Starting phenix.real_space_refine on Sat Sep 12 14:13:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xnz_22274/09_2026/6xnz_22274.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xnz_22274/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6xnz_22274/09_2026/6xnz_22274.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xnz_22274/09_2026/6xnz_22274.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xnz_22274/09_2026/6xnz_22274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xnz_22274/09_2026/6xnz_22274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xnz_22274/09_2026/6xnz_22274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xnz_22274/09_2026/6xnz_22274.map" } 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-2.2.1-6174/lib/python3.11/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: 3.68, per 1000 atoms: 0.22 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: 1.51 Conformation dependent library (CDL) restraints added in 579.6 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: 2.19 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: 3.45 Time building geometry restraints manager: 1.89 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=" O3' DC J 26 " pdb=" P DC J 27 " ideal model delta sigma weight residual 1.607 1.662 -0.055 1.20e-02 6.94e+03 2.10e+01 bond pdb=" O3' DC x 41 " pdb=" P DT x 42 " ideal model delta sigma weight residual 1.607 1.659 -0.052 1.20e-02 6.94e+03 1.87e+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: 2537 0.156 - 0.312: 47 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 19.920 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 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= 0.817 Angle : 1.101 41.670 23686 Z= 0.683 Chirality : 0.060 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/Z covalent geometry : bond 0.01102 / 0.81 (17156) covalent geometry : angle 0.99874 / 0.68 (23682) hydrogen bonds : bond 0.14783 / 10.45 ( 613) hydrogen bonds : angle 8.44440 / 6.07 ( 1617) metal coordination : bond 0.11909 / 8.71 ( 8) metal coordination : angle 35.64946 / 17.80 ( 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 : 0.614 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: 0.6728 (ttt-90) REVERT: A 916 PHE cc_start: 0.7639 (t80) cc_final: 0.7227 (t80) REVERT: A 926 TYR cc_start: 0.7492 (p90) cc_final: 0.4037 (p90) REVERT: A 970 ARG cc_start: 0.6383 (mtp85) cc_final: 0.5788 (mtp85) REVERT: B 102 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7507 (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: 0.7231 (p0) REVERT: C 847 MET cc_start: 0.6777 (mmm) cc_final: 0.6567 (mmm) REVERT: C 859 THR cc_start: 0.7414 (OUTLIER) cc_final: 0.7211 (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: 0.7255 (m-80) outliers start: 27 outliers final: 5 residues processed: 349 average time/residue: 0.1590 time to fit residues: 80.5140 Evaluate side-chains 222 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 A residue 972 ARG 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: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 633 HIS A 647 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS A 763 ASN 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 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 222 HIS D 265 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.137430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.123584 restraints weight = 34943.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.125858 restraints weight = 21783.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.127452 restraints weight = 15306.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.128399 restraints weight = 11739.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.129295 restraints weight = 9764.341| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 17164 Z= 0.235 Angle : 0.873 20.464 23686 Z= 0.462 Chirality : 0.051 0.249 2589 Planarity : 0.007 0.070 2647 Dihedral : 23.057 157.312 3198 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.62 % Favored : 88.32 % Rotamer: Outliers : 2.43 % Allowed : 13.98 % Favored : 83.59 % 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: -4.67 (0.16), residues: 1773 helix: -2.40 (0.18), residues: 546 sheet: -3.88 (0.28), residues: 233 loop : -3.43 (0.16), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 73 TYR 0.055 0.003 TYR B 80 PHE 0.030 0.003 PHE A 475 TRP 0.025 0.003 TRP C 829 HIS 0.012 0.002 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (17156) covalent geometry : angle 0.86119 / 0.46 (23682) hydrogen bonds : bond 0.06216 / 4.25 ( 613) hydrogen bonds : angle 6.80571 / 4.96 ( 1617) metal coordination : bond 0.06896 / 4.70 ( 8) metal coordination : angle 10.88510 / 5.44 ( 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 305 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 LEU cc_start: 0.8687 (tt) cc_final: 0.8476 (tt) REVERT: A 855 ARG cc_start: 0.7288 (mtt90) cc_final: 0.6998 (mtm-85) REVERT: A 858 MET cc_start: 0.7656 (mmt) cc_final: 0.7092 (mmt) REVERT: A 886 TYR cc_start: 0.6857 (t80) cc_final: 0.6455 (t80) REVERT: A 916 PHE cc_start: 0.7560 (t80) cc_final: 0.7088 (t80) REVERT: A 926 TYR cc_start: 0.7716 (p90) cc_final: 0.5125 (p90) REVERT: A 970 ARG cc_start: 0.6534 (mtp85) cc_final: 0.6176 (ttm110) REVERT: B 1 MET cc_start: 0.1859 (mpp) cc_final: 0.0765 (mmt) REVERT: B 74 TYR cc_start: 0.8315 (m-80) cc_final: 0.7907 (m-80) REVERT: B 172 TRP cc_start: 0.8150 (t-100) cc_final: 0.7800 (t-100) REVERT: B 321 ASN cc_start: 0.7926 (p0) cc_final: 0.7665 (p0) REVERT: C 848 MET cc_start: 0.7239 (mmm) cc_final: 0.6913 (mmt) REVERT: D 16 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: D 206 PHE cc_start: 0.7618 (m-80) cc_final: 0.7408 (m-80) outliers start: 38 outliers final: 19 residues processed: 295 average time/residue: 0.1419 time to fit residues: 63.1526 Evaluate side-chains 236 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 89 HIS 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 631 ILE Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 239 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 116 optimal weight: 1.9990 chunk 178 optimal weight: 30.0000 chunk 105 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 182 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN B 232 ASN B 335 ASN C 818 HIS C 975 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 265 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.132094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.117229 restraints weight = 36089.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.119528 restraints weight = 22614.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.121141 restraints weight = 16080.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.122257 restraints weight = 12465.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.123074 restraints weight = 10313.573| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 17164 Z= 0.323 Angle : 0.890 20.976 23686 Z= 0.471 Chirality : 0.052 0.230 2589 Planarity : 0.006 0.060 2647 Dihedral : 23.121 157.731 3184 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.52 % Favored : 87.48 % Rotamer: Outliers : 3.77 % Allowed : 18.20 % Favored : 78.03 % 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: -4.44 (0.17), residues: 1773 helix: -2.18 (0.18), residues: 548 sheet: -3.95 (0.26), residues: 259 loop : -3.19 (0.17), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 969 TYR 0.025 0.003 TYR B 80 PHE 0.020 0.003 PHE C 622 TRP 0.030 0.003 TRP C 829 HIS 0.012 0.002 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.32 (17156) covalent geometry : angle 0.87805 / 0.47 (23682) hydrogen bonds : bond 0.06519 / 4.43 ( 613) hydrogen bonds : angle 6.64035 / 4.84 ( 1617) metal coordination : bond 0.07236 / 5.01 ( 8) metal coordination : angle 11.20209 / 5.65 ( 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 294 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 0.638 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 600 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7434 (t70) REVERT: A 682 MET cc_start: 0.8020 (mtp) cc_final: 0.7818 (mtm) REVERT: A 738 SER cc_start: 0.6593 (OUTLIER) cc_final: 0.6228 (p) REVERT: A 830 GLN cc_start: 0.7292 (mm-40) cc_final: 0.6922 (mm-40) REVERT: A 855 ARG cc_start: 0.7588 (mtt90) cc_final: 0.7302 (mtm-85) REVERT: A 916 PHE cc_start: 0.7734 (t80) cc_final: 0.7442 (t80) REVERT: B 197 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7255 (mm) REVERT: B 321 ASN cc_start: 0.8108 (p0) cc_final: 0.7898 (p0) REVERT: C 702 PHE cc_start: 0.7712 (m-80) cc_final: 0.7424 (m-80) REVERT: C 790 SER cc_start: 0.7929 (t) cc_final: 0.7664 (m) REVERT: C 841 MET cc_start: 0.4506 (mmp) cc_final: 0.4280 (mmp) REVERT: C 842 ASN cc_start: 0.8119 (m-40) cc_final: 0.7890 (m-40) REVERT: C 847 MET cc_start: 0.6647 (mpp) cc_final: 0.6048 (tpp) REVERT: C 974 MET cc_start: 0.7243 (ttt) cc_final: 0.6956 (ttt) REVERT: D 206 PHE cc_start: 0.7727 (m-80) cc_final: 0.7515 (m-80) REVERT: D 285 MET cc_start: 0.6729 (mpp) cc_final: 0.6324 (mtm) REVERT: D 299 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7807 (mp) REVERT: D 302 MET cc_start: 0.6493 (tmm) cc_final: 0.6095 (ttm) outliers start: 59 outliers final: 29 residues processed: 281 average time/residue: 0.1433 time to fit residues: 60.6078 Evaluate side-chains 229 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 600 ASP Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 5 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 120 VAL 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 292 LEU Chi-restraints excluded: chain C residue 472 VAL 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 708 ASP Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 299 ILE 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: 3.9990 chunk 67 optimal weight: 10.0000 chunk 155 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 183 optimal weight: 30.0000 chunk 43 optimal weight: 0.0170 chunk 32 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 overall best weight: 0.7436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 ASN B 47 HIS ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 222 HIS D 265 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.139151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.124638 restraints weight = 35021.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.126998 restraints weight = 21685.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.128693 restraints weight = 15246.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.129891 restraints weight = 11666.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.130635 restraints weight = 9474.937| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17164 Z= 0.178 Angle : 0.781 15.343 23686 Z= 0.414 Chirality : 0.049 0.253 2589 Planarity : 0.006 0.054 2647 Dihedral : 23.057 158.656 3181 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 2.62 % Allowed : 21.33 % Favored : 76.05 % 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: -3.99 (0.17), residues: 1773 helix: -1.88 (0.19), residues: 547 sheet: -3.72 (0.28), residues: 234 loop : -2.90 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 703 TYR 0.024 0.002 TYR A 725 PHE 0.026 0.002 PHE C 557 TRP 0.027 0.002 TRP C 829 HIS 0.012 0.002 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (17156) covalent geometry : angle 0.77395 / 0.41 (23682) hydrogen bonds : bond 0.05481 / 3.71 ( 613) hydrogen bonds : angle 6.37687 / 4.64 ( 1617) metal coordination : bond 0.03362 / 2.30 ( 8) metal coordination : angle 8.34329 / 4.33 ( 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 303 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 262 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 658 MET cc_start: 0.7893 (mpp) cc_final: 0.7410 (mpp) REVERT: A 858 MET cc_start: 0.7807 (mmt) cc_final: 0.6977 (mmt) REVERT: A 916 PHE cc_start: 0.7556 (t80) cc_final: 0.7265 (t80) REVERT: A 940 LEU cc_start: 0.8312 (mp) cc_final: 0.7916 (mp) REVERT: A 994 TYR cc_start: 0.8181 (t80) cc_final: 0.7484 (t80) REVERT: B 91 TYR cc_start: 0.7039 (m-80) cc_final: 0.5991 (m-80) REVERT: B 321 ASN cc_start: 0.8054 (p0) cc_final: 0.7852 (p0) REVERT: B 322 MET cc_start: 0.6368 (mpp) cc_final: 0.6070 (mpp) REVERT: C 605 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8463 (p) REVERT: C 841 MET cc_start: 0.4636 (mmp) cc_final: 0.4232 (mmp) REVERT: C 847 MET cc_start: 0.6401 (mpp) cc_final: 0.5886 (tpp) REVERT: C 848 MET cc_start: 0.7213 (mmm) cc_final: 0.6913 (mmt) REVERT: D 73 ARG cc_start: 0.6854 (ptt-90) cc_final: 0.6480 (ptt-90) REVERT: D 206 PHE cc_start: 0.7354 (m-80) cc_final: 0.7086 (m-80) REVERT: D 285 MET cc_start: 0.6375 (mpp) cc_final: 0.6001 (mtm) REVERT: D 299 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7590 (mp) outliers start: 41 outliers final: 23 residues processed: 296 average time/residue: 0.1279 time to fit residues: 58.8830 Evaluate side-chains 244 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 605 VAL Chi-restraints excluded: chain A residue 638 VAL 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 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 316 ILE 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 631 ILE Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 883 MET 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: 4.9990 chunk 174 optimal weight: 6.9990 chunk 74 optimal weight: 0.2980 chunk 136 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 GLN A1000 GLN B 16 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN C 473 ASN C 515 HIS C 961 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.132804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.117838 restraints weight = 35525.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.120084 restraints weight = 22524.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.121683 restraints weight = 16149.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.122752 restraints weight = 12576.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.123618 restraints weight = 10441.562| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 17164 Z= 0.308 Angle : 0.853 18.119 23686 Z= 0.446 Chirality : 0.050 0.236 2589 Planarity : 0.006 0.052 2647 Dihedral : 23.144 158.472 3180 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 4.09 % Allowed : 22.48 % Favored : 73.44 % 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: -3.94 (0.17), residues: 1773 helix: -1.73 (0.19), residues: 547 sheet: -3.78 (0.27), residues: 241 loop : -2.90 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 703 TYR 0.021 0.003 TYR D 68 PHE 0.021 0.003 PHE A 475 TRP 0.033 0.003 TRP C 829 HIS 0.010 0.002 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.31 (17156) covalent geometry : angle 0.84338 / 0.44 (23682) hydrogen bonds : bond 0.06021 / 4.09 ( 613) hydrogen bonds : angle 6.34918 / 4.61 ( 1617) metal coordination : bond 0.06897 / 4.77 ( 8) metal coordination : angle 9.83712 / 4.76 ( 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 278 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 214 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 658 MET cc_start: 0.8060 (mpp) cc_final: 0.6732 (mtm) REVERT: A 855 ARG cc_start: 0.7679 (mtt90) cc_final: 0.7345 (mtm-85) REVERT: A 858 MET cc_start: 0.8055 (mmt) cc_final: 0.7163 (mmt) REVERT: A 877 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 916 PHE cc_start: 0.7752 (t80) cc_final: 0.7377 (t80) REVERT: A 956 TRP cc_start: 0.8649 (m100) cc_final: 0.8091 (m100) REVERT: B 91 TYR cc_start: 0.7308 (m-80) cc_final: 0.6897 (m-80) REVERT: B 197 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7421 (mm) REVERT: B 232 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7391 (p0) REVERT: B 234 TYR cc_start: 0.7398 (m-80) cc_final: 0.7108 (m-80) REVERT: C 605 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8640 (p) REVERT: C 847 MET cc_start: 0.6626 (mpp) cc_final: 0.5956 (tpp) REVERT: C 969 ARG cc_start: 0.8713 (ttm110) cc_final: 0.8421 (tpp80) REVERT: D 16 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7979 (pt0) REVERT: D 206 PHE cc_start: 0.7560 (m-80) cc_final: 0.7314 (m-80) REVERT: D 299 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7766 (mp) outliers start: 64 outliers final: 40 residues processed: 267 average time/residue: 0.1263 time to fit residues: 52.1470 Evaluate side-chains 237 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 598 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 638 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 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 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 197 LEU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU 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 518 GLU 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 631 ILE Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 712 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 124 optimal weight: 0.3980 chunk 157 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN B 23 ASN ** B 101 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.137706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.123600 restraints weight = 34978.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.125823 restraints weight = 22288.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.127411 restraints weight = 15800.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.128527 restraints weight = 12206.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.129185 restraints weight = 10003.324| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17164 Z= 0.174 Angle : 0.779 13.972 23686 Z= 0.407 Chirality : 0.048 0.249 2589 Planarity : 0.005 0.053 2647 Dihedral : 23.075 159.258 3180 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 3.32 % Allowed : 23.18 % 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: -3.63 (0.18), residues: 1773 helix: -1.48 (0.19), residues: 554 sheet: -3.66 (0.27), residues: 240 loop : -2.69 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 972 TYR 0.025 0.002 TYR A 481 PHE 0.015 0.002 PHE C 557 TRP 0.027 0.002 TRP C 829 HIS 0.010 0.002 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (17156) covalent geometry : angle 0.77176 / 0.41 (23682) hydrogen bonds : bond 0.05172 / 3.52 ( 613) hydrogen bonds : angle 6.19290 / 4.49 ( 1617) metal coordination : bond 0.04265 / 2.83 ( 8) metal coordination : angle 8.02370 / 4.24 ( 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 295 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 480 GLN cc_start: 0.6404 (mt0) cc_final: 0.6201 (mt0) REVERT: A 658 MET cc_start: 0.8159 (mpp) cc_final: 0.7006 (mpp) REVERT: A 711 LEU cc_start: 0.8640 (tt) cc_final: 0.8399 (tt) REVERT: A 858 MET cc_start: 0.7717 (mmt) cc_final: 0.6718 (mmt) REVERT: A 916 PHE cc_start: 0.7537 (t80) cc_final: 0.7271 (t80) REVERT: A 940 LEU cc_start: 0.8514 (mp) cc_final: 0.8104 (mp) REVERT: A 949 ARG cc_start: 0.7790 (ttt180) cc_final: 0.7542 (tmm-80) REVERT: A 956 TRP cc_start: 0.8533 (m100) cc_final: 0.8122 (m100) REVERT: A 972 ARG cc_start: 0.6313 (ttp80) cc_final: 0.6021 (ttp80) REVERT: B 91 TYR cc_start: 0.7032 (m-80) cc_final: 0.6407 (m-80) REVERT: B 196 ILE cc_start: 0.6857 (tp) cc_final: 0.6563 (tp) REVERT: C 466 VAL cc_start: 0.8292 (t) cc_final: 0.7969 (p) REVERT: C 558 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7379 (ttp-110) REVERT: C 605 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8448 (p) REVERT: C 711 LEU cc_start: 0.9058 (tt) cc_final: 0.8842 (tt) REVERT: C 841 MET cc_start: 0.5026 (mmp) cc_final: 0.4807 (mmp) REVERT: C 847 MET cc_start: 0.6598 (mpp) cc_final: 0.5877 (tpp) REVERT: C 849 MET cc_start: 0.6378 (tpt) cc_final: 0.6147 (tpp) REVERT: C 1001 LYS cc_start: 0.7488 (mmmt) cc_final: 0.7162 (mmtt) REVERT: D 99 PRO cc_start: 0.8828 (Cg_exo) cc_final: 0.8497 (Cg_endo) REVERT: D 206 PHE cc_start: 0.7397 (m-80) cc_final: 0.7121 (m-80) REVERT: D 299 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7616 (mp) outliers start: 52 outliers final: 32 residues processed: 283 average time/residue: 0.1247 time to fit residues: 55.6226 Evaluate side-chains 243 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 569 ASP Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 638 VAL 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 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ASP 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 558 ARG Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 712 VAL 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 145 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 144 optimal weight: 0.0070 chunk 94 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 179 optimal weight: 20.0000 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN D 23 ASN ** D 94 HIS ** 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 = 0.4081 r_free = 0.4081 target = 0.139124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.125106 restraints weight = 34900.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.127316 restraints weight = 22063.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.128904 restraints weight = 15671.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.130073 restraints weight = 12080.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.130914 restraints weight = 9849.716| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17164 Z= 0.168 Angle : 0.757 13.624 23686 Z= 0.397 Chirality : 0.048 0.330 2589 Planarity : 0.005 0.052 2647 Dihedral : 23.033 159.773 3180 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 3.13 % Allowed : 23.88 % Favored : 72.99 % 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: -3.39 (0.18), residues: 1773 helix: -1.32 (0.20), residues: 557 sheet: -3.44 (0.27), residues: 251 loop : -2.52 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 703 TYR 0.033 0.002 TYR A 481 PHE 0.026 0.002 PHE C 698 TRP 0.027 0.002 TRP C 829 HIS 0.009 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (17156) covalent geometry : angle 0.75257 / 0.40 (23682) hydrogen bonds : bond 0.04968 / 3.36 ( 613) hydrogen bonds : angle 6.06283 / 4.38 ( 1617) metal coordination : bond 0.03508 / 2.38 ( 8) metal coordination : angle 6.63854 / 3.49 ( 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 283 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 480 GLN cc_start: 0.6233 (mt0) cc_final: 0.6025 (mt0) REVERT: A 545 VAL cc_start: 0.8604 (p) cc_final: 0.8125 (p) REVERT: A 658 MET cc_start: 0.8160 (mpp) cc_final: 0.6631 (mpp) REVERT: A 711 LEU cc_start: 0.8564 (tt) cc_final: 0.8361 (tt) REVERT: A 858 MET cc_start: 0.7847 (mmt) cc_final: 0.6738 (mmt) REVERT: A 916 PHE cc_start: 0.7434 (t80) cc_final: 0.7215 (t80) REVERT: A 940 LEU cc_start: 0.8422 (mp) cc_final: 0.7992 (mp) REVERT: A 949 ARG cc_start: 0.7678 (ttt180) cc_final: 0.7371 (tmm-80) REVERT: A 972 ARG cc_start: 0.6239 (ttp80) cc_final: 0.5975 (ttp-110) REVERT: B 56 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6565 (tppt) REVERT: B 196 ILE cc_start: 0.6661 (tp) cc_final: 0.6405 (tp) REVERT: C 466 VAL cc_start: 0.8322 (t) cc_final: 0.7887 (p) REVERT: C 558 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7327 (ttp-110) REVERT: C 605 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8196 (p) REVERT: C 711 LEU cc_start: 0.9006 (tt) cc_final: 0.8777 (tt) REVERT: C 785 ILE cc_start: 0.7868 (mp) cc_final: 0.7578 (mt) REVERT: C 841 MET cc_start: 0.4951 (mmp) cc_final: 0.4738 (mmp) REVERT: C 847 MET cc_start: 0.6657 (mpp) cc_final: 0.5956 (tpp) REVERT: D 99 PRO cc_start: 0.8813 (Cg_exo) cc_final: 0.8461 (Cg_endo) REVERT: D 206 PHE cc_start: 0.7341 (m-80) cc_final: 0.6998 (m-80) outliers start: 49 outliers final: 34 residues processed: 271 average time/residue: 0.1286 time to fit residues: 54.3017 Evaluate side-chains 247 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 563 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 638 VAL 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 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 175 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 322 MET 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 558 ARG 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 708 ASP Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain D residue 145 VAL 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: 0.8980 chunk 86 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 178 optimal weight: 40.0000 chunk 139 optimal weight: 3.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 763 ASN B 16 GLN ** B 101 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.138582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.124476 restraints weight = 34923.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.126669 restraints weight = 22242.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.128244 restraints weight = 15851.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.129172 restraints weight = 12291.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.130124 restraints weight = 10291.682| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17164 Z= 0.178 Angle : 0.751 14.316 23686 Z= 0.394 Chirality : 0.047 0.295 2589 Planarity : 0.005 0.069 2647 Dihedral : 23.021 160.159 3180 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 3.58 % Allowed : 23.69 % Favored : 72.73 % 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: -3.25 (0.18), residues: 1773 helix: -1.17 (0.20), residues: 556 sheet: -3.33 (0.28), residues: 249 loop : -2.47 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 703 TYR 0.029 0.002 TYR A 481 PHE 0.020 0.002 PHE D 29 TRP 0.028 0.002 TRP C 829 HIS 0.008 0.002 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (17156) covalent geometry : angle 0.74844 / 0.39 (23682) hydrogen bonds : bond 0.04929 / 3.34 ( 613) hydrogen bonds : angle 5.99559 / 4.34 ( 1617) metal coordination : bond 0.03079 / 2.09 ( 8) metal coordination : angle 4.67607 / 2.40 ( 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 279 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 VAL cc_start: 0.8819 (p) cc_final: 0.8612 (p) REVERT: A 658 MET cc_start: 0.8085 (mpp) cc_final: 0.6669 (mpp) REVERT: A 711 LEU cc_start: 0.8575 (tt) cc_final: 0.8363 (tt) REVERT: A 858 MET cc_start: 0.7853 (mmt) cc_final: 0.6716 (mmt) REVERT: A 916 PHE cc_start: 0.7526 (t80) cc_final: 0.7214 (t80) REVERT: A 940 LEU cc_start: 0.8446 (mp) cc_final: 0.7880 (mp) REVERT: A 972 ARG cc_start: 0.6103 (ttp80) cc_final: 0.5853 (ttp-110) REVERT: B 196 ILE cc_start: 0.6721 (tp) cc_final: 0.6475 (tp) REVERT: C 466 VAL cc_start: 0.8275 (t) cc_final: 0.7835 (p) REVERT: C 558 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7290 (ttp-110) REVERT: C 605 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8195 (p) REVERT: C 711 LEU cc_start: 0.9044 (tt) cc_final: 0.8802 (tt) REVERT: C 785 ILE cc_start: 0.7936 (mp) cc_final: 0.7578 (mt) REVERT: C 847 MET cc_start: 0.6765 (mpp) cc_final: 0.5992 (tpp) REVERT: C 858 MET cc_start: 0.6534 (mmp) cc_final: 0.6095 (mmp) REVERT: C 883 MET cc_start: 0.7950 (tpp) cc_final: 0.7295 (mmm) REVERT: D 99 PRO cc_start: 0.8845 (Cg_exo) cc_final: 0.8472 (Cg_endo) REVERT: D 206 PHE cc_start: 0.7256 (m-80) cc_final: 0.6991 (m-80) outliers start: 56 outliers final: 40 residues processed: 265 average time/residue: 0.1271 time to fit residues: 52.6865 Evaluate side-chains 253 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 563 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 688 THR 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 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 142 ILE 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 258 VAL 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 477 SER Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 558 ARG 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 712 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain D residue 145 VAL 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: 6.9990 chunk 124 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.139799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.126328 restraints weight = 34813.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.128423 restraints weight = 22425.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.129934 restraints weight = 16048.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.130979 restraints weight = 12419.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.131818 restraints weight = 10210.856| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17164 Z= 0.168 Angle : 0.759 15.347 23686 Z= 0.397 Chirality : 0.047 0.284 2589 Planarity : 0.005 0.055 2647 Dihedral : 23.021 160.465 3180 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.38 % Allowed : 24.33 % Favored : 72.29 % 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: -3.11 (0.19), residues: 1773 helix: -1.07 (0.20), residues: 556 sheet: -3.25 (0.28), residues: 251 loop : -2.37 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 703 TYR 0.028 0.002 TYR A 481 PHE 0.026 0.002 PHE A 971 TRP 0.027 0.002 TRP C 829 HIS 0.008 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (17156) covalent geometry : angle 0.75824 / 0.40 (23682) hydrogen bonds : bond 0.04807 / 3.25 ( 613) hydrogen bonds : angle 6.01866 / 4.34 ( 1617) metal coordination : bond 0.02271 / 1.53 ( 8) metal coordination : angle 3.26160 / 1.69 ( 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 287 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 234 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 480 GLN cc_start: 0.6272 (mt0) cc_final: 0.6043 (mt0) REVERT: A 602 MET cc_start: 0.6583 (ttt) cc_final: 0.6330 (ttt) REVERT: A 658 MET cc_start: 0.8080 (mpp) cc_final: 0.6612 (mpp) REVERT: A 858 MET cc_start: 0.7772 (mmt) cc_final: 0.6601 (mmt) REVERT: A 940 LEU cc_start: 0.8389 (mp) cc_final: 0.7850 (mp) REVERT: B 56 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6527 (tppt) REVERT: C 466 VAL cc_start: 0.8176 (t) cc_final: 0.7802 (p) REVERT: C 558 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7270 (ttp-110) REVERT: C 605 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8140 (p) REVERT: C 711 LEU cc_start: 0.8949 (tt) cc_final: 0.8698 (tt) REVERT: C 785 ILE cc_start: 0.7776 (mp) cc_final: 0.7373 (mt) REVERT: C 842 ASN cc_start: 0.7753 (m-40) cc_final: 0.7402 (m110) REVERT: C 847 MET cc_start: 0.6733 (mpp) cc_final: 0.6000 (tpp) REVERT: C 849 MET cc_start: 0.6407 (tpt) cc_final: 0.6102 (tpp) REVERT: C 858 MET cc_start: 0.6426 (mmp) cc_final: 0.6085 (mmp) REVERT: D 99 PRO cc_start: 0.8833 (Cg_exo) cc_final: 0.8474 (Cg_endo) REVERT: D 206 PHE cc_start: 0.7199 (m-80) cc_final: 0.6953 (m-80) outliers start: 53 outliers final: 42 residues processed: 273 average time/residue: 0.1273 time to fit residues: 54.5041 Evaluate side-chains 253 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 563 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 807 ILE 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 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 142 ILE 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 258 VAL 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 477 SER Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 558 ARG 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 712 VAL 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 145 VAL 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: 7.9990 chunk 153 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 164 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 147 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 180 optimal weight: 50.0000 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 665 HIS B 16 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 GLN ** C1000 GLN ** 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 = 0.4081 r_free = 0.4081 target = 0.139257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.125823 restraints weight = 34534.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.127850 restraints weight = 22202.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.129324 restraints weight = 15946.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.130395 restraints weight = 12400.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.131108 restraints weight = 10210.566| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17164 Z= 0.179 Angle : 0.761 14.589 23686 Z= 0.400 Chirality : 0.047 0.293 2589 Planarity : 0.005 0.063 2647 Dihedral : 23.036 160.658 3180 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 3.58 % Allowed : 24.52 % Favored : 71.90 % 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: -3.10 (0.19), residues: 1773 helix: -1.07 (0.20), residues: 555 sheet: -3.22 (0.29), residues: 254 loop : -2.36 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 703 TYR 0.028 0.002 TYR A 481 PHE 0.036 0.002 PHE A 916 TRP 0.028 0.002 TRP C 829 HIS 0.008 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (17156) covalent geometry : angle 0.75958 / 0.40 (23682) hydrogen bonds : bond 0.04820 / 3.27 ( 613) hydrogen bonds : angle 5.99503 / 4.33 ( 1617) metal coordination : bond 0.02383 / 1.60 ( 8) metal coordination : angle 3.49808 / 1.72 ( 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 280 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 224 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 658 MET cc_start: 0.8128 (mpp) cc_final: 0.7363 (mtm) REVERT: A 984 MET cc_start: 0.6763 (mmp) cc_final: 0.6544 (mmp) REVERT: B 56 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6519 (tppt) REVERT: B 284 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8024 (ttm-80) REVERT: C 466 VAL cc_start: 0.8193 (t) cc_final: 0.7815 (p) REVERT: C 558 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7262 (ttp-110) REVERT: C 605 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8109 (p) REVERT: C 711 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8698 (tt) REVERT: C 785 ILE cc_start: 0.8009 (mp) cc_final: 0.7636 (mt) REVERT: C 842 ASN cc_start: 0.7794 (m-40) cc_final: 0.7421 (m110) REVERT: C 847 MET cc_start: 0.6774 (mpp) cc_final: 0.5928 (tpp) REVERT: C 849 MET cc_start: 0.6499 (tpt) cc_final: 0.6169 (tpp) REVERT: D 99 PRO cc_start: 0.8938 (Cg_exo) cc_final: 0.8568 (Cg_endo) REVERT: D 206 PHE cc_start: 0.7215 (m-80) cc_final: 0.6978 (m-80) outliers start: 56 outliers final: 45 residues processed: 266 average time/residue: 0.1299 time to fit residues: 53.9555 Evaluate side-chains 263 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 563 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 598 SER 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 638 VAL Chi-restraints excluded: chain A residue 665 HIS Chi-restraints excluded: chain A residue 688 THR 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 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 175 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 284 ARG Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 326 THR 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 558 ARG Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 592 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 711 LEU Chi-restraints excluded: chain C residue 712 VAL 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 145 VAL 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: 40.0000 chunk 59 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 106 optimal weight: 0.0980 chunk 102 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 665 HIS ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.139804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.126242 restraints weight = 34659.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.128315 restraints weight = 22449.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.129830 restraints weight = 16173.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.130944 restraints weight = 12538.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.131711 restraints weight = 10250.400| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17164 Z= 0.174 Angle : 0.765 14.606 23686 Z= 0.400 Chirality : 0.047 0.306 2589 Planarity : 0.005 0.059 2647 Dihedral : 23.016 160.815 3180 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 23.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 3.32 % Allowed : 24.46 % Favored : 72.22 % 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: -3.04 (0.19), residues: 1773 helix: -1.02 (0.21), residues: 553 sheet: -3.16 (0.29), residues: 252 loop : -2.33 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 703 TYR 0.041 0.002 TYR A 485 PHE 0.039 0.002 PHE A 916 TRP 0.054 0.003 TRP A 956 HIS 0.020 0.002 HIS A 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (17156) covalent geometry : angle 0.76344 / 0.40 (23682) hydrogen bonds : bond 0.04700 / 3.18 ( 613) hydrogen bonds : angle 5.97660 / 4.31 ( 1617) metal coordination : bond 0.02465 / 1.62 ( 8) metal coordination : angle 3.27125 / 1.59 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2612.86 seconds wall clock time: 46 minutes 33.75 seconds (2793.75 seconds total)