Starting phenix.real_space_refine on Sat Jul 4 23:18:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7crp_30455/07_2026/7crp_30455.cif Found real_map, /net/cci-nas-00/data/ceres_data/7crp_30455/07_2026/7crp_30455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7crp_30455/07_2026/7crp_30455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7crp_30455/07_2026/7crp_30455.map" model { file = "/net/cci-nas-00/data/ceres_data/7crp_30455/07_2026/7crp_30455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7crp_30455/07_2026/7crp_30455.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7crp_30455/07_2026/7crp_30455.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7crp_30455/07_2026/7crp_30455.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12071 atoms to isotropic. 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 3 6.06 5 P 336 5.49 5 S 29 5.16 5 C 8245 2.51 5 N 2788 2.21 5 O 3432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14833 Number of models: 1 Model: "" Number of chains: 12 Chain: "M" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 833 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'NLE:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 803 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'NLE:plan-1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "A" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3420 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "K" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3468 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "I" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1755 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14347 SG CYS I1226 39.089 63.619 56.304 1.00 79.83 S ATOM 14705 SG CYS I1273 35.850 64.429 53.660 1.00 94.82 S ATOM 14721 SG CYS I1275 38.268 64.272 51.140 1.00 82.68 S ATOM 13309 SG CYS I1098 60.107 91.817 70.409 1.00 57.92 S ATOM 13382 SG CYS I1108 59.101 92.880 65.735 1.00 57.74 S ATOM 13424 SG CYS I1114 58.558 89.544 67.760 1.00 50.22 S ATOM 13382 SG CYS I1108 59.101 92.880 65.735 1.00 57.74 S ATOM 13542 SG CYS I1128 58.192 96.211 67.575 1.00 60.95 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N SAM I1501 " occ=0.93 ... (25 atoms not shown) pdb=" O4' SAM I1501 " occ=0.93 Time building chain proxies: 2.77, per 1000 atoms: 0.19 Number of scatterers: 14833 At special positions: 0 Unit cell: (136.08, 150.12, 172.8, 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 3 29.99 S 29 16.00 P 336 15.00 O 3432 8.00 N 2788 7.00 C 8245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 398.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I1502 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1273 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1275 " pdb="ZN ZN I1502 " - pdb=" SG CYS I1226 " pdb=" ZN I1503 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1098 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1114 " pdb="ZN ZN I1503 " - pdb=" SG CYS I1108 " pdb=" ZN I1504 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1128 " pdb="ZN ZN I1504 " - pdb=" SG CYS I1108 " 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 59.2% alpha, 0.0% beta 120 base pairs and 292 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.830A pdb=" N LEU M 48 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU M 50 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN M 55 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER M 57 " --> pdb=" O ARG M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 77 removed outlier: 3.696A pdb=" N LEU M 70 " --> pdb=" O PRO M 66 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL M 71 " --> pdb=" O PHE M 67 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG M 72 " --> pdb=" O GLN M 68 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.685A pdb=" N NLE M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN M 93 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU M 94 " --> pdb=" O NLE M 90 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA M 95 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU M 97 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU M 105 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN M 108 " --> pdb=" O PHE M 104 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS M 110 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 removed outlier: 4.197A pdb=" N ILE M 124 " --> pdb=" O NLE M 120 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN M 125 " --> pdb=" O PRO M 121 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 42 removed outlier: 4.427A pdb=" N GLY B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N THR B 30 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS B 31 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 3.608A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.668A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.217A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.631A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 21' Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.569A pdb=" N HIS C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.769A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU C 61 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 66 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 97 removed outlier: 3.751A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLU C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLU C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.356A pdb=" N LEU C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.594A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.744A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 120 removed outlier: 3.721A pdb=" N THR D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Proline residue: D 100 - end of helix removed outlier: 6.308A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.587A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.781A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.083A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N NLE E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU E 94 " --> pdb=" O NLE E 90 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.989A pdb=" N ILE E 124 " --> pdb=" O NLE E 120 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 41 removed outlier: 5.327A pdb=" N GLY F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N THR F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS F 31 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Proline residue: F 32 - end of helix removed outlier: 3.510A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.048A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.103A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.808A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 16 through 21' Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.740A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.902A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 58 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 97 removed outlier: 3.730A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU G 91 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLU G 92 " --> pdb=" O ARG G 88 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU G 93 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 4.017A pdb=" N LEU G 116 " --> pdb=" O GLN G 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 116' Processing helix chain 'H' and resid 34 through 46 removed outlier: 4.264A pdb=" N TYR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 4.217A pdb=" N SER H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 121 removed outlier: 3.795A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR H 93 " --> pdb=" O ARG H 89 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG H 96 " --> pdb=" O GLN H 92 " (cutoff:3.500A) Proline residue: H 100 - end of helix removed outlier: 6.451A pdb=" N LEU H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 1091 through 1095 removed outlier: 4.506A pdb=" N ILE I1095 " --> pdb=" O ASP I1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1091 through 1095' Processing helix chain 'I' and resid 1114 through 1119 removed outlier: 3.708A pdb=" N LEU I1119 " --> pdb=" O LEU I1115 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1142 removed outlier: 4.642A pdb=" N LYS I1141 " --> pdb=" O GLN I1137 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG I1142 " --> pdb=" O CYS I1138 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1137 through 1142' Processing helix chain 'I' and resid 1180 through 1194 removed outlier: 3.998A pdb=" N GLU I1193 " --> pdb=" O LYS I1189 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN I1194 " --> pdb=" O ARG I1190 " (cutoff:3.500A) Processing helix chain 'I' and resid 1217 through 1222 removed outlier: 4.719A pdb=" N PHE I1221 " --> pdb=" O ASN I1217 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N MET I1222 " --> pdb=" O TYR I1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1217 through 1222' 223 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 313 hydrogen bonds 626 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 292 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 1.45 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: 2802 1.33 - 1.45: 5045 1.45 - 1.57: 7227 1.57 - 1.69: 670 1.69 - 1.81: 41 Bond restraints: 15785 Sorted by residual: bond pdb=" C3' DT K 116 " pdb=" C2' DT K 116 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C1' DC K 69 " pdb=" N1 DC K 69 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" C3' DC A 94 " pdb=" C2' DC A 94 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT A 173 " pdb=" C2' DT A 173 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" N1 DC A 102 " pdb=" C6 DC A 102 " ideal model delta sigma weight residual 1.367 1.347 0.020 6.00e-03 2.78e+04 1.08e+01 ... (remaining 15780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 21247 1.77 - 3.54: 1410 3.54 - 5.31: 76 5.31 - 7.09: 20 7.09 - 8.86: 8 Bond angle restraints: 22761 Sorted by residual: angle pdb=" N LYS I1181 " pdb=" CA LYS I1181 " pdb=" C LYS I1181 " ideal model delta sigma weight residual 111.11 118.33 -7.22 1.20e+00 6.94e-01 3.62e+01 angle pdb=" N VAL M 117 " pdb=" CA VAL M 117 " pdb=" C VAL M 117 " ideal model delta sigma weight residual 113.71 108.43 5.28 9.50e-01 1.11e+00 3.09e+01 angle pdb=" N3 DT A 52 " pdb=" C4 DT A 52 " pdb=" O4 DT A 52 " ideal model delta sigma weight residual 119.90 122.77 -2.87 6.00e-01 2.78e+00 2.28e+01 angle pdb=" N3 DT K 103 " pdb=" C4 DT K 103 " pdb=" O4 DT K 103 " ideal model delta sigma weight residual 119.90 122.67 -2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" N3 DT A 95 " pdb=" C4 DT A 95 " pdb=" O4 DT A 95 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 ... (remaining 22756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 6913 33.94 - 67.87: 1669 67.87 - 101.81: 19 101.81 - 135.75: 1 135.75 - 169.68: 1 Dihedral angle restraints: 8603 sinusoidal: 5707 harmonic: 2896 Sorted by residual: dihedral pdb=" CA HIS E 39 " pdb=" C HIS E 39 " pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASP I1146 " pdb=" C ASP I1146 " pdb=" N ALA I1147 " pdb=" CA ALA I1147 " ideal model delta harmonic sigma weight residual -180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA PRO I1145 " pdb=" C PRO I1145 " pdb=" N ASP I1146 " pdb=" CA ASP I1146 " ideal model delta harmonic sigma weight residual 180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 8600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1647 0.045 - 0.090: 775 0.090 - 0.134: 129 0.134 - 0.179: 19 0.179 - 0.224: 2 Chirality restraints: 2572 Sorted by residual: chirality pdb=" CA LYS I1181 " pdb=" N LYS I1181 " pdb=" C LYS I1181 " pdb=" CB LYS I1181 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ARG C 35 " pdb=" N ARG C 35 " pdb=" C ARG C 35 " pdb=" CB ARG C 35 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA SER C 113 " pdb=" N SER C 113 " pdb=" C SER C 113 " pdb=" CB SER C 113 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.98e-01 ... (remaining 2569 not shown) Planarity restraints: 1729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR I1144 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO I1145 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO I1145 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I1145 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE I1076 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" C ILE I1076 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE I1076 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS I1077 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C NLE E 120 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO E 121 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.025 5.00e-02 4.00e+02 ... (remaining 1726 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 1 2.16 - 2.85: 4177 2.85 - 3.53: 16631 3.53 - 4.22: 37115 4.22 - 4.90: 57155 Nonbonded interactions: 115079 Sorted by model distance: nonbonded pdb=" NZ LYS G 119 " pdb=" OE2 GLU I1111 " model vdw 1.478 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.193 3.040 nonbonded pdb=" NZ LYS G 119 " pdb=" CD GLU I1111 " model vdw 2.224 3.350 nonbonded pdb=" O HIS I1224 " pdb=" N6 SAM I1501 " model vdw 2.263 3.120 nonbonded pdb=" O ALA I1212 " pdb=" NH2 ARG I1220 " model vdw 2.279 3.120 ... (remaining 115074 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 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 27 through 121) } ncs_group { reference = chain 'E' selection = (chain 'M' and resid 37 through 134) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.93 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.230 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.010 0.650 15793 Z= 0.661 Angle : 0.889 8.857 22761 Z= 0.731 Chirality : 0.049 0.224 2572 Planarity : 0.005 0.054 1729 Dihedral : 27.057 169.684 6737 Min Nonbonded Distance : 1.478 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.05 % Favored : 91.85 % Rotamer: Outliers : 0.96 % Allowed : 5.17 % Favored : 93.87 % 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: -5.47 (0.18), residues: 969 helix: -3.46 (0.15), residues: 511 sheet: -3.13 (0.83), residues: 16 loop : -3.84 (0.20), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 35 TYR 0.018 0.002 TYR I1261 PHE 0.015 0.002 PHE F 61 TRP 0.012 0.003 TRP I1157 HIS 0.007 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.62 (15785) covalent geometry : angle 0.88937 / 0.73 (22761) hydrogen bonds : bond 0.14364 / 9.55 ( 536) hydrogen bonds : angle 4.77227 / 3.02 ( 1295) metal coordination : bond 0.28782 / 18.77 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: D 31 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7960 (mmtt) REVERT: D 83 ARG cc_start: 0.8347 (mmt-90) cc_final: 0.8133 (mmt180) REVERT: G 112 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8769 (mm110) REVERT: H 39 TYR cc_start: 0.8324 (t80) cc_final: 0.8115 (t80) outliers start: 8 outliers final: 3 residues processed: 133 average time/residue: 0.1770 time to fit residues: 30.8867 Evaluate side-chains 115 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1262 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 50.0000 chunk 55 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN F 25 ASN G 31 HIS H 60 ASN I1135 GLN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1137 GLN I1192 HIS I1229 ASN I1233 GLN I1238 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.184904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.141865 restraints weight = 17240.027| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.88 r_work: 0.2955 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15793 Z= 0.148 Angle : 0.645 9.577 22761 Z= 0.381 Chirality : 0.047 0.298 2572 Planarity : 0.004 0.054 1729 Dihedral : 30.053 172.870 4787 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.96 % Allowed : 8.65 % Favored : 90.38 % 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: -4.26 (0.21), residues: 969 helix: -2.39 (0.19), residues: 512 sheet: -3.01 (0.84), residues: 16 loop : -3.35 (0.21), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 42 TYR 0.011 0.001 TYR I1261 PHE 0.016 0.001 PHE I1170 TRP 0.012 0.002 TRP I1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.15 (15785) covalent geometry : angle 0.64521 / 0.38 (22761) hydrogen bonds : bond 0.06755 / 4.35 ( 536) hydrogen bonds : angle 2.83105 / 1.86 ( 1295) metal coordination : bond 0.00780 / 0.55 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: M 133 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8013 (mt-10) REVERT: D 31 LYS cc_start: 0.8344 (mtmp) cc_final: 0.7813 (mtpp) REVERT: D 56 MET cc_start: 0.8878 (tpp) cc_final: 0.8416 (mmt) REVERT: D 83 ARG cc_start: 0.8646 (mmt-90) cc_final: 0.8437 (mmt180) REVERT: G 112 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8919 (mm110) REVERT: H 39 TYR cc_start: 0.8772 (t80) cc_final: 0.8563 (t80) outliers start: 8 outliers final: 6 residues processed: 122 average time/residue: 0.1689 time to fit residues: 27.3799 Evaluate side-chains 115 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 1087 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 44 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 30.0000 chunk 56 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN E 39 HIS ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.186562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.144266 restraints weight = 17526.433| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.91 r_work: 0.2971 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15793 Z= 0.134 Angle : 0.576 8.357 22761 Z= 0.348 Chirality : 0.043 0.303 2572 Planarity : 0.004 0.056 1729 Dihedral : 30.133 174.957 4777 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.20 % Allowed : 9.98 % Favored : 88.82 % 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: -3.44 (0.22), residues: 969 helix: -1.70 (0.21), residues: 513 sheet: -2.73 (0.86), residues: 16 loop : -2.98 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 42 TYR 0.009 0.001 TYR H 118 PHE 0.009 0.001 PHE D 67 TRP 0.011 0.002 TRP I1157 HIS 0.004 0.000 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.13 (15785) covalent geometry : angle 0.57605 / 0.35 (22761) hydrogen bonds : bond 0.05901 / 3.78 ( 536) hydrogen bonds : angle 2.60138 / 1.71 ( 1295) metal coordination : bond 0.00923 / 0.63 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: M 133 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8118 (mt-10) REVERT: D 31 LYS cc_start: 0.8197 (mtmp) cc_final: 0.7768 (mtpt) REVERT: D 56 MET cc_start: 0.8796 (tpp) cc_final: 0.8301 (mmt) REVERT: D 83 ARG cc_start: 0.8622 (mmt-90) cc_final: 0.8419 (mmt180) REVERT: G 112 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8870 (mm110) REVERT: H 39 TYR cc_start: 0.8685 (t80) cc_final: 0.8452 (t80) outliers start: 10 outliers final: 9 residues processed: 117 average time/residue: 0.1688 time to fit residues: 26.2359 Evaluate side-chains 118 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1205 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 83 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 117 optimal weight: 0.0470 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.184099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.142154 restraints weight = 17368.357| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.97 r_work: 0.2936 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15793 Z= 0.164 Angle : 0.606 8.573 22761 Z= 0.357 Chirality : 0.045 0.291 2572 Planarity : 0.004 0.058 1729 Dihedral : 30.192 175.887 4777 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.44 % Allowed : 11.06 % Favored : 87.50 % 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: -3.26 (0.23), residues: 969 helix: -1.56 (0.21), residues: 514 sheet: -1.94 (0.99), residues: 16 loop : -2.91 (0.23), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 42 TYR 0.012 0.001 TYR I1261 PHE 0.011 0.002 PHE F 61 TRP 0.011 0.002 TRP I1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (15785) covalent geometry : angle 0.60627 / 0.36 (22761) hydrogen bonds : bond 0.06646 / 4.24 ( 536) hydrogen bonds : angle 2.62678 / 1.74 ( 1295) metal coordination : bond 0.00206 / 0.12 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: M 133 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8021 (mt-10) REVERT: D 31 LYS cc_start: 0.8323 (mtmp) cc_final: 0.7906 (mtpt) REVERT: G 112 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8887 (mm110) REVERT: H 39 TYR cc_start: 0.8717 (t80) cc_final: 0.8487 (t80) REVERT: I 1228 PRO cc_start: 0.6297 (Cg_endo) cc_final: 0.5999 (Cg_exo) outliers start: 12 outliers final: 10 residues processed: 129 average time/residue: 0.1533 time to fit residues: 26.7730 Evaluate side-chains 126 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1204 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1106 ASN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.184234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.140885 restraints weight = 17325.318| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.77 r_work: 0.2919 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15793 Z= 0.161 Angle : 0.607 12.077 22761 Z= 0.356 Chirality : 0.045 0.289 2572 Planarity : 0.004 0.056 1729 Dihedral : 30.201 176.051 4777 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.52 % Allowed : 10.82 % Favored : 86.66 % 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: -3.13 (0.23), residues: 969 helix: -1.47 (0.21), residues: 515 sheet: -1.50 (1.06), residues: 16 loop : -2.85 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.011 0.001 TYR I1261 PHE 0.010 0.001 PHE F 61 TRP 0.017 0.004 TRP I1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (15785) covalent geometry : angle 0.60700 / 0.36 (22761) hydrogen bonds : bond 0.06504 / 4.14 ( 536) hydrogen bonds : angle 2.61989 / 1.73 ( 1295) metal coordination : bond 0.00237 / 0.15 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: M 133 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8118 (mt-10) REVERT: D 31 LYS cc_start: 0.8322 (mtmp) cc_final: 0.7926 (mtpt) REVERT: E 73 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8527 (tt0) REVERT: G 112 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8905 (mm110) REVERT: H 39 TYR cc_start: 0.8712 (t80) cc_final: 0.8490 (t80) REVERT: I 1228 PRO cc_start: 0.6233 (Cg_endo) cc_final: 0.5982 (Cg_exo) outliers start: 21 outliers final: 18 residues processed: 130 average time/residue: 0.1425 time to fit residues: 25.4211 Evaluate side-chains 134 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1106 ASN Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1205 THR Chi-restraints excluded: chain I residue 1251 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1106 ASN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.183509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137067 restraints weight = 17231.628| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.87 r_work: 0.2903 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 15793 Z= 0.183 Angle : 0.624 9.549 22761 Z= 0.363 Chirality : 0.046 0.282 2572 Planarity : 0.005 0.057 1729 Dihedral : 30.216 176.049 4777 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.40 % Allowed : 11.54 % Favored : 86.06 % 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: -3.14 (0.23), residues: 969 helix: -1.52 (0.21), residues: 519 sheet: -0.88 (1.17), residues: 16 loop : -2.84 (0.24), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.013 0.001 TYR I1261 PHE 0.012 0.002 PHE F 61 TRP 0.015 0.003 TRP I1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (15785) covalent geometry : angle 0.62369 / 0.36 (22761) hydrogen bonds : bond 0.06885 / 4.38 ( 536) hydrogen bonds : angle 2.66580 / 1.76 ( 1295) metal coordination : bond 0.00231 / 0.16 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: D 31 LYS cc_start: 0.8410 (mtmp) cc_final: 0.8034 (mtpt) REVERT: E 73 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8573 (tt0) REVERT: G 112 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8977 (mm110) outliers start: 20 outliers final: 17 residues processed: 131 average time/residue: 0.1565 time to fit residues: 28.2406 Evaluate side-chains 136 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1205 THR Chi-restraints excluded: chain I residue 1251 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 63 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 74 optimal weight: 50.0000 chunk 108 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1106 ASN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.184313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138110 restraints weight = 17250.561| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.98 r_work: 0.2880 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15793 Z= 0.148 Angle : 0.603 9.416 22761 Z= 0.354 Chirality : 0.045 0.281 2572 Planarity : 0.004 0.056 1729 Dihedral : 30.203 175.699 4777 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.28 % Allowed : 12.26 % Favored : 85.46 % 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: -2.95 (0.23), residues: 969 helix: -1.31 (0.21), residues: 515 sheet: -0.70 (1.23), residues: 16 loop : -2.81 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 42 TYR 0.011 0.001 TYR I1261 PHE 0.009 0.001 PHE D 67 TRP 0.015 0.003 TRP I1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (15785) covalent geometry : angle 0.60262 / 0.35 (22761) hydrogen bonds : bond 0.06376 / 4.05 ( 536) hydrogen bonds : angle 2.65604 / 1.75 ( 1295) metal coordination : bond 0.00189 / 0.12 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8167 (mt-10) REVERT: D 31 LYS cc_start: 0.8410 (mtmp) cc_final: 0.8021 (mtpt) REVERT: E 73 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8699 (tt0) REVERT: G 112 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8988 (mm110) outliers start: 19 outliers final: 17 residues processed: 131 average time/residue: 0.1385 time to fit residues: 24.8726 Evaluate side-chains 135 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1205 THR Chi-restraints excluded: chain I residue 1251 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 62 optimal weight: 0.0040 chunk 96 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 8 optimal weight: 0.0010 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1106 ASN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.185002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.140607 restraints weight = 17281.674| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.01 r_work: 0.2873 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 15793 Z= 0.133 Angle : 0.588 9.536 22761 Z= 0.348 Chirality : 0.044 0.282 2572 Planarity : 0.004 0.055 1729 Dihedral : 30.200 175.851 4777 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.28 % Allowed : 12.38 % Favored : 85.34 % 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: -2.85 (0.24), residues: 969 helix: -1.22 (0.21), residues: 513 sheet: -0.69 (1.24), residues: 16 loop : -2.77 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 42 TYR 0.010 0.001 TYR I1261 PHE 0.010 0.001 PHE D 67 TRP 0.015 0.002 TRP I1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.13 (15785) covalent geometry : angle 0.58751 / 0.35 (22761) hydrogen bonds : bond 0.06107 / 3.89 ( 536) hydrogen bonds : angle 2.63959 / 1.74 ( 1295) metal coordination : bond 0.00162 / 0.11 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8105 (mt-10) REVERT: D 31 LYS cc_start: 0.8349 (mtmp) cc_final: 0.7940 (mtpt) REVERT: E 73 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8582 (tt0) REVERT: G 112 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8918 (mm110) outliers start: 19 outliers final: 14 residues processed: 129 average time/residue: 0.1540 time to fit residues: 27.2935 Evaluate side-chains 130 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1205 THR Chi-restraints excluded: chain I residue 1251 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 37 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 0.0030 chunk 71 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 50.0000 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1106 ASN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.183996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.140316 restraints weight = 17329.550| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.16 r_work: 0.2908 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15793 Z= 0.176 Angle : 0.618 8.554 22761 Z= 0.360 Chirality : 0.046 0.276 2572 Planarity : 0.005 0.057 1729 Dihedral : 30.208 176.151 4777 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.04 % Allowed : 12.74 % Favored : 85.22 % 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: -2.91 (0.24), residues: 969 helix: -1.32 (0.21), residues: 516 sheet: -0.59 (1.27), residues: 16 loop : -2.74 (0.25), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.013 0.001 TYR I1261 PHE 0.012 0.002 PHE F 61 TRP 0.014 0.003 TRP I1157 HIS 0.005 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (15785) covalent geometry : angle 0.61756 / 0.36 (22761) hydrogen bonds : bond 0.06798 / 4.32 ( 536) hydrogen bonds : angle 2.66362 / 1.76 ( 1295) metal coordination : bond 0.00360 / 0.23 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8040 (mt-10) REVERT: D 31 LYS cc_start: 0.8417 (mtmp) cc_final: 0.8009 (mtpt) REVERT: E 73 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8599 (tt0) REVERT: G 112 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8941 (mm110) outliers start: 17 outliers final: 14 residues processed: 129 average time/residue: 0.1538 time to fit residues: 27.2265 Evaluate side-chains 130 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1251 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 95 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1106 ASN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.183902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138521 restraints weight = 17253.771| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.03 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15793 Z= 0.150 Angle : 0.606 8.600 22761 Z= 0.355 Chirality : 0.045 0.275 2572 Planarity : 0.005 0.056 1729 Dihedral : 30.211 176.268 4777 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.04 % Allowed : 12.74 % Favored : 85.22 % 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: -2.88 (0.24), residues: 969 helix: -1.29 (0.21), residues: 515 sheet: -0.58 (1.27), residues: 16 loop : -2.73 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.013 0.001 TYR I1261 PHE 0.010 0.001 PHE F 61 TRP 0.013 0.002 TRP I1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (15785) covalent geometry : angle 0.60587 / 0.35 (22761) hydrogen bonds : bond 0.06644 / 4.23 ( 536) hydrogen bonds : angle 2.65751 / 1.76 ( 1295) metal coordination : bond 0.00287 / 0.20 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1938 Ramachandran restraints generated. 969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7367 (mt-10) REVERT: D 31 LYS cc_start: 0.8226 (mtmp) cc_final: 0.7987 (mtpt) REVERT: G 112 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8778 (mm110) REVERT: I 1080 LYS cc_start: 0.7645 (mmtp) cc_final: 0.7442 (mmtt) outliers start: 17 outliers final: 15 residues processed: 128 average time/residue: 0.1544 time to fit residues: 27.0855 Evaluate side-chains 132 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Chi-restraints excluded: chain I residue 1204 VAL Chi-restraints excluded: chain I residue 1251 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 19 optimal weight: 0.0770 chunk 47 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 92 optimal weight: 50.0000 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1106 ASN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1229 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.184089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.141966 restraints weight = 17245.074| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.23 r_work: 0.2928 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15793 Z= 0.166 Angle : 0.610 8.559 22761 Z= 0.356 Chirality : 0.045 0.276 2572 Planarity : 0.005 0.056 1729 Dihedral : 30.207 176.174 4777 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.04 % Allowed : 12.98 % Favored : 84.98 % 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: -2.85 (0.24), residues: 969 helix: -1.26 (0.21), residues: 515 sheet: -0.55 (1.28), residues: 16 loop : -2.73 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 42 TYR 0.012 0.001 TYR I1261 PHE 0.011 0.001 PHE F 61 TRP 0.013 0.002 TRP I1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (15785) covalent geometry : angle 0.61011 / 0.36 (22761) hydrogen bonds : bond 0.06642 / 4.23 ( 536) hydrogen bonds : angle 2.65038 / 1.75 ( 1295) metal coordination : bond 0.00255 / 0.17 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3851.67 seconds wall clock time: 66 minutes 9.39 seconds (3969.39 seconds total)