Starting phenix.real_space_refine on Thu Mar 5 17:25:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7crp_30455/03_2026/7crp_30455.cif Found real_map, /net/cci-nas-00/data/ceres_data/7crp_30455/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7crp_30455/03_2026/7crp_30455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7crp_30455/03_2026/7crp_30455.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7crp_30455/03_2026/7crp_30455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7crp_30455/03_2026/7crp_30455.map" } 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-5986/lib/python3.9/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: 3.09, per 1000 atoms: 0.21 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: 1.20 Conformation dependent library (CDL) restraints added in 406.7 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: 2.18 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: 2.83 Time building geometry restraints manager: 1.55 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=" N ARG D 30 " pdb=" CA ARG D 30 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.74e+00 bond pdb=" CA LYS I1077 " pdb=" C LYS I1077 " ideal model delta sigma weight residual 1.519 1.557 -0.037 1.32e-02 5.74e+03 8.06e+00 bond pdb=" C2 SAM I1501 " pdb=" N3 SAM I1501 " ideal model delta sigma weight residual 1.322 1.376 -0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" C8 SAM I1501 " pdb=" N7 SAM I1501 " ideal model delta sigma weight residual 1.298 1.350 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C2 SAM I1501 " pdb=" N1 SAM I1501 " ideal model delta sigma weight residual 1.329 1.380 -0.051 2.00e-02 2.50e+03 6.62e+00 ... (remaining 15780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 21898 1.77 - 3.54: 765 3.54 - 5.31: 70 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=" C THR D 29 " pdb=" N ARG D 30 " pdb=" CA ARG D 30 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N ARG C 35 " pdb=" CA ARG C 35 " pdb=" C ARG C 35 " ideal model delta sigma weight residual 111.82 116.82 -5.00 1.16e+00 7.43e-01 1.86e+01 angle pdb=" N ARG D 30 " pdb=" CA ARG D 30 " pdb=" CB ARG D 30 " ideal model delta sigma weight residual 110.49 117.33 -6.84 1.69e+00 3.50e-01 1.64e+01 ... (remaining 22756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 6935 33.94 - 67.87: 1679 67.87 - 101.81: 19 101.81 - 135.75: 1 135.75 - 169.68: 1 Dihedral angle restraints: 8635 sinusoidal: 5739 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 8632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1866 0.045 - 0.090: 607 0.090 - 0.134: 79 0.134 - 0.179: 18 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.050 Find NCS groups from input model: 0.160 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.009 0.650 15793 Z= 0.363 Angle : 0.759 8.857 22761 Z= 0.450 Chirality : 0.043 0.224 2572 Planarity : 0.005 0.054 1729 Dihedral : 27.070 169.684 6769 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 covalent geometry : bond 0.00650 (15785) covalent geometry : angle 0.75942 (22761) hydrogen bonds : bond 0.14364 ( 536) hydrogen bonds : angle 4.77227 ( 1295) metal coordination : bond 0.28782 ( 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 : 0.340 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: 0.1905 time to fit residues: 32.7296 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 : 0.348 ------------------------------------------------------------------------------- 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: 7.9990 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: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 20.0000 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4071 r_free = 0.4071 target = 0.184689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.140199 restraints weight = 17253.095| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.03 r_work: 0.2899 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- 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 = 0.93 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 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15793 Z= 0.160 Angle : 0.600 9.497 22761 Z= 0.352 Chirality : 0.037 0.155 2572 Planarity : 0.004 0.054 1729 Dihedral : 29.789 171.094 4819 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.84 % Allowed : 8.65 % Favored : 90.50 % 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: -4.19 (0.21), residues: 969 helix: -2.34 (0.19), residues: 509 sheet: -2.98 (0.85), residues: 16 loop : -3.31 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.010 0.001 TYR I1261 PHE 0.017 0.001 PHE I1170 TRP 0.012 0.002 TRP I1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00338 (15785) covalent geometry : angle 0.59972 (22761) hydrogen bonds : bond 0.05976 ( 536) hydrogen bonds : angle 2.72840 ( 1295) metal coordination : bond 0.01468 ( 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 123 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: D 31 LYS cc_start: 0.8444 (mtmp) cc_final: 0.7936 (mtpp) REVERT: D 56 MET cc_start: 0.8928 (tpp) cc_final: 0.8478 (mmt) REVERT: G 112 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8983 (mm110) outliers start: 7 outliers final: 5 residues processed: 120 average time/residue: 0.1817 time to fit residues: 28.4735 Evaluate side-chains 113 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0060 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 overall best weight: 2.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 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 = 0.184188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.141436 restraints weight = 17462.456| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.02 r_work: 0.2963 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15793 Z= 0.174 Angle : 0.578 7.600 22761 Z= 0.339 Chirality : 0.036 0.149 2572 Planarity : 0.004 0.056 1729 Dihedral : 29.745 172.158 4809 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.20 % Allowed : 10.58 % Favored : 88.22 % 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: -3.57 (0.22), residues: 969 helix: -1.80 (0.21), residues: 513 sheet: -2.68 (0.86), residues: 16 loop : -3.05 (0.22), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 42 TYR 0.011 0.001 TYR H 118 PHE 0.012 0.002 PHE H 67 TRP 0.011 0.002 TRP I1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00383 (15785) covalent geometry : angle 0.57828 (22761) hydrogen bonds : bond 0.05833 ( 536) hydrogen bonds : angle 2.56241 ( 1295) metal coordination : bond 0.00394 ( 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 : 0.403 Fit side-chains revert: symmetry clash REVERT: M 133 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8017 (mt-10) REVERT: D 31 LYS cc_start: 0.8281 (mtmp) cc_final: 0.7851 (mtpt) REVERT: G 112 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8876 (mm110) outliers start: 10 outliers final: 8 residues processed: 117 average time/residue: 0.1701 time to fit residues: 26.4244 Evaluate side-chains 117 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 96 ARG Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 1087 ILE Chi-restraints excluded: chain I residue 1161 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 83 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 117 optimal weight: 0.0270 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4067 r_free = 0.4067 target = 0.184241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.142238 restraints weight = 17383.059| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.96 r_work: 0.2948 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15793 Z= 0.154 Angle : 0.563 7.244 22761 Z= 0.333 Chirality : 0.035 0.152 2572 Planarity : 0.004 0.060 1729 Dihedral : 29.736 172.202 4809 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.92 % Allowed : 10.82 % Favored : 87.26 % 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: -3.30 (0.23), residues: 969 helix: -1.57 (0.21), residues: 513 sheet: -2.34 (0.91), residues: 16 loop : -2.95 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 77 TYR 0.010 0.001 TYR I1261 PHE 0.018 0.001 PHE I1170 TRP 0.011 0.002 TRP I1157 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00327 (15785) covalent geometry : angle 0.56322 (22761) hydrogen bonds : bond 0.05564 ( 536) hydrogen bonds : angle 2.55524 ( 1295) metal coordination : bond 0.00286 ( 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 132 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: M 133 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8041 (mt-10) REVERT: D 31 LYS cc_start: 0.8328 (mtmp) cc_final: 0.7909 (mtpt) REVERT: G 112 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8884 (mm110) REVERT: I 1228 PRO cc_start: 0.6311 (Cg_endo) cc_final: 0.6052 (Cg_exo) outliers start: 16 outliers final: 13 residues processed: 126 average time/residue: 0.1559 time to fit residues: 26.4133 Evaluate side-chains 122 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 G residue 113 SER Chi-restraints excluded: chain H residue 57 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 125 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4074 r_free = 0.4074 target = 0.184870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140057 restraints weight = 17335.111| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.98 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1291 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= 0.147 Angle : 0.559 13.070 22761 Z= 0.329 Chirality : 0.035 0.150 2572 Planarity : 0.004 0.058 1729 Dihedral : 29.718 172.449 4809 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.92 % Allowed : 11.66 % Favored : 86.42 % 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: -3.08 (0.23), residues: 969 helix: -1.38 (0.21), residues: 513 sheet: -2.07 (0.96), residues: 16 loop : -2.86 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 42 TYR 0.010 0.001 TYR I1261 PHE 0.009 0.001 PHE D 67 TRP 0.021 0.004 TRP I1157 HIS 0.004 0.000 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00310 (15785) covalent geometry : angle 0.55938 (22761) hydrogen bonds : bond 0.05303 ( 536) hydrogen bonds : angle 2.50733 ( 1295) metal coordination : bond 0.00219 ( 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 133 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: M 133 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8021 (mt-10) REVERT: D 31 LYS cc_start: 0.8134 (mtmp) cc_final: 0.7901 (mtpt) REVERT: E 73 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7814 (tt0) REVERT: G 112 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8737 (mm110) outliers start: 16 outliers final: 15 residues processed: 126 average time/residue: 0.1533 time to fit residues: 25.8804 Evaluate side-chains 131 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 96 ARG Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 117 VAL 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 57 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4048 r_free = 0.4048 target = 0.182424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139658 restraints weight = 17233.613| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.90 r_work: 0.2895 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15793 Z= 0.224 Angle : 0.613 9.089 22761 Z= 0.355 Chirality : 0.038 0.148 2572 Planarity : 0.005 0.058 1729 Dihedral : 29.779 172.239 4809 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.52 % Allowed : 11.42 % 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: -3.24 (0.23), residues: 969 helix: -1.59 (0.21), residues: 518 sheet: -1.63 (0.95), residues: 18 loop : -2.87 (0.24), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 42 TYR 0.015 0.002 TYR I1261 PHE 0.012 0.002 PHE F 61 TRP 0.016 0.003 TRP I1157 HIS 0.005 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00513 (15785) covalent geometry : angle 0.61259 (22761) hydrogen bonds : bond 0.06805 ( 536) hydrogen bonds : angle 2.63779 ( 1295) metal coordination : bond 0.00234 ( 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: 21 poor density : 117 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: D 31 LYS cc_start: 0.8527 (mtmp) cc_final: 0.8122 (mtpt) REVERT: E 73 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8669 (tt0) REVERT: G 112 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8988 (mm110) REVERT: I 1106 ASN cc_start: 0.6868 (OUTLIER) cc_final: 0.6591 (p0) outliers start: 21 outliers final: 16 residues processed: 132 average time/residue: 0.1480 time to fit residues: 26.4759 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 : 0.364 ------------------------------------------------------------------------------- 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 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 57 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 1251 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 63 optimal weight: 7.9990 chunk 127 optimal weight: 30.0000 chunk 117 optimal weight: 20.0000 chunk 107 optimal weight: 0.0980 chunk 24 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 74 optimal weight: 40.0000 chunk 108 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4074 r_free = 0.4074 target = 0.184897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.140734 restraints weight = 17313.430| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.96 r_work: 0.2902 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1380 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= 0.154 Angle : 0.563 9.090 22761 Z= 0.332 Chirality : 0.035 0.145 2572 Planarity : 0.004 0.056 1729 Dihedral : 29.720 172.624 4809 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.16 % Allowed : 12.02 % Favored : 85.82 % 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: -2.85 (0.24), residues: 969 helix: -1.21 (0.21), residues: 514 sheet: -1.12 (1.15), residues: 16 loop : -2.77 (0.24), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.010 0.001 TYR I1261 PHE 0.009 0.001 PHE D 67 TRP 0.014 0.002 TRP I1157 HIS 0.003 0.000 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00326 (15785) covalent geometry : angle 0.56340 (22761) hydrogen bonds : bond 0.05448 ( 536) hydrogen bonds : angle 2.52168 ( 1295) metal coordination : bond 0.00251 ( 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 137 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8044 (mt-10) REVERT: D 31 LYS cc_start: 0.8376 (mtmp) cc_final: 0.7965 (mtpt) REVERT: E 73 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8571 (tt0) REVERT: G 112 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8916 (mm110) outliers start: 18 outliers final: 14 residues processed: 131 average time/residue: 0.1585 time to fit residues: 27.9792 Evaluate side-chains 131 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 111 ILE 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 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 Chi-restraints excluded: chain I residue 1255 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 108 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.0470 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4079 r_free = 0.4079 target = 0.185361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.141123 restraints weight = 17342.467| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.89 r_work: 0.2947 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15793 Z= 0.146 Angle : 0.555 8.888 22761 Z= 0.328 Chirality : 0.035 0.155 2572 Planarity : 0.004 0.055 1729 Dihedral : 29.706 172.869 4809 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.04 % Allowed : 12.26 % Favored : 85.70 % 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: -2.61 (0.24), residues: 969 helix: -0.99 (0.22), residues: 513 sheet: -0.77 (1.23), residues: 16 loop : -2.70 (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 0.009 0.001 PHE D 67 TRP 0.014 0.002 TRP I1157 HIS 0.003 0.000 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00300 (15785) covalent geometry : angle 0.55520 (22761) hydrogen bonds : bond 0.05207 ( 536) hydrogen bonds : angle 2.49750 ( 1295) metal coordination : bond 0.00237 ( 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 134 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8151 (mt-10) REVERT: D 31 LYS cc_start: 0.8416 (mtmp) cc_final: 0.8031 (mtpt) REVERT: E 73 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8666 (tt0) REVERT: G 112 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8970 (mm110) outliers start: 17 outliers final: 16 residues processed: 129 average time/residue: 0.1517 time to fit residues: 26.5743 Evaluate side-chains 132 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 H residue 57 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 1229 ASN Chi-restraints excluded: chain I residue 1251 ILE Chi-restraints excluded: chain I residue 1255 MET 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: 10.0000 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 0.0970 chunk 91 optimal weight: 20.0000 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4086 r_free = 0.4086 target = 0.186014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.141459 restraints weight = 17412.538| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.20 r_work: 0.2871 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15793 Z= 0.145 Angle : 0.546 8.535 22761 Z= 0.322 Chirality : 0.035 0.147 2572 Planarity : 0.004 0.054 1729 Dihedral : 29.665 173.598 4809 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.04 % Allowed : 12.14 % Favored : 85.82 % 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: -2.41 (0.24), residues: 969 helix: -0.81 (0.22), residues: 514 sheet: -0.61 (1.24), residues: 16 loop : -2.63 (0.25), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.009 0.001 TYR I1261 PHE 0.009 0.001 PHE D 67 TRP 0.013 0.002 TRP I1157 HIS 0.003 0.000 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00308 (15785) covalent geometry : angle 0.54563 (22761) hydrogen bonds : bond 0.05007 ( 536) hydrogen bonds : angle 2.41816 ( 1295) metal coordination : bond 0.00144 ( 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 136 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8182 (mt-10) REVERT: M 133 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8266 (mt-10) REVERT: D 31 LYS cc_start: 0.8359 (mtmp) cc_final: 0.7932 (mtpt) REVERT: D 56 MET cc_start: 0.8867 (mmt) cc_final: 0.8535 (mmt) REVERT: E 73 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8772 (tt0) REVERT: G 112 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8957 (mm110) outliers start: 17 outliers final: 15 residues processed: 129 average time/residue: 0.1542 time to fit residues: 26.8178 Evaluate side-chains 134 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 H residue 57 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 1255 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 95 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1106 ASN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.184469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.140062 restraints weight = 17333.515| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.21 r_work: 0.2915 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15793 Z= 0.184 Angle : 0.570 8.110 22761 Z= 0.333 Chirality : 0.036 0.147 2572 Planarity : 0.004 0.055 1729 Dihedral : 29.679 173.861 4809 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.04 % Allowed : 12.14 % Favored : 85.82 % 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: -2.55 (0.24), residues: 969 helix: -0.95 (0.21), residues: 516 sheet: -0.56 (1.25), residues: 16 loop : -2.66 (0.25), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 42 TYR 0.012 0.001 TYR I1261 PHE 0.010 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 covalent geometry : bond 0.00414 (15785) covalent geometry : angle 0.57046 (22761) hydrogen bonds : bond 0.05744 ( 536) hydrogen bonds : angle 2.48013 ( 1295) metal coordination : bond 0.00258 ( 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 133 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: M 105 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8067 (mt-10) REVERT: D 31 LYS cc_start: 0.8395 (mtmp) cc_final: 0.7960 (mtpt) REVERT: D 56 MET cc_start: 0.8886 (mmt) cc_final: 0.8534 (mmt) REVERT: E 73 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8644 (tt0) REVERT: G 112 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8928 (mm110) outliers start: 17 outliers final: 16 residues processed: 127 average time/residue: 0.1597 time to fit residues: 27.3761 Evaluate side-chains 132 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 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 H residue 57 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 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: 10.0000 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1106 ASN ** I1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.184538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.141087 restraints weight = 17290.277| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.95 r_work: 0.2945 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- 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 = 0.78 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 = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15793 Z= 0.174 Angle : 0.566 8.175 22761 Z= 0.331 Chirality : 0.036 0.147 2572 Planarity : 0.004 0.055 1729 Dihedral : 29.677 173.788 4809 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.04 % Allowed : 12.14 % Favored : 85.82 % 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: -2.54 (0.24), residues: 969 helix: -0.95 (0.21), residues: 516 sheet: -0.51 (1.26), residues: 16 loop : -2.66 (0.25), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.012 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 covalent geometry : bond 0.00385 (15785) covalent geometry : angle 0.56617 (22761) hydrogen bonds : bond 0.05705 ( 536) hydrogen bonds : angle 2.47293 ( 1295) metal coordination : bond 0.00286 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3813.94 seconds wall clock time: 65 minutes 23.91 seconds (3923.91 seconds total)