138983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.125436 restraints weight = 35030.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.127487 restraints weight = 22580.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.128965 restraints weight = 16282.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.129972 restraints weight = 12671.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.130791 restraints weight = 10545.589| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17164 Z= 0.187 Angle : 0.751 15.223 23686 Z= 0.390 Chirality : 0.045 0.212 2589 Planarity : 0.005 0.058 2647 Dihedral : 23.027 158.823 3180 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 3.38 % Allowed : 23.69 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.19), residues: 1773 helix: -0.81 (0.21), residues: 562 sheet: -3.39 (0.29), residues: 243 loop : -2.45 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 703 TYR 0.022 0.002 TYR A 725 PHE 0.034 0.002 PHE D 206 TRP 0.029 0.002 TRP A 956 HIS 0.011 0.002 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00430 (17156) covalent geometry : angle 0.74960 (23682) hydrogen bonds : bond 0.04556 ( 613) hydrogen bonds : angle 5.92934 ( 1617) metal coordination : bond 0.02463 ( 8) metal coordination : angle 3.57084 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 658 MET cc_start: 0.8159 (mpp) cc_final: 0.7339 (mtm) REVERT: A 803 GLU cc_start: 0.6809 (tp30) cc_final: 0.6551 (tp30) REVERT: A 974 MET cc_start: 0.6452 (ptp) cc_final: 0.6016 (ptm) REVERT: A 983 GLU cc_start: 0.6098 (pt0) cc_final: 0.5764 (tp30) REVERT: A 1003 MET cc_start: 0.7710 (mmm) cc_final: 0.7506 (tpt) REVERT: C 466 VAL cc_start: 0.8202 (t) cc_final: 0.7787 (p) REVERT: C 605 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8150 (p) REVERT: C 785 ILE cc_start: 0.7875 (mp) cc_final: 0.7324 (mt) REVERT: C 842 ASN cc_start: 0.7676 (m-40) cc_final: 0.7399 (m-40) REVERT: C 847 MET cc_start: 0.6886 (tpp) cc_final: 0.6472 (mpp) REVERT: C 849 MET cc_start: 0.6577 (tpt) cc_final: 0.6257 (tpp) REVERT: D 99 PRO cc_start: 0.8858 (Cg_exo) cc_final: 0.8615 (Cg_endo) REVERT: D 177 ASP cc_start: 0.7159 (m-30) cc_final: 0.6941 (m-30) outliers start: 53 outliers final: 40 residues processed: 268 average time/residue: 0.1146 time to fit residues: 48.4380 Evaluate side-chains 253 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 120 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 175 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.137127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.123013 restraints weight = 35251.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.125150 restraints weight = 22545.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.126679 restraints weight = 16194.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.127761 restraints weight = 12601.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.128416 restraints weight = 10435.637| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17164 Z= 0.220 Angle : 0.772 15.238 23686 Z= 0.401 Chirality : 0.046 0.207 2589 Planarity : 0.005 0.061 2647 Dihedral : 23.048 158.620 3180 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 3.07 % Allowed : 24.39 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.19), residues: 1773 helix: -0.87 (0.21), residues: 559 sheet: -3.30 (0.29), residues: 246 loop : -2.46 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 915 TYR 0.022 0.002 TYR A 725 PHE 0.027 0.002 PHE D 206 TRP 0.027 0.002 TRP C 829 HIS 0.011 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00508 (17156) covalent geometry : angle 0.77129 (23682) hydrogen bonds : bond 0.04761 ( 613) hydrogen bonds : angle 5.97620 ( 1617) metal coordination : bond 0.02916 ( 8) metal coordination : angle 3.03169 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 658 MET cc_start: 0.7875 (mpp) cc_final: 0.6896 (mtm) REVERT: A 974 MET cc_start: 0.6617 (ptp) cc_final: 0.6268 (ptm) REVERT: A 983 GLU cc_start: 0.6217 (pt0) cc_final: 0.5782 (tp30) REVERT: C 466 VAL cc_start: 0.8253 (t) cc_final: 0.7867 (p) REVERT: C 578 MET cc_start: 0.6525 (ttt) cc_final: 0.6287 (mtm) REVERT: C 605 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8143 (p) REVERT: C 711 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8734 (tt) REVERT: C 785 ILE cc_start: 0.8202 (mp) cc_final: 0.7697 (mt) REVERT: C 842 ASN cc_start: 0.7809 (m-40) cc_final: 0.7542 (m-40) REVERT: C 847 MET cc_start: 0.6937 (tpp) cc_final: 0.6537 (mpp) REVERT: C 849 MET cc_start: 0.6730 (tpt) cc_final: 0.6423 (tpp) REVERT: D 99 PRO cc_start: 0.8882 (Cg_exo) cc_final: 0.8640 (Cg_endo) outliers start: 48 outliers final: 41 residues processed: 265 average time/residue: 0.1108 time to fit residues: 46.6301 Evaluate side-chains 260 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 937 HIS Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain C residue 473 ASN Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 17 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.139852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.126386 restraints weight = 34909.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.128413 restraints weight = 22577.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.129882 restraints weight = 16325.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.130993 restraints weight = 12700.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.131603 restraints weight = 10435.987| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17164 Z= 0.177 Angle : 0.754 13.746 23686 Z= 0.391 Chirality : 0.045 0.215 2589 Planarity : 0.005 0.062 2647 Dihedral : 23.023 158.814 3180 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 2.81 % Allowed : 24.78 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.19), residues: 1773 helix: -0.79 (0.21), residues: 557 sheet: -3.04 (0.30), residues: 251 loop : -2.42 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 703 TYR 0.022 0.002 TYR A 725 PHE 0.028 0.002 PHE D 206 TRP 0.023 0.002 TRP C 829 HIS 0.009 0.001 HIS D 207 Details of bonding type rmsd covalent geometry : bond 0.00408 (17156) covalent geometry : angle 0.75257 (23682) hydrogen bonds : bond 0.04402 ( 613) hydrogen bonds : angle 5.92897 ( 1617) metal coordination : bond 0.02031 ( 8) metal coordination : angle 3.18729 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 658 MET cc_start: 0.7808 (mpp) cc_final: 0.6939 (mtm) REVERT: A 974 MET cc_start: 0.6270 (ptp) cc_final: 0.5910 (ptm) REVERT: A 983 GLU cc_start: 0.6099 (pt0) cc_final: 0.5871 (tp30) REVERT: C 466 VAL cc_start: 0.8072 (t) cc_final: 0.7630 (p) REVERT: C 578 MET cc_start: 0.6319 (ttt) cc_final: 0.6074 (mtm) REVERT: C 605 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.8072 (p) REVERT: C 711 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8600 (tt) REVERT: C 785 ILE cc_start: 0.8220 (mp) cc_final: 0.7771 (mt) REVERT: C 842 ASN cc_start: 0.7584 (m-40) cc_final: 0.7329 (m-40) REVERT: C 847 MET cc_start: 0.7047 (tpp) cc_final: 0.6552 (mpp) REVERT: C 849 MET cc_start: 0.6569 (tpt) cc_final: 0.6365 (tpp) REVERT: D 99 PRO cc_start: 0.8824 (Cg_exo) cc_final: 0.8580 (Cg_endo) outliers start: 44 outliers final: 37 residues processed: 274 average time/residue: 0.1176 time to fit residues: 49.4673 Evaluate side-chains 253 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 937 HIS Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 181 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 102 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 335 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.142071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.128844 restraints weight = 34499.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.130920 restraints weight = 22119.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.132396 restraints weight = 15807.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.133402 restraints weight = 12265.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.134225 restraints weight = 10128.849| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17164 Z= 0.161 Angle : 0.744 14.790 23686 Z= 0.385 Chirality : 0.044 0.213 2589 Planarity : 0.005 0.060 2647 Dihedral : 22.965 159.090 3180 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 2.36 % Allowed : 25.67 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.83 (0.19), residues: 1773 helix: -0.64 (0.21), residues: 552 sheet: -2.99 (0.30), residues: 254 loop : -2.35 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 703 TYR 0.021 0.002 TYR A 725 PHE 0.024 0.002 PHE D 206 TRP 0.022 0.002 TRP C 829 HIS 0.008 0.001 HIS C 766 Details of bonding type rmsd covalent geometry : bond 0.00368 (17156) covalent geometry : angle 0.74251 (23682) hydrogen bonds : bond 0.04245 ( 613) hydrogen bonds : angle 5.85646 ( 1617) metal coordination : bond 0.01550 ( 8) metal coordination : angle 3.23095 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2364.80 seconds wall clock time: 42 minutes 10.69 seconds (2530.69 seconds total)