Starting phenix.real_space_refine on Sat Mar 7 06:03:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rl4_54030/03_2026/9rl4_54030.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rl4_54030/03_2026/9rl4_54030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rl4_54030/03_2026/9rl4_54030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rl4_54030/03_2026/9rl4_54030.map" model { file = "/net/cci-nas-00/data/ceres_data/9rl4_54030/03_2026/9rl4_54030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rl4_54030/03_2026/9rl4_54030.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.010 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 1 6.06 5 P 283 5.49 5 S 137 5.16 5 C 23076 2.51 5 N 6894 2.21 5 O 7734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38125 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 4517 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 477} Link IDs: {'PTRANS': 24, 'TRANS': 738} Chain breaks: 5 Unresolved non-hydrogen bonds: 1833 Unresolved non-hydrogen angles: 2334 Unresolved non-hydrogen dihedrals: 1526 Unresolved non-hydrogen chiralities: 169 Planarities with less than four sites: {'ASP:plan': 28, 'GLN:plan1': 25, 'ARG:plan': 37, 'TYR:plan': 20, 'GLU:plan': 40, 'HIS:plan': 16, 'ASN:plan1': 24, 'TRP:plan': 8, 'PHE:plan': 23} Unresolved non-hydrogen planarities: 1031 Chain: "J" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3109 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 21, 'TRANS': 378} Chain breaks: 1 Chain: "K" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2784 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 18, 'TRANS': 338} Chain breaks: 1 Chain: "L" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3671 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 440} Chain breaks: 4 Chain: "M" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2375 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 2 Chain: "N" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2194 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 3 Chain: "O" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2666 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 19, 'TRANS': 312} Chain breaks: 3 Chain: "P" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2744 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PTRANS': 19, 'TRANS': 361} Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 553 Unresolved non-hydrogen dihedrals: 352 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'ARG:plan': 8, 'PHE:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 16, 'GLU:plan': 9, 'TRP:plan': 2, 'TYR:plan': 3, 'GLN:plan1': 4, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 248 Chain: "Q" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 860 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "R" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 580 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "V" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 363 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 7, 'GLU:plan': 5, 'PHE:plan': 5, 'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "W" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 378 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 5, 'TRANS': 68} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 11, 'ASN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 7, 'HIS:plan': 3, 'ASP:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 165 Chain: "X" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2889 Classifications: {'DNA': 142} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 141} Chain: "Y" Number of atoms: 2930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2930 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {'PTD': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PTD:plan-1': 3, 'PTD:plan-2': 3} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PTD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "N" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {'PTD': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PTD:plan-1': 3, 'PTD:plan-2': 3} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18714 SG CYS L2094 79.214 149.872 80.082 1.00 77.09 S Time building chain proxies: 8.92, per 1000 atoms: 0.23 Number of scatterers: 38125 At special positions: 0 Unit cell: (228.995, 222.235, 146.185, 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 1 29.99 S 137 16.00 P 283 15.00 O 7734 8.00 N 6894 7.00 C 23076 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2019 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2090 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2021 " pdb="ZN ZN L2301 " - pdb=" SG CYS L2094 " Number of angles added : 3 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8254 Finding SS restraints... Secondary structure from input PDB file: 211 helices and 37 sheets defined 63.6% alpha, 7.8% beta 142 base pairs and 272 stacking pairs defined. Time for finding SS restraints: 5.09 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.895A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.652A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.440A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.537A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.510A pdb=" N GLN D 48 " --> pdb=" O LYS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.935A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.706A pdb=" N ASP E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.463A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'I' and resid 362 through 387 removed outlier: 3.543A pdb=" N ILE I 366 " --> pdb=" O ASP I 362 " (cutoff:3.500A) Processing helix chain 'I' and resid 393 through 429 removed outlier: 4.815A pdb=" N ASN I 411 " --> pdb=" O LEU I 407 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE I 412 " --> pdb=" O ARG I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 435 removed outlier: 3.997A pdb=" N ASN I 435 " --> pdb=" O THR I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 440 removed outlier: 3.771A pdb=" N LYS I 440 " --> pdb=" O LYS I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 512 removed outlier: 4.102A pdb=" N LYS I 455 " --> pdb=" O ARG I 451 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN I 459 " --> pdb=" O LYS I 455 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLN I 460 " --> pdb=" O LEU I 456 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS I 461 " --> pdb=" O GLU I 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE I 462 " --> pdb=" O LYS I 458 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA I 503 " --> pdb=" O LYS I 499 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU I 512 " --> pdb=" O HIS I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 513 through 517 removed outlier: 3.900A pdb=" N LYS I 516 " --> pdb=" O ARG I 513 " (cutoff:3.500A) Processing helix chain 'I' and resid 546 through 558 Processing helix chain 'I' and resid 732 through 736 Processing helix chain 'I' and resid 741 through 745 Processing helix chain 'I' and resid 755 through 771 Processing helix chain 'I' and resid 784 through 799 Processing helix chain 'I' and resid 811 through 826 removed outlier: 4.478A pdb=" N SER I 816 " --> pdb=" O LEU I 812 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASN I 817 " --> pdb=" O SER I 813 " (cutoff:3.500A) Processing helix chain 'I' and resid 837 through 843 Processing helix chain 'I' and resid 844 through 850 Processing helix chain 'I' and resid 860 through 866 removed outlier: 3.647A pdb=" N ILE I 864 " --> pdb=" O TYR I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 866 through 871 Processing helix chain 'I' and resid 882 through 887 Processing helix chain 'I' and resid 891 through 900 removed outlier: 3.504A pdb=" N GLN I 895 " --> pdb=" O CYS I 891 " (cutoff:3.500A) Processing helix chain 'I' and resid 918 through 929 removed outlier: 3.971A pdb=" N TRP I 922 " --> pdb=" O LEU I 918 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU I 924 " --> pdb=" O GLU I 920 " (cutoff:3.500A) Processing helix chain 'I' and resid 935 through 939 Processing helix chain 'I' and resid 961 through 973 removed outlier: 4.213A pdb=" N ILE I 965 " --> pdb=" O THR I 961 " (cutoff:3.500A) Processing helix chain 'I' and resid 980 through 984 Processing helix chain 'I' and resid 1001 through 1015 removed outlier: 3.650A pdb=" N HIS I1010 " --> pdb=" O VAL I1006 " (cutoff:3.500A) Processing helix chain 'I' and resid 1037 through 1048 Processing helix chain 'I' and resid 1049 through 1051 No H-bonds generated for 'chain 'I' and resid 1049 through 1051' Processing helix chain 'I' and resid 1052 through 1064 Processing helix chain 'I' and resid 1072 through 1079 removed outlier: 3.843A pdb=" N TYR I1076 " --> pdb=" O GLY I1072 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER I1079 " --> pdb=" O LEU I1075 " (cutoff:3.500A) Processing helix chain 'I' and resid 1079 through 1095 removed outlier: 4.081A pdb=" N ARG I1087 " --> pdb=" O GLU I1083 " (cutoff:3.500A) Proline residue: I1090 - end of helix Processing helix chain 'I' and resid 1106 through 1120 removed outlier: 4.279A pdb=" N THR I1110 " --> pdb=" O THR I1106 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE I1111 " --> pdb=" O SER I1107 " (cutoff:3.500A) Processing helix chain 'I' and resid 1133 through 1144 Processing helix chain 'I' and resid 1157 through 1161 Processing helix chain 'I' and resid 1179 through 1188 removed outlier: 4.269A pdb=" N ASP I1183 " --> pdb=" O ASN I1179 " (cutoff:3.500A) Processing helix chain 'I' and resid 1209 through 1219 removed outlier: 3.914A pdb=" N LYS I1213 " --> pdb=" O SER I1209 " (cutoff:3.500A) Processing helix chain 'I' and resid 1268 through 1274 removed outlier: 4.021A pdb=" N MET I1272 " --> pdb=" O THR I1268 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE I1273 " --> pdb=" O VAL I1269 " (cutoff:3.500A) Processing helix chain 'I' and resid 1276 through 1284 Processing helix chain 'I' and resid 1285 through 1294 Processing helix chain 'I' and resid 1295 through 1297 No H-bonds generated for 'chain 'I' and resid 1295 through 1297' Processing helix chain 'I' and resid 1310 through 1316 removed outlier: 3.662A pdb=" N ILE I1314 " --> pdb=" O LEU I1310 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS I1316 " --> pdb=" O SER I1312 " (cutoff:3.500A) Processing helix chain 'I' and resid 1351 through 1361 removed outlier: 3.529A pdb=" N ILE I1359 " --> pdb=" O TRP I1355 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 12 Processing helix chain 'J' and resid 71 through 76 Processing helix chain 'J' and resid 95 through 110 Processing helix chain 'J' and resid 114 through 118 Processing helix chain 'J' and resid 129 through 143 Processing helix chain 'J' and resid 154 through 162 Processing helix chain 'J' and resid 189 through 192 Processing helix chain 'J' and resid 198 through 213 Processing helix chain 'J' and resid 219 through 221 No H-bonds generated for 'chain 'J' and resid 219 through 221' Processing helix chain 'J' and resid 247 through 267 removed outlier: 3.563A pdb=" N VAL J 258 " --> pdb=" O MET J 254 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU J 267 " --> pdb=" O GLN J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 280 Processing helix chain 'J' and resid 299 through 310 Proline residue: J 305 - end of helix removed outlier: 4.591A pdb=" N LEU J 308 " --> pdb=" O ILE J 304 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE J 309 " --> pdb=" O PRO J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 314 Processing helix chain 'J' and resid 324 through 336 Processing helix chain 'J' and resid 340 through 346 Processing helix chain 'J' and resid 352 through 357 Processing helix chain 'J' and resid 359 through 372 Processing helix chain 'J' and resid 385 through 391 Processing helix chain 'J' and resid 391 through 401 Processing helix chain 'J' and resid 402 through 403 No H-bonds generated for 'chain 'J' and resid 402 through 403' Processing helix chain 'J' and resid 404 through 409 Processing helix chain 'J' and resid 413 through 419 removed outlier: 3.574A pdb=" N GLY J 419 " --> pdb=" O GLU J 415 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 Processing helix chain 'K' and resid 78 through 92 removed outlier: 3.910A pdb=" N MET K 82 " --> pdb=" O ASN K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 101 Processing helix chain 'K' and resid 112 through 126 Processing helix chain 'K' and resid 137 through 145 Processing helix chain 'K' and resid 172 through 175 Processing helix chain 'K' and resid 181 through 196 Processing helix chain 'K' and resid 204 through 217 removed outlier: 3.665A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 233 Processing helix chain 'K' and resid 234 through 237 Processing helix chain 'K' and resid 252 through 260 Proline residue: K 258 - end of helix Processing helix chain 'K' and resid 261 through 262 No H-bonds generated for 'chain 'K' and resid 261 through 262' Processing helix chain 'K' and resid 263 through 268 Processing helix chain 'K' and resid 273 through 284 Processing helix chain 'K' and resid 286 through 296 removed outlier: 4.576A pdb=" N LYS K 291 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP K 292 " --> pdb=" O ASP K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 306 removed outlier: 4.228A pdb=" N TYR K 306 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 337 through 349 Processing helix chain 'K' and resid 350 through 355 Processing helix chain 'K' and resid 359 through 366 Processing helix chain 'K' and resid 369 through 374 removed outlier: 3.606A pdb=" N CYS K 374 " --> pdb=" O VAL K 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 1645 through 1649 Processing helix chain 'L' and resid 1660 through 1665 Processing helix chain 'L' and resid 1668 through 1678 Processing helix chain 'L' and resid 1680 through 1697 Processing helix chain 'L' and resid 1700 through 1704 Processing helix chain 'L' and resid 1711 through 1729 Processing helix chain 'L' and resid 1731 through 1735 removed outlier: 4.078A pdb=" N GLU L1735 " --> pdb=" O LYS L1732 " (cutoff:3.500A) Processing helix chain 'L' and resid 1740 through 1745 removed outlier: 3.967A pdb=" N LEU L1744 " --> pdb=" O GLY L1740 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU L1745 " --> pdb=" O GLN L1741 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1740 through 1745' Processing helix chain 'L' and resid 1840 through 1846 Processing helix chain 'L' and resid 1971 through 1992 Processing helix chain 'L' and resid 1996 through 2003 removed outlier: 4.138A pdb=" N GLU L2000 " --> pdb=" O GLY L1996 " (cutoff:3.500A) Processing helix chain 'L' and resid 2004 through 2017 removed outlier: 4.577A pdb=" N LEU L2016 " --> pdb=" O GLY L2012 " (cutoff:3.500A) Processing helix chain 'L' and resid 2049 through 2068 Processing helix chain 'L' and resid 2077 through 2094 Proline residue: L2083 - end of helix removed outlier: 3.504A pdb=" N VAL L2093 " --> pdb=" O LEU L2089 " (cutoff:3.500A) Processing helix chain 'L' and resid 2113 through 2126 Processing helix chain 'L' and resid 2128 through 2137 Processing helix chain 'L' and resid 2140 through 2157 removed outlier: 3.520A pdb=" N ASP L2157 " --> pdb=" O ARG L2153 " (cutoff:3.500A) Processing helix chain 'L' and resid 2160 through 2178 Processing helix chain 'L' and resid 2178 through 2187 Processing helix chain 'L' and resid 2190 through 2210 Processing helix chain 'L' and resid 2227 through 2243 Processing helix chain 'L' and resid 2244 through 2249 removed outlier: 4.644A pdb=" N ASN L2247 " --> pdb=" O VAL L2244 " (cutoff:3.500A) Processing helix chain 'L' and resid 2254 through 2264 Processing helix chain 'L' and resid 2268 through 2284 removed outlier: 3.659A pdb=" N VAL L2274 " --> pdb=" O LEU L2270 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 36 Processing helix chain 'M' and resid 41 through 47 Processing helix chain 'M' and resid 56 through 66 Processing helix chain 'M' and resid 79 through 84 Processing helix chain 'M' and resid 93 through 100 Processing helix chain 'M' and resid 173 through 182 removed outlier: 3.689A pdb=" N GLN M 182 " --> pdb=" O GLU M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 226 Processing helix chain 'M' and resid 229 through 248 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 289 through 302 Processing helix chain 'M' and resid 304 through 326 Processing helix chain 'M' and resid 327 through 329 No H-bonds generated for 'chain 'M' and resid 327 through 329' Processing helix chain 'M' and resid 342 through 350 removed outlier: 4.327A pdb=" N GLN M 348 " --> pdb=" O GLY M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 357 through 381 Processing helix chain 'N' and resid 427 through 431 Processing helix chain 'N' and resid 440 through 446 Processing helix chain 'N' and resid 447 through 450 Processing helix chain 'N' and resid 458 through 475 Processing helix chain 'N' and resid 482 through 490 removed outlier: 3.521A pdb=" N CYS N 486 " --> pdb=" O THR N 482 " (cutoff:3.500A) Processing helix chain 'N' and resid 493 through 507 Processing helix chain 'N' and resid 603 through 617 Processing helix chain 'N' and resid 620 through 628 Processing helix chain 'N' and resid 631 through 641 Processing helix chain 'N' and resid 672 through 682 Processing helix chain 'N' and resid 685 through 701 Processing helix chain 'N' and resid 702 through 703 No H-bonds generated for 'chain 'N' and resid 702 through 703' Processing helix chain 'N' and resid 858 through 858 No H-bonds generated for 'chain 'N' and resid 858 through 858' Processing helix chain 'N' and resid 859 through 951 removed outlier: 3.569A pdb=" N HIS N 905 " --> pdb=" O ILE N 901 " (cutoff:3.500A) Processing helix chain 'O' and resid 439 through 446 Processing helix chain 'O' and resid 447 through 450 Processing helix chain 'O' and resid 458 through 475 Processing helix chain 'O' and resid 482 through 490 removed outlier: 3.668A pdb=" N ASN O 489 " --> pdb=" O ALA O 485 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 507 Processing helix chain 'O' and resid 602 through 616 removed outlier: 3.843A pdb=" N MET O 615 " --> pdb=" O GLU O 611 " (cutoff:3.500A) Processing helix chain 'O' and resid 619 through 628 Processing helix chain 'O' and resid 631 through 642 Processing helix chain 'O' and resid 645 through 650 Processing helix chain 'O' and resid 656 through 661 removed outlier: 3.598A pdb=" N TYR O 661 " --> pdb=" O PRO O 658 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 684 removed outlier: 4.267A pdb=" N PHE O 679 " --> pdb=" O SER O 675 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER O 682 " --> pdb=" O ALA O 678 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL O 683 " --> pdb=" O PHE O 679 " (cutoff:3.500A) Processing helix chain 'O' and resid 685 through 705 removed outlier: 3.756A pdb=" N GLU O 705 " --> pdb=" O SER O 701 " (cutoff:3.500A) Processing helix chain 'O' and resid 709 through 717 Processing helix chain 'O' and resid 859 through 950 removed outlier: 3.601A pdb=" N GLU O 943 " --> pdb=" O LEU O 939 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 131 Processing helix chain 'P' and resid 134 through 139 Processing helix chain 'P' and resid 143 through 174 Processing helix chain 'P' and resid 218 through 223 removed outlier: 3.978A pdb=" N LYS P 223 " --> pdb=" O SER P 219 " (cutoff:3.500A) Processing helix chain 'P' and resid 224 through 226 No H-bonds generated for 'chain 'P' and resid 224 through 226' Processing helix chain 'P' and resid 232 through 235 Processing helix chain 'P' and resid 245 through 250 Processing helix chain 'P' and resid 298 through 306 Processing helix chain 'P' and resid 312 through 326 Processing helix chain 'P' and resid 355 through 363 removed outlier: 4.741A pdb=" N GLN P 359 " --> pdb=" O SER P 355 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA P 363 " --> pdb=" O GLN P 359 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 385 removed outlier: 3.529A pdb=" N LYS P 385 " --> pdb=" O PRO P 381 " (cutoff:3.500A) Processing helix chain 'P' and resid 399 through 413 Processing helix chain 'P' and resid 414 through 447 Processing helix chain 'P' and resid 447 through 468 Processing helix chain 'P' and resid 472 through 478 removed outlier: 4.007A pdb=" N ARG P 478 " --> pdb=" O GLU P 474 " (cutoff:3.500A) Processing helix chain 'P' and resid 479 through 485 removed outlier: 3.714A pdb=" N GLN P 484 " --> pdb=" O PHE P 481 " (cutoff:3.500A) Proline residue: P 485 - end of helix Processing helix chain 'P' and resid 486 through 505 Processing helix chain 'Q' and resid 186 through 207 Processing helix chain 'Q' and resid 220 through 275 Processing helix chain 'R' and resid 14 through 39 Processing helix chain 'R' and resid 58 through 62 Processing helix chain 'V' and resid 139 through 160 Processing helix chain 'V' and resid 163 through 176 Processing helix chain 'V' and resid 180 through 189 Processing helix chain 'V' and resid 193 through 210 Proline residue: V 202 - end of helix Processing helix chain 'W' and resid 46 through 63 removed outlier: 3.535A pdb=" N GLY W 54 " --> pdb=" O VAL W 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 82 Processing helix chain 'W' and resid 83 through 105 Proline residue: W 89 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.987A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.013A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.788A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.995A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.039A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'I' and resid 831 through 834 removed outlier: 6.785A pdb=" N VAL I 832 " --> pdb=" O LEU I 857 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N THR I 859 " --> pdb=" O VAL I 832 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N TYR I 834 " --> pdb=" O THR I 859 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET I 878 " --> pdb=" O LEU I 907 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU I 909 " --> pdb=" O MET I 878 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL I 880 " --> pdb=" O LEU I 909 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY I 775 " --> pdb=" O ARG I 906 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE I 776 " --> pdb=" O LEU I 977 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 992 through 998 removed outlier: 6.518A pdb=" N VAL I 992 " --> pdb=" O VAL I1201 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ARG I1203 " --> pdb=" O VAL I 992 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR I 994 " --> pdb=" O ARG I1203 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS I1205 " --> pdb=" O TYR I 994 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE I 996 " --> pdb=" O CYS I1205 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL I1171 " --> pdb=" O LEU I1202 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU I1204 " --> pdb=" O VAL I1171 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE I1173 " --> pdb=" O LEU I1204 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N THR I1206 " --> pdb=" O ILE I1173 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU I1100 " --> pdb=" O ILE I1172 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU I1124 " --> pdb=" O LEU I1153 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N SER I1155 " --> pdb=" O LEU I1124 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LEU I1126 " --> pdb=" O SER I1155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 1016 through 1018 Processing sheet with id=AB5, first strand: chain 'J' and resid 35 through 38 removed outlier: 6.396A pdb=" N LEU J 14 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N SER J 123 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N PHE J 16 " --> pdb=" O SER J 123 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL J 120 " --> pdb=" O PHE J 150 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N CYS J 152 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET J 122 " --> pdb=" O CYS J 152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 67 through 69 Processing sheet with id=AB7, first strand: chain 'J' and resid 88 through 89 Processing sheet with id=AB8, first strand: chain 'J' and resid 186 through 187 Processing sheet with id=AB9, first strand: chain 'J' and resid 186 through 187 removed outlier: 6.265A pdb=" N VAL J 348 " --> pdb=" O ILE J 381 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 223 through 227 removed outlier: 6.591A pdb=" N LYS J 238 " --> pdb=" O ALA J 224 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS J 226 " --> pdb=" O ASN J 236 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN J 236 " --> pdb=" O LYS J 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 285 through 289 Processing sheet with id=AC3, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.633A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AC7, first strand: chain 'K' and resid 169 through 170 removed outlier: 6.299A pdb=" N THR K 297 " --> pdb=" O ILE K 330 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AC9, first strand: chain 'L' and resid 1814 through 1816 Processing sheet with id=AD1, first strand: chain 'M' and resid 17 through 18 Processing sheet with id=AD2, first strand: chain 'M' and resid 186 through 195 Processing sheet with id=AD3, first strand: chain 'M' and resid 261 through 270 Processing sheet with id=AD4, first strand: chain 'N' and resid 424 through 426 Processing sheet with id=AD5, first strand: chain 'N' and resid 437 through 439 removed outlier: 6.735A pdb=" N VAL N 438 " --> pdb=" O LEU R 71 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 523 through 524 Processing sheet with id=AD7, first strand: chain 'P' and resid 269 through 275 Processing sheet with id=AD8, first strand: chain 'P' and resid 255 through 259 removed outlier: 3.505A pdb=" N SER P 239 " --> pdb=" O MET P 287 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 309 through 311 Processing sheet with id=AE1, first strand: chain 'P' and resid 336 through 338 2067 hydrogen bonds defined for protein. 5874 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 358 hydrogen bonds 716 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 272 stacking parallelities Total time for adding SS restraints: 12.67 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7707 1.33 - 1.45: 9793 1.45 - 1.57: 21049 1.57 - 1.69: 566 1.69 - 1.81: 230 Bond restraints: 39345 Sorted by residual: bond pdb=" C LYS N 897 " pdb=" O LYS N 897 " ideal model delta sigma weight residual 1.236 1.290 -0.054 1.15e-02 7.56e+03 2.18e+01 bond pdb=" C LYS P 156 " pdb=" O LYS P 156 " ideal model delta sigma weight residual 1.236 1.283 -0.047 1.15e-02 7.56e+03 1.66e+01 bond pdb=" C LYS M 296 " pdb=" O LYS M 296 " ideal model delta sigma weight residual 1.236 1.282 -0.045 1.15e-02 7.56e+03 1.54e+01 bond pdb=" CA LYS P 156 " pdb=" C LYS P 156 " ideal model delta sigma weight residual 1.524 1.575 -0.051 1.32e-02 5.74e+03 1.48e+01 bond pdb=" C LYS O 885 " pdb=" O LYS O 885 " ideal model delta sigma weight residual 1.236 1.277 -0.040 1.15e-02 7.56e+03 1.23e+01 ... (remaining 39340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.27: 54502 5.27 - 10.53: 26 10.53 - 15.80: 0 15.80 - 21.07: 0 21.07 - 26.33: 1 Bond angle restraints: 54529 Sorted by residual: angle pdb=" CD LYS L1811 " pdb=" CE LYS L1811 " pdb=" NZ LYS L1811 " ideal model delta sigma weight residual 111.90 138.23 -26.33 3.20e+00 9.77e-02 6.77e+01 angle pdb=" N LYS A 123 " pdb=" CA LYS A 123 " pdb=" CB LYS A 123 " ideal model delta sigma weight residual 110.06 117.74 -7.68 1.50e+00 4.44e-01 2.62e+01 angle pdb=" N LYS H 44 " pdb=" CA LYS H 44 " pdb=" CB LYS H 44 " ideal model delta sigma weight residual 109.94 117.38 -7.44 1.49e+00 4.50e-01 2.49e+01 angle pdb=" N LYS O 885 " pdb=" CA LYS O 885 " pdb=" CB LYS O 885 " ideal model delta sigma weight residual 110.01 116.42 -6.41 1.45e+00 4.76e-01 1.95e+01 angle pdb=" C2' DC X 24 " pdb=" C1' DC X 24 " pdb=" N1 DC X 24 " ideal model delta sigma weight residual 113.50 119.53 -6.03 1.50e+00 4.44e-01 1.61e+01 ... (remaining 54524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.56: 21624 32.56 - 65.12: 1516 65.12 - 97.68: 48 97.68 - 130.23: 0 130.23 - 162.79: 1 Dihedral angle restraints: 23189 sinusoidal: 10516 harmonic: 12673 Sorted by residual: dihedral pdb=" CA GLY J 292 " pdb=" C GLY J 292 " pdb=" N TYR J 293 " pdb=" CA TYR J 293 " ideal model delta harmonic sigma weight residual 180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA TYR J 69 " pdb=" C TYR J 69 " pdb=" N ILE J 70 " pdb=" CA ILE J 70 " ideal model delta harmonic sigma weight residual -180.00 -151.70 -28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA THR I1363 " pdb=" C THR I1363 " pdb=" N LEU I1364 " pdb=" CA LEU I1364 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 23186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 5134 0.081 - 0.163: 983 0.163 - 0.244: 106 0.244 - 0.326: 26 0.326 - 0.407: 4 Chirality restraints: 6253 Sorted by residual: chirality pdb=" CA LYS H 47 " pdb=" N LYS H 47 " pdb=" C LYS H 47 " pdb=" CB LYS H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA LYS O 885 " pdb=" N LYS O 885 " pdb=" C LYS O 885 " pdb=" CB LYS O 885 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA LYS D 47 " pdb=" N LYS D 47 " pdb=" C LYS D 47 " pdb=" CB LYS D 47 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 6250 not shown) Planarity restraints: 6106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC X 24 " 0.068 2.00e-02 2.50e+03 3.32e-02 2.47e+01 pdb=" N1 DC X 24 " -0.061 2.00e-02 2.50e+03 pdb=" C2 DC X 24 " -0.010 2.00e-02 2.50e+03 pdb=" O2 DC X 24 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC X 24 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DC X 24 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC X 24 " 0.033 2.00e-02 2.50e+03 pdb=" C5 DC X 24 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC X 24 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG Y 116 " -0.064 2.00e-02 2.50e+03 2.74e-02 2.26e+01 pdb=" N9 DG Y 116 " 0.064 2.00e-02 2.50e+03 pdb=" C8 DG Y 116 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG Y 116 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG Y 116 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG Y 116 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG Y 116 " -0.021 2.00e-02 2.50e+03 pdb=" N1 DG Y 116 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DG Y 116 " -0.005 2.00e-02 2.50e+03 pdb=" N2 DG Y 116 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DG Y 116 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG Y 116 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA X 88 " -0.066 2.00e-02 2.50e+03 2.84e-02 2.22e+01 pdb=" N9 DA X 88 " 0.058 2.00e-02 2.50e+03 pdb=" C8 DA X 88 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DA X 88 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA X 88 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA X 88 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA X 88 " -0.030 2.00e-02 2.50e+03 pdb=" N1 DA X 88 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA X 88 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DA X 88 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DA X 88 " 0.010 2.00e-02 2.50e+03 ... (remaining 6103 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8910 2.81 - 3.33: 36234 3.33 - 3.86: 65028 3.86 - 4.38: 76017 4.38 - 4.90: 118807 Nonbonded interactions: 304996 Sorted by model distance: nonbonded pdb=" O TYR J 6 " pdb=" NH1 ARG K 372 " model vdw 2.288 3.120 nonbonded pdb=" OD1 ASP M 369 " pdb=" N ARG M 370 " model vdw 2.357 3.120 nonbonded pdb=" O TYR J 416 " pdb=" N GLY J 419 " model vdw 2.408 3.120 nonbonded pdb=" OD1 ASP N 619 " pdb=" N ASN N 621 " model vdw 2.413 3.120 nonbonded pdb=" O ARG M 366 " pdb=" OD1 ASP M 369 " model vdw 2.423 3.040 ... (remaining 304991 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' selection = (chain 'E' and resid 41 through 201) } ncs_group { reference = (chain 'B' and resid 23 through 103) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 201) selection = (chain 'G' and (resid 10 through 117 or resid 201)) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 9.890 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: 0.030 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 44.790 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.008 0.172 39381 Z= 0.585 Angle : 0.893 26.335 54532 Z= 0.536 Chirality : 0.065 0.407 6253 Planarity : 0.009 0.127 6106 Dihedral : 18.233 162.792 14935 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.56 % Favored : 97.35 % Rotamer: Outliers : 0.49 % Allowed : 3.46 % Favored : 96.05 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.12), residues: 4264 helix: 0.18 (0.09), residues: 2476 sheet: 0.28 (0.28), residues: 289 loop : -0.24 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 60 TYR 0.024 0.003 TYR M 313 PHE 0.028 0.003 PHE P 495 TRP 0.024 0.003 TRP K 340 HIS 0.010 0.002 HIS I 508 Details of bonding type rmsd covalent geometry : bond 0.00602 (39345) covalent geometry : angle 0.89311 (54529) hydrogen bonds : bond 0.12345 ( 2421) hydrogen bonds : angle 5.69487 ( 6590) metal coordination : bond 0.04705 ( 4) metal coordination : angle 2.55483 ( 3) Misc. bond : bond 0.17020 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 803 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9014 (tttt) cc_final: 0.8793 (ttmm) REVERT: D 69 ASP cc_start: 0.8510 (t0) cc_final: 0.8275 (t0) REVERT: G 21 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7602 (mtm-85) REVERT: I 477 ASN cc_start: 0.8809 (m-40) cc_final: 0.8165 (m-40) REVERT: I 498 GLN cc_start: 0.8051 (tp40) cc_final: 0.7715 (tp40) REVERT: J 15 VAL cc_start: 0.9516 (t) cc_final: 0.9252 (p) REVERT: J 27 TYR cc_start: 0.8556 (m-80) cc_final: 0.7897 (m-10) REVERT: J 92 MET cc_start: 0.9086 (mtm) cc_final: 0.8785 (mtm) REVERT: J 109 MET cc_start: 0.9231 (mmm) cc_final: 0.8779 (mmm) REVERT: J 176 HIS cc_start: 0.6992 (m90) cc_final: 0.6732 (m90) REVERT: J 193 VAL cc_start: 0.8932 (t) cc_final: 0.8519 (m) REVERT: J 222 MET cc_start: 0.9085 (mtp) cc_final: 0.8717 (mtt) REVERT: J 345 TYR cc_start: 0.8653 (m-80) cc_final: 0.8433 (m-80) REVERT: J 349 ILE cc_start: 0.9443 (mt) cc_final: 0.9142 (mp) REVERT: J 388 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8487 (mt-10) REVERT: K 103 VAL cc_start: 0.9619 (t) cc_final: 0.9407 (p) REVERT: K 110 LEU cc_start: 0.9455 (mt) cc_final: 0.8758 (mt) REVERT: K 115 ASN cc_start: 0.8914 (m110) cc_final: 0.8193 (m-40) REVERT: K 121 GLN cc_start: 0.9317 (tt0) cc_final: 0.8993 (tm-30) REVERT: K 122 ILE cc_start: 0.9704 (mt) cc_final: 0.9476 (mt) REVERT: K 123 MET cc_start: 0.9482 (mmt) cc_final: 0.9218 (mmp) REVERT: K 195 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8585 (pt0) REVERT: K 280 ASN cc_start: 0.9681 (m-40) cc_final: 0.9226 (m110) REVERT: K 324 THR cc_start: 0.9051 (p) cc_final: 0.8566 (t) REVERT: L 1661 MET cc_start: 0.7827 (ttp) cc_final: 0.7525 (tmm) REVERT: L 1718 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7487 (mt-10) REVERT: L 1732 LYS cc_start: 0.9102 (ttmt) cc_final: 0.8807 (tttt) REVERT: L 1975 ASP cc_start: 0.8266 (t70) cc_final: 0.7996 (t0) REVERT: L 2203 LEU cc_start: 0.9064 (mt) cc_final: 0.8365 (mp) REVERT: M 38 MET cc_start: 0.8799 (mmt) cc_final: 0.8340 (mmm) REVERT: M 99 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8244 (mm) REVERT: M 178 GLU cc_start: 0.8742 (tp30) cc_final: 0.8519 (tp30) REVERT: M 350 CYS cc_start: 0.6814 (p) cc_final: 0.6452 (p) REVERT: O 480 TYR cc_start: 0.8652 (t80) cc_final: 0.8360 (t80) REVERT: O 523 MET cc_start: 0.8969 (mmm) cc_final: 0.8658 (mmm) REVERT: O 930 ASP cc_start: 0.8657 (t0) cc_final: 0.8369 (t0) REVERT: O 936 MET cc_start: 0.8838 (tpp) cc_final: 0.8611 (tpp) REVERT: P 148 MET cc_start: 0.8504 (mmm) cc_final: 0.8228 (mmt) REVERT: P 322 TYR cc_start: 0.9056 (t80) cc_final: 0.8735 (t80) REVERT: P 357 ILE cc_start: 0.9284 (mt) cc_final: 0.8820 (mm) REVERT: P 462 ASP cc_start: 0.8099 (m-30) cc_final: 0.7863 (m-30) REVERT: Q 238 GLN cc_start: 0.9227 (tp-100) cc_final: 0.8348 (tm-30) REVERT: Q 244 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8776 (mt-10) REVERT: Q 248 ILE cc_start: 0.9500 (pt) cc_final: 0.9243 (pt) REVERT: Q 263 THR cc_start: 0.9243 (m) cc_final: 0.9001 (m) REVERT: R 26 ASN cc_start: 0.8897 (m-40) cc_final: 0.8592 (m110) outliers start: 15 outliers final: 2 residues processed: 815 average time/residue: 0.2659 time to fit residues: 337.6538 Evaluate side-chains 520 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 517 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain N residue 619 ASP Chi-restraints excluded: chain P residue 414 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 30.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN D 50 HIS D 85 ASN F 94 GLN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN H 96 GLN I 460 GLN I 490 HIS J 327 HIS K 12 ASN K 353 GLN L1960 HIS L2100 GLN L2115 GLN M 278 GLN M 342 ASN M 348 GLN N 476 ASN ** N 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 513 GLN N 626 HIS N 638 HIS N 875 HIS P 308 HIS ** P 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 326 HIS Q 238 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.089663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.059754 restraints weight = 147096.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.061584 restraints weight = 65992.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.062767 restraints weight = 42747.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.063371 restraints weight = 33692.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.063773 restraints weight = 29708.643| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 39381 Z= 0.178 Angle : 0.673 16.091 54532 Z= 0.366 Chirality : 0.042 0.251 6253 Planarity : 0.005 0.050 6106 Dihedral : 21.504 171.000 7828 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.69 % Favored : 98.26 % Rotamer: Outliers : 1.76 % Allowed : 9.92 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.13), residues: 4264 helix: 1.68 (0.10), residues: 2496 sheet: 0.43 (0.28), residues: 316 loop : 0.08 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 366 TYR 0.036 0.002 TYR O 941 PHE 0.019 0.002 PHE N 639 TRP 0.013 0.001 TRP J 410 HIS 0.012 0.001 HIS N 875 Details of bonding type rmsd covalent geometry : bond 0.00386 (39345) covalent geometry : angle 0.67272 (54529) hydrogen bonds : bond 0.04821 ( 2421) hydrogen bonds : angle 4.23157 ( 6590) metal coordination : bond 0.00158 ( 4) metal coordination : angle 0.74308 ( 3) Misc. bond : bond 0.00550 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 548 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 ASP cc_start: 0.8615 (t0) cc_final: 0.8327 (t0) REVERT: E 53 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7767 (mtp-110) REVERT: G 74 ASN cc_start: 0.8667 (t0) cc_final: 0.8407 (t0) REVERT: H 43 TYR cc_start: 0.7330 (t80) cc_final: 0.7099 (t80) REVERT: I 487 LYS cc_start: 0.9346 (tppt) cc_final: 0.8928 (tppt) REVERT: I 488 GLU cc_start: 0.8736 (tp30) cc_final: 0.8155 (tp30) REVERT: I 501 THR cc_start: 0.8869 (p) cc_final: 0.8632 (t) REVERT: J 27 TYR cc_start: 0.8198 (m-80) cc_final: 0.7835 (m-80) REVERT: J 109 MET cc_start: 0.8865 (mmm) cc_final: 0.8533 (mmm) REVERT: J 162 ASN cc_start: 0.8699 (m-40) cc_final: 0.8373 (m110) REVERT: J 254 MET cc_start: 0.9181 (mmm) cc_final: 0.8936 (mmm) REVERT: K 82 MET cc_start: 0.8591 (tpt) cc_final: 0.8292 (tpt) REVERT: K 90 PHE cc_start: 0.9318 (m-80) cc_final: 0.8957 (m-10) REVERT: K 115 ASN cc_start: 0.8610 (m110) cc_final: 0.8316 (m-40) REVERT: K 189 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9237 (mt) REVERT: K 191 LYS cc_start: 0.9447 (tttt) cc_final: 0.9212 (ptpt) REVERT: K 263 GLN cc_start: 0.8529 (mp10) cc_final: 0.8262 (mp10) REVERT: K 276 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8792 (mt-10) REVERT: K 280 ASN cc_start: 0.9696 (m-40) cc_final: 0.9348 (m110) REVERT: K 313 MET cc_start: 0.9148 (mmm) cc_final: 0.8641 (tpt) REVERT: L 2276 CYS cc_start: 0.8850 (m) cc_final: 0.8601 (m) REVERT: M 38 MET cc_start: 0.8507 (mmt) cc_final: 0.8288 (mmm) REVERT: M 99 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8323 (mm) REVERT: M 321 TRP cc_start: 0.8586 (t60) cc_final: 0.8094 (t60) REVERT: M 375 MET cc_start: 0.7988 (mmm) cc_final: 0.7785 (mmm) REVERT: N 674 MET cc_start: 0.7861 (mmt) cc_final: 0.7637 (mmm) REVERT: O 930 ASP cc_start: 0.8748 (t0) cc_final: 0.8420 (t0) REVERT: P 154 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8065 (tm-30) REVERT: P 158 ASP cc_start: 0.8550 (m-30) cc_final: 0.7909 (m-30) REVERT: P 316 ILE cc_start: 0.9643 (OUTLIER) cc_final: 0.9038 (mt) REVERT: P 357 ILE cc_start: 0.9203 (mt) cc_final: 0.8856 (mt) REVERT: P 414 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8768 (pm20) REVERT: Q 225 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8996 (mm-40) REVERT: Q 230 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8800 (pt0) REVERT: Q 238 GLN cc_start: 0.9627 (tp40) cc_final: 0.9368 (tp-100) REVERT: Q 251 ARG cc_start: 0.9095 (ttm110) cc_final: 0.8712 (ptp-110) REVERT: Q 268 ASN cc_start: 0.9311 (m-40) cc_final: 0.8976 (m110) REVERT: R 26 ASN cc_start: 0.8792 (m-40) cc_final: 0.8541 (m110) outliers start: 54 outliers final: 24 residues processed: 579 average time/residue: 0.2384 time to fit residues: 222.3604 Evaluate side-chains 499 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 470 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 458 LYS Chi-restraints excluded: chain I residue 467 LYS Chi-restraints excluded: chain J residue 34 LYS Chi-restraints excluded: chain J residue 242 LYS Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain N residue 415 ASP Chi-restraints excluded: chain O residue 882 ARG Chi-restraints excluded: chain O residue 899 LEU Chi-restraints excluded: chain O residue 939 LEU Chi-restraints excluded: chain P residue 298 ASP Chi-restraints excluded: chain P residue 308 HIS Chi-restraints excluded: chain P residue 316 ILE Chi-restraints excluded: chain P residue 406 SER Chi-restraints excluded: chain P residue 414 GLN Chi-restraints excluded: chain P residue 441 MET Chi-restraints excluded: chain Q residue 230 GLN Chi-restraints excluded: chain R residue 42 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 213 optimal weight: 10.0000 chunk 366 optimal weight: 50.0000 chunk 338 optimal weight: 0.9990 chunk 307 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 347 optimal weight: 10.0000 chunk 402 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 GLN C 39 ASN D 48 GLN H 50 HIS ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 482 HIS ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1960 HIS L1997 ASN M 323 GLN N 604 GLN N 638 HIS N 875 HIS N 925 GLN O 489 ASN O 501 HIS O 513 GLN ** Q 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 238 GLN R 23 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.087346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.057188 restraints weight = 147818.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.058969 restraints weight = 66234.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.060116 restraints weight = 43192.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.060701 restraints weight = 34205.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.061107 restraints weight = 30313.677| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 39381 Z= 0.297 Angle : 0.674 11.198 54532 Z= 0.364 Chirality : 0.043 0.241 6253 Planarity : 0.005 0.056 6106 Dihedral : 21.651 166.644 7826 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.54 % Rotamer: Outliers : 2.90 % Allowed : 10.51 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.13), residues: 4264 helix: 1.85 (0.10), residues: 2510 sheet: 0.60 (0.28), residues: 324 loop : 0.04 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 257 TYR 0.031 0.002 TYR P 322 PHE 0.021 0.002 PHE J 201 TRP 0.024 0.002 TRP M 349 HIS 0.015 0.002 HIS R 61 Details of bonding type rmsd covalent geometry : bond 0.00670 (39345) covalent geometry : angle 0.67334 (54529) hydrogen bonds : bond 0.04924 ( 2421) hydrogen bonds : angle 4.14637 ( 6590) metal coordination : bond 0.03142 ( 4) metal coordination : angle 2.08211 ( 3) Misc. bond : bond 0.00824 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 489 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: D 69 ASP cc_start: 0.8676 (t0) cc_final: 0.8338 (t0) REVERT: G 74 ASN cc_start: 0.8763 (t0) cc_final: 0.8468 (t0) REVERT: I 467 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8653 (pptt) REVERT: I 487 LYS cc_start: 0.9454 (tppt) cc_final: 0.8950 (tppt) REVERT: J 27 TYR cc_start: 0.8243 (m-80) cc_final: 0.7703 (m-80) REVERT: J 34 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8032 (mmmt) REVERT: J 104 ASP cc_start: 0.8580 (m-30) cc_final: 0.8309 (m-30) REVERT: J 109 MET cc_start: 0.8896 (mmm) cc_final: 0.8558 (mmm) REVERT: J 162 ASN cc_start: 0.8836 (m-40) cc_final: 0.8569 (m-40) REVERT: J 254 MET cc_start: 0.9199 (mmm) cc_final: 0.8899 (mmm) REVERT: K 189 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9167 (mt) REVERT: K 191 LYS cc_start: 0.9292 (tttt) cc_final: 0.9036 (ttpp) REVERT: K 263 GLN cc_start: 0.8499 (mp10) cc_final: 0.8192 (mp10) REVERT: K 276 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8785 (mt-10) REVERT: K 280 ASN cc_start: 0.9697 (m-40) cc_final: 0.9381 (m110) REVERT: K 313 MET cc_start: 0.9173 (mmm) cc_final: 0.8681 (tpt) REVERT: K 373 LYS cc_start: 0.9042 (tptm) cc_final: 0.8700 (tppp) REVERT: L 2276 CYS cc_start: 0.8922 (m) cc_final: 0.8635 (m) REVERT: M 38 MET cc_start: 0.8515 (mmt) cc_final: 0.8275 (mmm) REVERT: M 99 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8441 (mm) REVERT: N 674 MET cc_start: 0.7993 (mmt) cc_final: 0.7741 (mmm) REVERT: O 480 TYR cc_start: 0.9092 (t80) cc_final: 0.8695 (t80) REVERT: O 930 ASP cc_start: 0.8775 (t0) cc_final: 0.8470 (t0) REVERT: P 317 GLN cc_start: 0.9323 (tt0) cc_final: 0.9068 (tm-30) REVERT: P 357 ILE cc_start: 0.9262 (mt) cc_final: 0.9051 (mt) REVERT: Q 225 GLN cc_start: 0.9250 (tm-30) cc_final: 0.9029 (tp-100) REVERT: Q 228 LYS cc_start: 0.9355 (mttp) cc_final: 0.9003 (mttp) REVERT: Q 230 GLN cc_start: 0.9197 (tt0) cc_final: 0.8864 (pt0) REVERT: Q 238 GLN cc_start: 0.9663 (tp-100) cc_final: 0.9386 (tp-100) REVERT: Q 259 PHE cc_start: 0.8649 (t80) cc_final: 0.8442 (t80) REVERT: Q 268 ASN cc_start: 0.9395 (m-40) cc_final: 0.9078 (m-40) REVERT: R 22 GLU cc_start: 0.8576 (tp30) cc_final: 0.8359 (tp30) REVERT: R 26 ASN cc_start: 0.8765 (m-40) cc_final: 0.7786 (m-40) outliers start: 89 outliers final: 51 residues processed: 545 average time/residue: 0.2420 time to fit residues: 213.5963 Evaluate side-chains 506 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 452 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 453 THR Chi-restraints excluded: chain I residue 458 LYS Chi-restraints excluded: chain I residue 467 LYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 1340 HIS Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 242 LYS Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 321 THR Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 383 ASN Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 272 CYS Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain L residue 1744 LEU Chi-restraints excluded: chain L residue 2109 ASN Chi-restraints excluded: chain L residue 2162 VAL Chi-restraints excluded: chain L residue 2281 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 378 LEU Chi-restraints excluded: chain N residue 415 ASP Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 680 LEU Chi-restraints excluded: chain N residue 683 VAL Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 882 ARG Chi-restraints excluded: chain O residue 899 LEU Chi-restraints excluded: chain O residue 939 LEU Chi-restraints excluded: chain P residue 298 ASP Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 441 MET Chi-restraints excluded: chain P residue 454 ASP Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 51 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 56 optimal weight: 0.6980 chunk 449 optimal weight: 2.9990 chunk 255 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 137 optimal weight: 50.0000 chunk 425 optimal weight: 40.0000 chunk 203 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 394 optimal weight: 4.9990 chunk 343 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN ** I 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 251 HIS K 121 GLN K 137 GLN ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1960 HIS N 638 HIS N 875 HIS N 925 GLN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.088254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.058217 restraints weight = 146594.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060033 restraints weight = 65328.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.061194 restraints weight = 42439.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.061815 restraints weight = 33620.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062149 restraints weight = 29648.253| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 39381 Z= 0.173 Angle : 0.606 11.522 54532 Z= 0.327 Chirality : 0.040 0.252 6253 Planarity : 0.004 0.066 6106 Dihedral : 21.681 168.351 7823 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.78 % Favored : 98.19 % Rotamer: Outliers : 2.25 % Allowed : 11.59 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.13), residues: 4264 helix: 2.07 (0.10), residues: 2501 sheet: 0.84 (0.29), residues: 324 loop : 0.06 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 229 TYR 0.028 0.002 TYR P 322 PHE 0.020 0.001 PHE Q 259 TRP 0.023 0.001 TRP I1355 HIS 0.008 0.001 HIS N 875 Details of bonding type rmsd covalent geometry : bond 0.00387 (39345) covalent geometry : angle 0.60579 (54529) hydrogen bonds : bond 0.04135 ( 2421) hydrogen bonds : angle 3.91372 ( 6590) metal coordination : bond 0.01174 ( 4) metal coordination : angle 1.55279 ( 3) Misc. bond : bond 0.00318 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 491 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 74 ASN cc_start: 0.8778 (t0) cc_final: 0.8452 (t0) REVERT: I 467 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8213 (pptt) REVERT: I 473 GLN cc_start: 0.8861 (tp-100) cc_final: 0.8380 (tp-100) REVERT: I 477 ASN cc_start: 0.8894 (m110) cc_final: 0.7998 (m110) REVERT: I 487 LYS cc_start: 0.9349 (tppt) cc_final: 0.8990 (tppt) REVERT: I 491 ARG cc_start: 0.8709 (mtm180) cc_final: 0.8467 (mtm180) REVERT: J 27 TYR cc_start: 0.8288 (m-80) cc_final: 0.7896 (m-80) REVERT: J 109 MET cc_start: 0.8863 (mmm) cc_final: 0.8527 (mmm) REVERT: J 162 ASN cc_start: 0.8796 (m-40) cc_final: 0.8532 (m-40) REVERT: J 254 MET cc_start: 0.9196 (mmm) cc_final: 0.8911 (mmm) REVERT: K 90 PHE cc_start: 0.9318 (m-80) cc_final: 0.8845 (m-10) REVERT: K 189 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9060 (mt) REVERT: K 191 LYS cc_start: 0.9276 (tttt) cc_final: 0.9015 (ttpp) REVERT: K 263 GLN cc_start: 0.8569 (mp10) cc_final: 0.8219 (mp10) REVERT: K 280 ASN cc_start: 0.9694 (m-40) cc_final: 0.9382 (m110) REVERT: K 313 MET cc_start: 0.9167 (mmm) cc_final: 0.8680 (tpt) REVERT: K 373 LYS cc_start: 0.9055 (tptm) cc_final: 0.8694 (tppp) REVERT: L 2266 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8801 (pp) REVERT: L 2276 CYS cc_start: 0.8867 (m) cc_final: 0.8601 (m) REVERT: M 38 MET cc_start: 0.8467 (mmt) cc_final: 0.8235 (mmm) REVERT: N 640 LEU cc_start: 0.9230 (mm) cc_final: 0.9007 (mm) REVERT: N 674 MET cc_start: 0.7920 (mmt) cc_final: 0.7654 (mmm) REVERT: O 930 ASP cc_start: 0.8774 (t0) cc_final: 0.8454 (t0) REVERT: P 357 ILE cc_start: 0.9236 (mt) cc_final: 0.8950 (mt) REVERT: Q 225 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8988 (tp-100) REVERT: Q 228 LYS cc_start: 0.9321 (mttp) cc_final: 0.8952 (mttp) REVERT: Q 230 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8848 (pt0) REVERT: Q 238 GLN cc_start: 0.9671 (tp-100) cc_final: 0.9414 (tp-100) REVERT: Q 268 ASN cc_start: 0.9459 (m-40) cc_final: 0.9158 (m-40) REVERT: R 26 ASN cc_start: 0.8777 (m-40) cc_final: 0.7892 (m-40) outliers start: 69 outliers final: 43 residues processed: 537 average time/residue: 0.2317 time to fit residues: 204.1864 Evaluate side-chains 499 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 452 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 453 THR Chi-restraints excluded: chain I residue 458 LYS Chi-restraints excluded: chain I residue 467 LYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 1340 HIS Chi-restraints excluded: chain J residue 242 LYS Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 383 ASN Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 137 GLN Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain L residue 1744 LEU Chi-restraints excluded: chain L residue 2109 ASN Chi-restraints excluded: chain L residue 2162 VAL Chi-restraints excluded: chain L residue 2263 VAL Chi-restraints excluded: chain L residue 2266 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain N residue 415 ASP Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 683 VAL Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 882 ARG Chi-restraints excluded: chain O residue 899 LEU Chi-restraints excluded: chain O residue 939 LEU Chi-restraints excluded: chain P residue 290 TYR Chi-restraints excluded: chain P residue 298 ASP Chi-restraints excluded: chain Q residue 230 GLN Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 51 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 142 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 390 optimal weight: 6.9990 chunk 263 optimal weight: 0.9980 chunk 435 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 413 optimal weight: 50.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 ASN D 96 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1960 HIS N 638 HIS ** N 925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 949 GLN O 632 GLN ** Q 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.087798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.057767 restraints weight = 147036.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.059573 restraints weight = 65491.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.060717 restraints weight = 42601.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.061354 restraints weight = 33703.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.061666 restraints weight = 29664.447| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 39381 Z= 0.197 Angle : 0.612 15.928 54532 Z= 0.329 Chirality : 0.040 0.255 6253 Planarity : 0.004 0.064 6106 Dihedral : 21.607 168.968 7821 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.95 % Favored : 98.03 % Rotamer: Outliers : 2.35 % Allowed : 12.27 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.13), residues: 4264 helix: 2.16 (0.10), residues: 2506 sheet: 0.97 (0.29), residues: 322 loop : 0.07 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 229 TYR 0.026 0.001 TYR I 489 PHE 0.029 0.001 PHE Q 259 TRP 0.021 0.001 TRP I1355 HIS 0.007 0.001 HIS L1960 Details of bonding type rmsd covalent geometry : bond 0.00444 (39345) covalent geometry : angle 0.61234 (54529) hydrogen bonds : bond 0.04140 ( 2421) hydrogen bonds : angle 3.88170 ( 6590) metal coordination : bond 0.01755 ( 4) metal coordination : angle 1.72318 ( 3) Misc. bond : bond 0.00173 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 473 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 74 ASN cc_start: 0.8725 (t0) cc_final: 0.8180 (t0) REVERT: I 464 GLN cc_start: 0.8270 (mt0) cc_final: 0.7954 (tm-30) REVERT: I 467 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8354 (pptt) REVERT: I 473 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8399 (tp-100) REVERT: I 477 ASN cc_start: 0.9077 (m110) cc_final: 0.8083 (m110) REVERT: I 487 LYS cc_start: 0.9370 (tppt) cc_final: 0.9098 (tppt) REVERT: I 488 GLU cc_start: 0.8846 (tp30) cc_final: 0.8419 (tp30) REVERT: I 491 ARG cc_start: 0.8718 (mtm180) cc_final: 0.8374 (mtm180) REVERT: J 27 TYR cc_start: 0.8353 (m-80) cc_final: 0.8103 (m-80) REVERT: J 34 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8497 (mmmt) REVERT: J 109 MET cc_start: 0.8841 (mmm) cc_final: 0.8514 (mmm) REVERT: J 152 CYS cc_start: 0.8903 (t) cc_final: 0.8545 (t) REVERT: J 162 ASN cc_start: 0.8780 (m-40) cc_final: 0.8531 (m-40) REVERT: J 254 MET cc_start: 0.9216 (mmm) cc_final: 0.8921 (mmm) REVERT: J 379 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8144 (pttt) REVERT: J 388 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8658 (mt-10) REVERT: K 189 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9073 (mt) REVERT: K 191 LYS cc_start: 0.9291 (tttt) cc_final: 0.9003 (ttpp) REVERT: K 263 GLN cc_start: 0.8630 (mp10) cc_final: 0.8273 (mp10) REVERT: K 280 ASN cc_start: 0.9696 (m-40) cc_final: 0.9386 (m110) REVERT: L 2266 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8820 (pp) REVERT: L 2276 CYS cc_start: 0.8880 (m) cc_final: 0.8592 (m) REVERT: M 220 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8133 (tm-30) REVERT: N 640 LEU cc_start: 0.9247 (mm) cc_final: 0.9022 (mm) REVERT: N 674 MET cc_start: 0.7950 (mmt) cc_final: 0.7676 (mmm) REVERT: O 914 ASP cc_start: 0.9204 (OUTLIER) cc_final: 0.8979 (p0) REVERT: O 930 ASP cc_start: 0.8802 (t0) cc_final: 0.8475 (t0) REVERT: P 149 ASP cc_start: 0.8793 (m-30) cc_final: 0.8567 (p0) REVERT: P 357 ILE cc_start: 0.9227 (mt) cc_final: 0.8994 (mt) REVERT: Q 230 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8867 (pt0) REVERT: Q 238 GLN cc_start: 0.9657 (tp-100) cc_final: 0.9356 (tm-30) REVERT: Q 268 ASN cc_start: 0.9438 (m-40) cc_final: 0.9166 (m-40) outliers start: 72 outliers final: 48 residues processed: 517 average time/residue: 0.2304 time to fit residues: 195.7889 Evaluate side-chains 498 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 444 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 453 THR Chi-restraints excluded: chain I residue 458 LYS Chi-restraints excluded: chain I residue 467 LYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 1340 HIS Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 242 LYS Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 379 LYS Chi-restraints excluded: chain J residue 383 ASN Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain L residue 1744 LEU Chi-restraints excluded: chain L residue 2109 ASN Chi-restraints excluded: chain L residue 2145 GLU Chi-restraints excluded: chain L residue 2162 VAL Chi-restraints excluded: chain L residue 2263 VAL Chi-restraints excluded: chain L residue 2266 LEU Chi-restraints excluded: chain L residue 2281 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 415 ASP Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 683 VAL Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 882 ARG Chi-restraints excluded: chain O residue 899 LEU Chi-restraints excluded: chain O residue 914 ASP Chi-restraints excluded: chain O residue 939 LEU Chi-restraints excluded: chain P residue 298 ASP Chi-restraints excluded: chain P residue 454 ASP Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 230 GLN Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 51 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 353 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 343 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 198 optimal weight: 0.1980 chunk 295 optimal weight: 2.9990 chunk 374 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 247 optimal weight: 0.0970 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 GLN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 476 ASN N 638 HIS ** N 925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.088487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.058676 restraints weight = 147616.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.060471 restraints weight = 64942.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.061488 restraints weight = 41762.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.062189 restraints weight = 33356.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062493 restraints weight = 29066.381| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39381 Z= 0.141 Angle : 0.592 10.951 54532 Z= 0.318 Chirality : 0.039 0.261 6253 Planarity : 0.004 0.062 6106 Dihedral : 21.491 170.202 7821 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.67 % Favored : 98.31 % Rotamer: Outliers : 2.15 % Allowed : 13.48 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.13), residues: 4264 helix: 2.24 (0.10), residues: 2506 sheet: 1.09 (0.29), residues: 322 loop : 0.10 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 229 TYR 0.022 0.001 TYR I 489 PHE 0.016 0.001 PHE N 639 TRP 0.020 0.001 TRP I1355 HIS 0.012 0.001 HIS R 61 Details of bonding type rmsd covalent geometry : bond 0.00310 (39345) covalent geometry : angle 0.59144 (54529) hydrogen bonds : bond 0.03816 ( 2421) hydrogen bonds : angle 3.77738 ( 6590) metal coordination : bond 0.00631 ( 4) metal coordination : angle 1.40778 ( 3) Misc. bond : bond 0.00156 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 487 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: C 62 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7571 (tp30) REVERT: G 74 ASN cc_start: 0.8722 (t0) cc_final: 0.8362 (t0) REVERT: G 92 GLU cc_start: 0.7145 (pm20) cc_final: 0.6351 (pm20) REVERT: I 464 GLN cc_start: 0.8273 (mt0) cc_final: 0.7906 (tm-30) REVERT: I 467 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8214 (pptt) REVERT: I 473 GLN cc_start: 0.8878 (tp-100) cc_final: 0.8314 (tp-100) REVERT: I 477 ASN cc_start: 0.9033 (m110) cc_final: 0.8091 (m110) REVERT: I 487 LYS cc_start: 0.9346 (tppt) cc_final: 0.9119 (tppt) REVERT: I 498 GLN cc_start: 0.8744 (tp40) cc_final: 0.7966 (tp40) REVERT: J 27 TYR cc_start: 0.8290 (m-80) cc_final: 0.7950 (m-80) REVERT: J 109 MET cc_start: 0.8768 (mmm) cc_final: 0.8455 (mmm) REVERT: J 152 CYS cc_start: 0.8841 (t) cc_final: 0.8579 (t) REVERT: J 162 ASN cc_start: 0.8682 (m-40) cc_final: 0.8425 (m110) REVERT: J 204 MET cc_start: 0.8620 (ptp) cc_final: 0.8135 (ptp) REVERT: J 257 CYS cc_start: 0.9308 (m) cc_final: 0.8954 (m) REVERT: J 379 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7975 (pttt) REVERT: J 388 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8593 (mt-10) REVERT: K 189 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9050 (mt) REVERT: K 263 GLN cc_start: 0.8677 (mp10) cc_final: 0.8306 (mp10) REVERT: K 280 ASN cc_start: 0.9687 (m-40) cc_final: 0.9356 (m110) REVERT: L 2276 CYS cc_start: 0.8864 (m) cc_final: 0.8588 (m) REVERT: M 220 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8126 (tm-30) REVERT: N 616 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.7340 (m-80) REVERT: N 640 LEU cc_start: 0.9270 (mm) cc_final: 0.9040 (mm) REVERT: N 674 MET cc_start: 0.8016 (mmt) cc_final: 0.7727 (mmm) REVERT: O 674 MET cc_start: 0.8826 (tpt) cc_final: 0.8494 (tpp) REVERT: O 914 ASP cc_start: 0.9199 (OUTLIER) cc_final: 0.8999 (p0) REVERT: O 930 ASP cc_start: 0.8758 (t0) cc_final: 0.8436 (t0) REVERT: P 357 ILE cc_start: 0.9217 (mt) cc_final: 0.9005 (mt) REVERT: P 404 MET cc_start: 0.8673 (mpp) cc_final: 0.8229 (mpp) REVERT: Q 195 ARG cc_start: 0.9025 (ttm-80) cc_final: 0.8756 (ttp80) REVERT: Q 230 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8822 (pt0) REVERT: Q 238 GLN cc_start: 0.9636 (tp-100) cc_final: 0.9382 (tm-30) REVERT: Q 239 ARG cc_start: 0.8955 (ptp-170) cc_final: 0.8634 (ptt-90) REVERT: Q 268 ASN cc_start: 0.9413 (m-40) cc_final: 0.9159 (m-40) REVERT: R 22 GLU cc_start: 0.8621 (tp30) cc_final: 0.8333 (tp30) REVERT: R 26 ASN cc_start: 0.8890 (m-40) cc_final: 0.8576 (m110) outliers start: 66 outliers final: 45 residues processed: 531 average time/residue: 0.2328 time to fit residues: 203.1934 Evaluate side-chains 501 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 450 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 453 THR Chi-restraints excluded: chain I residue 458 LYS Chi-restraints excluded: chain I residue 467 LYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 1340 HIS Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 242 LYS Chi-restraints excluded: chain J residue 379 LYS Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain L residue 1744 LEU Chi-restraints excluded: chain L residue 2109 ASN Chi-restraints excluded: chain L residue 2145 GLU Chi-restraints excluded: chain L residue 2162 VAL Chi-restraints excluded: chain L residue 2263 VAL Chi-restraints excluded: chain L residue 2281 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 378 LEU Chi-restraints excluded: chain N residue 415 ASP Chi-restraints excluded: chain N residue 616 TYR Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 683 VAL Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 882 ARG Chi-restraints excluded: chain O residue 899 LEU Chi-restraints excluded: chain O residue 914 ASP Chi-restraints excluded: chain P residue 298 ASP Chi-restraints excluded: chain P residue 454 ASP Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 230 GLN Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 233 optimal weight: 8.9990 chunk 370 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 249 optimal weight: 4.9990 chunk 432 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 277 optimal weight: 0.9980 chunk 236 optimal weight: 0.0370 chunk 163 optimal weight: 0.0000 chunk 214 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 638 HIS N 925 GLN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 621 ASN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.088496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.058734 restraints weight = 148386.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060535 restraints weight = 65222.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061658 restraints weight = 41873.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.062319 restraints weight = 32948.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.062647 restraints weight = 28811.407| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39381 Z= 0.150 Angle : 0.600 14.407 54532 Z= 0.321 Chirality : 0.039 0.256 6253 Planarity : 0.004 0.060 6106 Dihedral : 21.384 171.403 7821 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.83 % Favored : 98.15 % Rotamer: Outliers : 2.12 % Allowed : 14.13 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.13), residues: 4264 helix: 2.27 (0.10), residues: 2515 sheet: 1.12 (0.29), residues: 324 loop : 0.12 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG Q 229 TYR 0.036 0.001 TYR B 89 PHE 0.031 0.001 PHE M 17 TRP 0.028 0.001 TRP I1355 HIS 0.007 0.001 HIS R 61 Details of bonding type rmsd covalent geometry : bond 0.00334 (39345) covalent geometry : angle 0.60033 (54529) hydrogen bonds : bond 0.03778 ( 2421) hydrogen bonds : angle 3.75925 ( 6590) metal coordination : bond 0.00958 ( 4) metal coordination : angle 1.47993 ( 3) Misc. bond : bond 0.00090 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 477 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 75 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7762 (tm-30) REVERT: C 62 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7526 (tp30) REVERT: E 58 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.7788 (t) REVERT: E 60 GLU cc_start: 0.8874 (pm20) cc_final: 0.8462 (pm20) REVERT: G 74 ASN cc_start: 0.8740 (t0) cc_final: 0.8214 (t0) REVERT: G 76 LYS cc_start: 0.9169 (mttp) cc_final: 0.8840 (mtpp) REVERT: I 464 GLN cc_start: 0.8274 (mt0) cc_final: 0.7904 (tm-30) REVERT: I 467 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8441 (pptt) REVERT: I 473 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8317 (tp-100) REVERT: I 477 ASN cc_start: 0.9046 (m110) cc_final: 0.8109 (m110) REVERT: I 487 LYS cc_start: 0.9340 (tppt) cc_final: 0.8937 (tppt) REVERT: I 488 GLU cc_start: 0.8836 (tp30) cc_final: 0.8181 (tp30) REVERT: I 491 ARG cc_start: 0.8721 (mtm180) cc_final: 0.8319 (mtm-85) REVERT: I 498 GLN cc_start: 0.8767 (tp40) cc_final: 0.7953 (tp40) REVERT: J 27 TYR cc_start: 0.8321 (m-80) cc_final: 0.7975 (m-80) REVERT: J 109 MET cc_start: 0.8767 (mmm) cc_final: 0.8450 (mmm) REVERT: J 152 CYS cc_start: 0.8835 (t) cc_final: 0.8571 (t) REVERT: J 162 ASN cc_start: 0.8650 (m-40) cc_final: 0.8392 (m110) REVERT: J 204 MET cc_start: 0.8632 (ptp) cc_final: 0.8142 (ptp) REVERT: J 257 CYS cc_start: 0.9307 (m) cc_final: 0.8925 (m) REVERT: J 282 MET cc_start: 0.5059 (mmt) cc_final: 0.4446 (mpp) REVERT: J 379 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8033 (pttt) REVERT: K 189 LEU cc_start: 0.9491 (mt) cc_final: 0.8924 (mt) REVERT: K 191 LYS cc_start: 0.9479 (ptmt) cc_final: 0.9219 (ptmm) REVERT: K 257 CYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8474 (t) REVERT: K 263 GLN cc_start: 0.8695 (mp10) cc_final: 0.8346 (mp10) REVERT: L 2276 CYS cc_start: 0.8873 (m) cc_final: 0.8583 (m) REVERT: M 220 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8137 (tm-30) REVERT: N 616 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: N 640 LEU cc_start: 0.9288 (mm) cc_final: 0.9053 (mm) REVERT: N 674 MET cc_start: 0.8010 (mmt) cc_final: 0.7715 (mmm) REVERT: O 914 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8849 (p0) REVERT: O 930 ASP cc_start: 0.8754 (t0) cc_final: 0.8432 (t0) REVERT: P 149 ASP cc_start: 0.8690 (m-30) cc_final: 0.8423 (m-30) REVERT: P 357 ILE cc_start: 0.9219 (mt) cc_final: 0.9013 (mt) REVERT: Q 195 ARG cc_start: 0.9041 (ttm-80) cc_final: 0.8768 (ttp80) REVERT: Q 230 GLN cc_start: 0.9203 (tt0) cc_final: 0.8943 (tt0) REVERT: Q 238 GLN cc_start: 0.9626 (tp-100) cc_final: 0.9386 (tm-30) REVERT: Q 268 ASN cc_start: 0.9406 (m-40) cc_final: 0.9163 (m-40) REVERT: R 22 GLU cc_start: 0.8581 (tp30) cc_final: 0.8255 (tp30) REVERT: R 26 ASN cc_start: 0.8865 (m-40) cc_final: 0.8536 (m110) outliers start: 65 outliers final: 46 residues processed: 520 average time/residue: 0.2360 time to fit residues: 201.3221 Evaluate side-chains 508 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 456 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 453 THR Chi-restraints excluded: chain I residue 458 LYS Chi-restraints excluded: chain I residue 467 LYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 242 LYS Chi-restraints excluded: chain J residue 379 LYS Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain L residue 1744 LEU Chi-restraints excluded: chain L residue 1831 LEU Chi-restraints excluded: chain L residue 2145 GLU Chi-restraints excluded: chain L residue 2162 VAL Chi-restraints excluded: chain L residue 2281 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 378 LEU Chi-restraints excluded: chain N residue 415 ASP Chi-restraints excluded: chain N residue 616 TYR Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 683 VAL Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 882 ARG Chi-restraints excluded: chain O residue 899 LEU Chi-restraints excluded: chain O residue 914 ASP Chi-restraints excluded: chain P residue 298 ASP Chi-restraints excluded: chain P residue 454 ASP Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 68 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 78 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 306 optimal weight: 0.9980 chunk 273 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 279 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 HIS K 121 GLN ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 638 HIS ** N 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 925 GLN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 923 GLN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.088376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.058620 restraints weight = 147562.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.060413 restraints weight = 65203.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.061530 restraints weight = 41954.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.062177 restraints weight = 32999.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.062502 restraints weight = 28949.890| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 39381 Z= 0.156 Angle : 0.613 17.762 54532 Z= 0.327 Chirality : 0.039 0.259 6253 Planarity : 0.004 0.060 6106 Dihedral : 21.353 172.385 7821 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.78 % Favored : 98.19 % Rotamer: Outliers : 2.06 % Allowed : 15.11 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.13), residues: 4264 helix: 2.28 (0.10), residues: 2514 sheet: 1.14 (0.30), residues: 325 loop : 0.13 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG Q 229 TYR 0.035 0.001 TYR B 89 PHE 0.027 0.001 PHE Q 259 TRP 0.030 0.001 TRP I1355 HIS 0.013 0.001 HIS N 875 Details of bonding type rmsd covalent geometry : bond 0.00348 (39345) covalent geometry : angle 0.61326 (54529) hydrogen bonds : bond 0.03762 ( 2421) hydrogen bonds : angle 3.76006 ( 6590) metal coordination : bond 0.01093 ( 4) metal coordination : angle 1.50074 ( 3) Misc. bond : bond 0.00093 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 475 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7730 (tm-30) REVERT: B 85 MET cc_start: 0.8605 (tpp) cc_final: 0.8012 (mmm) REVERT: C 62 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7546 (tp30) REVERT: G 74 ASN cc_start: 0.8720 (t0) cc_final: 0.8251 (t0) REVERT: G 76 LYS cc_start: 0.9163 (mttp) cc_final: 0.8857 (mtpp) REVERT: I 464 GLN cc_start: 0.8275 (mt0) cc_final: 0.7897 (tm-30) REVERT: I 467 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8420 (pptt) REVERT: I 473 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8249 (tp-100) REVERT: I 477 ASN cc_start: 0.9071 (m110) cc_final: 0.8213 (m110) REVERT: I 487 LYS cc_start: 0.9347 (tppt) cc_final: 0.8956 (tppt) REVERT: I 488 GLU cc_start: 0.8853 (tp30) cc_final: 0.8156 (tp30) REVERT: I 491 ARG cc_start: 0.8708 (mtm180) cc_final: 0.8310 (mtm-85) REVERT: I 498 GLN cc_start: 0.8783 (tp40) cc_final: 0.8095 (tp40) REVERT: J 27 TYR cc_start: 0.8327 (m-80) cc_final: 0.8049 (m-80) REVERT: J 109 MET cc_start: 0.8758 (mmm) cc_final: 0.8442 (mmm) REVERT: J 152 CYS cc_start: 0.8842 (t) cc_final: 0.8578 (t) REVERT: J 162 ASN cc_start: 0.8632 (m-40) cc_final: 0.8350 (m110) REVERT: J 204 MET cc_start: 0.8653 (ptp) cc_final: 0.8203 (ptp) REVERT: J 257 CYS cc_start: 0.9310 (m) cc_final: 0.8963 (m) REVERT: K 189 LEU cc_start: 0.9499 (mt) cc_final: 0.8924 (mt) REVERT: K 191 LYS cc_start: 0.9502 (ptmt) cc_final: 0.9284 (ptmm) REVERT: K 257 CYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8642 (t) REVERT: K 263 GLN cc_start: 0.8705 (mp10) cc_final: 0.8384 (mp10) REVERT: L 2231 MET cc_start: 0.8389 (mmp) cc_final: 0.8014 (mmm) REVERT: L 2276 CYS cc_start: 0.8875 (m) cc_final: 0.8587 (m) REVERT: M 220 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8144 (tm-30) REVERT: N 640 LEU cc_start: 0.9288 (mm) cc_final: 0.9052 (mm) REVERT: N 674 MET cc_start: 0.7898 (mmt) cc_final: 0.7604 (mmm) REVERT: N 944 MET cc_start: 0.8602 (mtt) cc_final: 0.8382 (ttm) REVERT: O 915 ARG cc_start: 0.8971 (ttp-110) cc_final: 0.8484 (ptp90) REVERT: O 930 ASP cc_start: 0.8749 (t0) cc_final: 0.8418 (t0) REVERT: Q 195 ARG cc_start: 0.9053 (ttm-80) cc_final: 0.8778 (ttp80) REVERT: Q 230 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8870 (tm-30) REVERT: Q 238 GLN cc_start: 0.9624 (tp-100) cc_final: 0.9391 (tm-30) REVERT: Q 259 PHE cc_start: 0.8683 (t80) cc_final: 0.8472 (t80) REVERT: R 22 GLU cc_start: 0.8595 (tp30) cc_final: 0.8242 (tp30) REVERT: R 26 ASN cc_start: 0.8876 (m-40) cc_final: 0.8546 (m110) outliers start: 63 outliers final: 47 residues processed: 518 average time/residue: 0.2196 time to fit residues: 188.0841 Evaluate side-chains 503 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 453 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 458 LYS Chi-restraints excluded: chain I residue 467 LYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 242 LYS Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain L residue 1744 LEU Chi-restraints excluded: chain L residue 1831 LEU Chi-restraints excluded: chain L residue 2109 ASN Chi-restraints excluded: chain L residue 2145 GLU Chi-restraints excluded: chain L residue 2162 VAL Chi-restraints excluded: chain L residue 2281 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 378 LEU Chi-restraints excluded: chain N residue 415 ASP Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 683 VAL Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 882 ARG Chi-restraints excluded: chain O residue 899 LEU Chi-restraints excluded: chain P residue 298 ASP Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 230 GLN Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 68 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 177 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 359 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 282 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 405 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 HIS J 110 HIS ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 489 ASN N 638 HIS ** N 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.088287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058521 restraints weight = 148506.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.060336 restraints weight = 65268.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.061451 restraints weight = 41858.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.062097 restraints weight = 32847.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.062432 restraints weight = 28878.345| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 39381 Z= 0.156 Angle : 0.627 14.280 54532 Z= 0.332 Chirality : 0.039 0.296 6253 Planarity : 0.004 0.064 6106 Dihedral : 21.331 173.373 7821 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.04 % Favored : 97.94 % Rotamer: Outliers : 1.70 % Allowed : 15.40 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.13), residues: 4264 helix: 2.34 (0.10), residues: 2495 sheet: 1.15 (0.30), residues: 325 loop : 0.17 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG Q 229 TYR 0.024 0.001 TYR O 616 PHE 0.021 0.001 PHE Q 259 TRP 0.032 0.001 TRP I1355 HIS 0.012 0.001 HIS N 875 Details of bonding type rmsd covalent geometry : bond 0.00349 (39345) covalent geometry : angle 0.62740 (54529) hydrogen bonds : bond 0.03734 ( 2421) hydrogen bonds : angle 3.76874 ( 6590) metal coordination : bond 0.01059 ( 4) metal coordination : angle 1.53193 ( 3) Misc. bond : bond 0.00140 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 466 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 75 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7719 (tm-30) REVERT: C 62 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7555 (tp30) REVERT: G 74 ASN cc_start: 0.8680 (t0) cc_final: 0.8238 (t0) REVERT: G 76 LYS cc_start: 0.9162 (mttp) cc_final: 0.8869 (mtpp) REVERT: I 464 GLN cc_start: 0.8293 (mt0) cc_final: 0.7904 (tm-30) REVERT: I 467 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8458 (pptt) REVERT: I 473 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8280 (tp-100) REVERT: I 477 ASN cc_start: 0.9057 (m110) cc_final: 0.8116 (m110) REVERT: I 487 LYS cc_start: 0.9345 (tppt) cc_final: 0.8971 (tppt) REVERT: I 488 GLU cc_start: 0.8837 (tp30) cc_final: 0.8133 (tp30) REVERT: I 491 ARG cc_start: 0.8700 (mtm180) cc_final: 0.8310 (mtm-85) REVERT: I 498 GLN cc_start: 0.8771 (tp40) cc_final: 0.8075 (tp40) REVERT: J 27 TYR cc_start: 0.8305 (m-80) cc_final: 0.7952 (m-80) REVERT: J 109 MET cc_start: 0.8751 (mmm) cc_final: 0.8444 (mmm) REVERT: J 162 ASN cc_start: 0.8576 (m-40) cc_final: 0.8293 (m110) REVERT: J 204 MET cc_start: 0.8658 (ptp) cc_final: 0.8198 (ptp) REVERT: J 257 CYS cc_start: 0.9301 (m) cc_final: 0.8962 (m) REVERT: J 282 MET cc_start: 0.4850 (mmt) cc_final: 0.4420 (mpp) REVERT: K 189 LEU cc_start: 0.9506 (mt) cc_final: 0.8884 (mt) REVERT: K 191 LYS cc_start: 0.9510 (ptmt) cc_final: 0.9287 (ptmm) REVERT: K 257 CYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8590 (t) REVERT: K 263 GLN cc_start: 0.8726 (mp10) cc_final: 0.8400 (mp10) REVERT: L 2231 MET cc_start: 0.8394 (mmp) cc_final: 0.8017 (mmm) REVERT: L 2276 CYS cc_start: 0.8837 (m) cc_final: 0.8577 (m) REVERT: M 220 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8168 (tm-30) REVERT: M 349 TRP cc_start: 0.7880 (m100) cc_final: 0.7350 (m100) REVERT: N 616 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.7269 (m-80) REVERT: N 640 LEU cc_start: 0.9295 (mm) cc_final: 0.9050 (mm) REVERT: N 674 MET cc_start: 0.7872 (mmt) cc_final: 0.7569 (mmm) REVERT: N 944 MET cc_start: 0.8500 (mtt) cc_final: 0.8277 (ttm) REVERT: O 915 ARG cc_start: 0.8971 (ttp-110) cc_final: 0.8565 (ptp-170) REVERT: O 930 ASP cc_start: 0.8737 (t0) cc_final: 0.8404 (t0) REVERT: Q 195 ARG cc_start: 0.9065 (ttm-80) cc_final: 0.8797 (ttp80) REVERT: Q 230 GLN cc_start: 0.9189 (tt0) cc_final: 0.8931 (tt0) REVERT: Q 238 GLN cc_start: 0.9621 (tp-100) cc_final: 0.9382 (tm-30) REVERT: Q 259 PHE cc_start: 0.8693 (t80) cc_final: 0.8485 (t80) REVERT: Q 264 ASP cc_start: 0.9010 (m-30) cc_final: 0.8639 (p0) REVERT: R 22 GLU cc_start: 0.8595 (tp30) cc_final: 0.8234 (tp30) REVERT: R 26 ASN cc_start: 0.8842 (m-40) cc_final: 0.8480 (m110) outliers start: 52 outliers final: 46 residues processed: 500 average time/residue: 0.2253 time to fit residues: 187.3716 Evaluate side-chains 506 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 457 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 458 LYS Chi-restraints excluded: chain I residue 467 LYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 242 LYS Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain L residue 1744 LEU Chi-restraints excluded: chain L residue 1831 LEU Chi-restraints excluded: chain L residue 2109 ASN Chi-restraints excluded: chain L residue 2145 GLU Chi-restraints excluded: chain L residue 2162 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 415 ASP Chi-restraints excluded: chain N residue 616 TYR Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 683 VAL Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 882 ARG Chi-restraints excluded: chain O residue 899 LEU Chi-restraints excluded: chain P residue 298 ASP Chi-restraints excluded: chain P residue 355 SER Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 68 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 412 optimal weight: 0.0980 chunk 59 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 448 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 447 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 638 HIS ** N 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.088650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.058995 restraints weight = 147322.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060799 restraints weight = 64927.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061931 restraints weight = 41694.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.062587 restraints weight = 32735.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.062921 restraints weight = 28668.754| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39381 Z= 0.143 Angle : 0.646 13.724 54532 Z= 0.339 Chirality : 0.039 0.293 6253 Planarity : 0.004 0.062 6106 Dihedral : 21.271 174.571 7821 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.97 % Favored : 98.01 % Rotamer: Outliers : 1.53 % Allowed : 15.73 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.13), residues: 4264 helix: 2.35 (0.10), residues: 2490 sheet: 1.20 (0.30), residues: 325 loop : 0.17 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG Q 229 TYR 0.036 0.001 TYR B 89 PHE 0.022 0.001 PHE Q 259 TRP 0.037 0.001 TRP I1355 HIS 0.012 0.001 HIS N 875 Details of bonding type rmsd covalent geometry : bond 0.00318 (39345) covalent geometry : angle 0.64586 (54529) hydrogen bonds : bond 0.03638 ( 2421) hydrogen bonds : angle 3.77153 ( 6590) metal coordination : bond 0.00688 ( 4) metal coordination : angle 1.45566 ( 3) Misc. bond : bond 0.00151 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8528 Ramachandran restraints generated. 4264 Oldfield, 0 Emsley, 4264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 473 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7708 (tm-30) REVERT: C 62 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7542 (tp30) REVERT: G 74 ASN cc_start: 0.8679 (t0) cc_final: 0.8249 (t0) REVERT: G 76 LYS cc_start: 0.9162 (mttp) cc_final: 0.8882 (mtpp) REVERT: G 93 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7516 (mm-30) REVERT: H 106 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7186 (pm20) REVERT: I 464 GLN cc_start: 0.8287 (mt0) cc_final: 0.7898 (tm-30) REVERT: I 467 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8448 (pptt) REVERT: I 473 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8245 (tp-100) REVERT: I 477 ASN cc_start: 0.9060 (m110) cc_final: 0.8139 (m110) REVERT: I 487 LYS cc_start: 0.9342 (tppt) cc_final: 0.8995 (tppt) REVERT: I 488 GLU cc_start: 0.8832 (tp30) cc_final: 0.8121 (tp30) REVERT: I 491 ARG cc_start: 0.8702 (mtm180) cc_final: 0.8336 (mtm-85) REVERT: I 498 GLN cc_start: 0.8744 (tp40) cc_final: 0.8042 (tp40) REVERT: J 27 TYR cc_start: 0.8300 (m-80) cc_final: 0.7154 (m-80) REVERT: J 34 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8087 (tttt) REVERT: J 109 MET cc_start: 0.8739 (mmm) cc_final: 0.8432 (mmm) REVERT: J 152 CYS cc_start: 0.8745 (t) cc_final: 0.8532 (t) REVERT: J 162 ASN cc_start: 0.8568 (m-40) cc_final: 0.8270 (m110) REVERT: J 204 MET cc_start: 0.8642 (ptp) cc_final: 0.8203 (ptp) REVERT: J 254 MET cc_start: 0.9228 (mmm) cc_final: 0.8936 (mmm) REVERT: J 257 CYS cc_start: 0.9284 (m) cc_final: 0.8964 (m) REVERT: J 282 MET cc_start: 0.5279 (mmt) cc_final: 0.4758 (mpp) REVERT: K 189 LEU cc_start: 0.9498 (mt) cc_final: 0.8814 (mp) REVERT: K 191 LYS cc_start: 0.9504 (ptmt) cc_final: 0.9285 (ptmm) REVERT: K 257 CYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8736 (t) REVERT: K 263 GLN cc_start: 0.8733 (mp10) cc_final: 0.8409 (mp10) REVERT: L 2231 MET cc_start: 0.8353 (mmp) cc_final: 0.7948 (mmm) REVERT: L 2276 CYS cc_start: 0.8818 (m) cc_final: 0.8592 (m) REVERT: M 220 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8169 (tm-30) REVERT: M 349 TRP cc_start: 0.7809 (m100) cc_final: 0.7344 (m100) REVERT: N 640 LEU cc_start: 0.9284 (mm) cc_final: 0.9040 (mm) REVERT: N 674 MET cc_start: 0.8015 (mmt) cc_final: 0.7702 (mmm) REVERT: N 944 MET cc_start: 0.8596 (mtt) cc_final: 0.8393 (ttm) REVERT: O 523 MET cc_start: 0.8498 (mmm) cc_final: 0.8134 (tpt) REVERT: O 915 ARG cc_start: 0.9009 (ttp-110) cc_final: 0.8518 (ptp90) REVERT: O 930 ASP cc_start: 0.8728 (t0) cc_final: 0.8394 (t0) REVERT: Q 195 ARG cc_start: 0.9058 (ttm-80) cc_final: 0.8730 (ttp80) REVERT: Q 225 GLN cc_start: 0.9358 (tm-30) cc_final: 0.9140 (mm110) REVERT: Q 230 GLN cc_start: 0.9181 (tt0) cc_final: 0.8968 (tt0) REVERT: Q 238 GLN cc_start: 0.9565 (tp-100) cc_final: 0.9363 (tm-30) REVERT: Q 259 PHE cc_start: 0.8713 (t80) cc_final: 0.8508 (t80) REVERT: R 22 GLU cc_start: 0.8588 (tp30) cc_final: 0.8221 (tp30) REVERT: R 26 ASN cc_start: 0.8833 (m-40) cc_final: 0.8492 (m110) outliers start: 47 outliers final: 43 residues processed: 506 average time/residue: 0.2351 time to fit residues: 196.3274 Evaluate side-chains 499 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 453 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 458 LYS Chi-restraints excluded: chain I residue 467 LYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 242 LYS Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain L residue 1676 LEU Chi-restraints excluded: chain L residue 1744 LEU Chi-restraints excluded: chain L residue 1831 LEU Chi-restraints excluded: chain L residue 2109 ASN Chi-restraints excluded: chain L residue 2145 GLU Chi-restraints excluded: chain L residue 2162 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 415 ASP Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 683 VAL Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 684 VAL Chi-restraints excluded: chain O residue 882 ARG Chi-restraints excluded: chain O residue 899 LEU Chi-restraints excluded: chain P residue 298 ASP Chi-restraints excluded: chain Q residue 206 ILE Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 68 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 455 random chunks: chunk 317 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 365 optimal weight: 0.0870 chunk 82 optimal weight: 2.9990 chunk 307 optimal weight: 0.6980 chunk 230 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 451 optimal weight: 3.9990 chunk 115 optimal weight: 40.0000 chunk 449 optimal weight: 3.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 638 HIS ** N 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.088657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059002 restraints weight = 148036.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060829 restraints weight = 65395.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.062003 restraints weight = 42245.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062649 restraints weight = 33274.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.063015 restraints weight = 29224.406| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 39381 Z= 0.145 Angle : 0.635 12.937 54532 Z= 0.335 Chirality : 0.039 0.254 6253 Planarity : 0.004 0.061 6106 Dihedral : 21.239 175.868 7821 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.09 % Favored : 97.89 % Rotamer: Outliers : 1.53 % Allowed : 15.96 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.13), residues: 4264 helix: 2.35 (0.10), residues: 2496 sheet: 1.20 (0.30), residues: 325 loop : 0.20 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG Q 229 TYR 0.029 0.001 TYR B 89 PHE 0.022 0.001 PHE Q 259 TRP 0.042 0.001 TRP I1355 HIS 0.011 0.001 HIS N 875 Details of bonding type rmsd covalent geometry : bond 0.00324 (39345) covalent geometry : angle 0.63473 (54529) hydrogen bonds : bond 0.03633 ( 2421) hydrogen bonds : angle 3.77467 ( 6590) metal coordination : bond 0.00809 ( 4) metal coordination : angle 1.47447 ( 3) Misc. bond : bond 0.00096 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11462.23 seconds wall clock time: 196 minutes 16.01 seconds (11776.01 seconds total)