Starting phenix.real_space_refine on Thu Aug 6 01:38:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihm_35449/08_2026/8ihm_35449.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihm_35449/08_2026/8ihm_35449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihm_35449/08_2026/8ihm_35449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihm_35449/08_2026/8ihm_35449.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihm_35449/08_2026/8ihm_35449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihm_35449/08_2026/8ihm_35449.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 317 5.49 5 S 12 5.16 5 C 7266 2.51 5 N 2473 2.21 5 O 3085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13153 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 607 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 801 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 711 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 779 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ML3:plan-1': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 609 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 760 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 639 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3216 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3280 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 154 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "N" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 841 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 2.87, per 1000 atoms: 0.22 Number of scatterers: 13153 At special positions: 0 Unit cell: (93.09, 140.17, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 317 15.00 O 3085 8.00 N 2473 7.00 C 7266 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: 0.96 Conformation dependent library (CDL) restraints added in 356.1 milliseconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 20 Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 23 Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 20 Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 23 Secondary structure from input PDB file: 39 helices and 9 sheets defined 65.6% alpha, 4.2% beta 150 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.569A pdb=" N ARG A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 115 removed outlier: 3.861A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.650A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.228A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.776A pdb=" N TYR B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.771A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 71 removed outlier: 4.651A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.560A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.561A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.553A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 74 removed outlier: 3.963A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 71 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 81 Processing helix chain 'D' and resid 88 through 99 removed outlier: 3.830A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.769A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.710A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.581A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.673A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.656A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.621A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.692A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.738A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 54 through 81 removed outlier: 3.778A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.533A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU H 97 " --> pdb=" O THR H 93 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.568A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 74 removed outlier: 4.358A pdb=" N GLY N 74 " --> pdb=" O GLU N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 131 removed outlier: 3.570A pdb=" N LYS N 108 " --> pdb=" O ASN N 104 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS N 119 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS N 120 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN N 125 " --> pdb=" O SER N 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.052A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.051A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.177A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.440A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.589A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'N' and resid 79 through 81 removed outlier: 3.588A pdb=" N LEU N 21 " --> pdb=" O HIS N 18 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA N 16 " --> pdb=" O TYR N 23 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS N 14 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU N 15 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 29 through 32 removed outlier: 4.445A pdb=" N ASP N 32 " --> pdb=" O MET N 37 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET N 37 " --> pdb=" O ASP N 32 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 388 hydrogen bonds 776 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.34 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: 2231 1.33 - 1.45: 4788 1.45 - 1.57: 6363 1.57 - 1.69: 632 1.69 - 1.81: 22 Bond restraints: 14036 Sorted by residual: bond pdb=" C3' DC I 8 " pdb=" O3' DC I 8 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.50e+01 bond pdb=" C3' DC I -4 " pdb=" O3' DC I -4 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" CA SER B 47 " pdb=" C SER B 47 " ideal model delta sigma weight residual 1.524 1.476 0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" C3' DC I -2 " pdb=" O3' DC I -2 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.26e+01 bond pdb=" C3' DT I 34 " pdb=" C2' DT I 34 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 ... (remaining 14031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 19702 2.30 - 4.60: 591 4.60 - 6.89: 31 6.89 - 9.19: 6 9.19 - 11.49: 2 Bond angle restraints: 20332 Sorted by residual: angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 111.81 102.06 9.75 8.60e-01 1.35e+00 1.29e+02 angle pdb=" N ARG N 98 " pdb=" CA ARG N 98 " pdb=" C ARG N 98 " ideal model delta sigma weight residual 109.72 98.23 11.49 1.60e+00 3.91e-01 5.15e+01 angle pdb=" N GLU A 97 " pdb=" CA GLU A 97 " pdb=" C GLU A 97 " ideal model delta sigma weight residual 111.40 103.25 8.15 1.22e+00 6.72e-01 4.46e+01 angle pdb=" N LEU E 48 " pdb=" CA LEU E 48 " pdb=" C LEU E 48 " ideal model delta sigma weight residual 111.14 104.49 6.65 1.08e+00 8.57e-01 3.80e+01 angle pdb=" O4' DG I 26 " pdb=" C4' DG I 26 " pdb=" C3' DG I 26 " ideal model delta sigma weight residual 106.00 102.63 3.37 6.00e-01 2.78e+00 3.16e+01 ... (remaining 20327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 6045 35.51 - 71.01: 1493 71.01 - 106.52: 42 106.52 - 142.02: 4 142.02 - 177.53: 3 Dihedral angle restraints: 7587 sinusoidal: 5027 harmonic: 2560 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -158.19 -21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C4' DC I -73 " pdb=" C3' DC I -73 " pdb=" O3' DC I -73 " pdb=" P DT I -72 " ideal model delta sinusoidal sigma weight residual -140.00 37.53 -177.53 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 56.50 163.50 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 7584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1360 0.037 - 0.074: 615 0.074 - 0.111: 228 0.111 - 0.148: 89 0.148 - 0.185: 9 Chirality restraints: 2301 Sorted by residual: chirality pdb=" C3' DC I -73 " pdb=" C4' DC I -73 " pdb=" O3' DC I -73 " pdb=" C2' DC I -73 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" C3' DC I 0 " pdb=" C4' DC I 0 " pdb=" O3' DC I 0 " pdb=" C2' DC I 0 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ARG N 98 " pdb=" N ARG N 98 " pdb=" C ARG N 98 " pdb=" CB ARG N 98 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 2298 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 63 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" C GLU F 63 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU F 63 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN F 64 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 66 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 8 " -0.027 2.00e-02 2.50e+03 1.23e-02 4.57e+00 pdb=" N9 DG J 8 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG J 8 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DG J 8 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG J 8 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG J 8 " -0.010 2.00e-02 2.50e+03 pdb=" O6 DG J 8 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DG J 8 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG J 8 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG J 8 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DG J 8 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG J 8 " 0.001 2.00e-02 2.50e+03 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3530 2.82 - 3.34: 13386 3.34 - 3.86: 25816 3.86 - 4.38: 29084 4.38 - 4.90: 39690 Nonbonded interactions: 111506 Sorted by model distance: nonbonded pdb=" O ILE M 54 " pdb=" OG1 THR M 55 " model vdw 2.297 3.040 nonbonded pdb=" C3' DT I 71 " pdb=" C1' DT I 71 " model vdw 2.319 3.120 nonbonded pdb=" OP1 DT I 12 " pdb=" N GLY N 83 " model vdw 2.365 3.120 nonbonded pdb=" N3 DC I -73 " pdb=" N2 DG J 74 " model vdw 2.372 3.200 nonbonded pdb=" O SER M 62 " pdb=" OG SER M 62 " model vdw 2.399 3.040 ... (remaining 111501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 45 or (resid 46 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 through 62 or (r \ esid 63 and (name N or name CA or name C or name O or name CB )) or resid 64 thr \ ough 70 or (resid 71 through 72 and (name N or name CA or name C or name O or na \ me CB )) or resid 73 through 81 or (resid 82 and (name N or name CA or name C or \ name O or name CB )) or resid 83 through 89 or (resid 90 through 91 and (name N \ or name CA or name C or name O or name CB )) or resid 92 through 96 or (resid 9 \ 7 through 98 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 9 or (resid 100 through 102 and (name N or name CA or name C or name O or name C \ B )) or resid 103 or (resid 104 through 108 and (name N or name CA or name C or \ name O or name CB )) or resid 109 through 134)) selection = (chain 'E' and (resid 38 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 74 or (r \ esid 75 and (name N or name CA or name C or name O )) or resid 76 through 87 or \ (resid 88 and (name N or name CA or name C or name O )) or resid 89 through 104 \ or (resid 105 through 108 and (name N or name CA or name C or name O or name CB \ )) or resid 109 through 114 or (resid 115 through 116 and (name N or name CA or \ name C or name O or name CB )) or resid 117 or (resid 118 and (name N or name CA \ or name C or name O or name CB )) or resid 119 or (resid 120 and (name N or nam \ e CA or name C or name O or name CB )) or resid 121 through 134)) } ncs_group { reference = (chain 'B' and (resid 22 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 29 or (resid 30 through 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 35 or (res \ id 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 50 or (resid 51 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 52 th \ rough 61 or (resid 62 and (name N or name CA or name C or name O or name CB )) o \ r resid 63 through 64 or (resid 65 through 67 and (name N or name CA or name C o \ r name O or name CB )) or resid 68 through 77 or (resid 78 through 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 or (resid 82 through \ 83 and (name N or name CA or name C or name O or name CB )) or resid 84 or (resi \ d 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 101)) selection = (chain 'F' and (resid 22 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 34 or (resid 35 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1)) or resid 36 through 44 or (resid 45 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 70 or (resid 71 and (n \ ame N or name CA or name C or name O or name CB )) or resid 72 or (resid 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 through 90 or ( \ resid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 th \ rough 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) o \ r resid 98 through 99 or (resid 100 and (name N or name CA or name C or name O o \ r name CB )) or resid 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 15 or (resid 16 and (name N or name CA or name \ C or name O )) or resid 17 through 24 or (resid 25 and (name N or name CA or nam \ e C or name O or name CB )) or resid 26 through 35 or (resid 36 and (name N or n \ ame CA or name C or name O or name CB )) or resid 37 through 40 or (resid 41 and \ (name N or name CA or name C or name O or name CB )) or resid 42 through 55 or \ (resid 56 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1)) or resid 57 or (resid 58 through 60 and (name N or name CA o \ r name C or name O or name CB )) or resid 61 through 62 or (resid 63 and (name N \ or name CA or name C or name O or name CB )) or resid 64 through 76 or (resid 7 \ 7 through 78 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 9 through 80 or (resid 81 and (name N or name CA or name C or name O or name CB \ )) or resid 82 through 84 or (resid 85 through 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 89 or (resid 90 and (name N or na \ me CA or name C or name O or name CB )) or resid 91 through 94 or (resid 95 and \ (name N or name CA or name C or name O or name CB )) or resid 96 through 114 or \ (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 116 \ through 117)) selection = (chain 'G' and (resid 12 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 48 or (resid 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 58 or (res \ id 59 through 60 and (name N or name CA or name C or name O or name CB )) or res \ id 61 through 77 or (resid 78 and (name N or name CA or name C or name O or name \ CB )) or resid 79 through 86 or (resid 87 and (name N or name CA or name C or n \ ame O or name CB )) or resid 88 through 100 or (resid 101 and (name N or name CA \ or name C or name O or name CB )) or resid 102 through 117)) } ncs_group { reference = (chain 'D' and ((resid 33 through 40 and (name N or name CA or name C or name O \ or name CB )) or resid 41 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 or (resid 57 through 61 and (n \ ame N or name CA or name C or name O or name CB )) or resid 62 through 84 or (re \ sid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 or ( \ resid 87 through 90 and (name N or name CA or name C or name O or name CB )) or \ resid 91 through 121)) selection = (chain 'H' and (resid 33 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 59 or (resid 60 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 64 or (res \ id 65 and (name N or name CA or name C or name O or name CB )) or resid 66 throu \ gh 83 or (resid 84 through 85 and (name N or name CA or name C or name O or name \ CB )) or resid 86 through 87 or (resid 88 through 90 and (name N or name CA or \ name C or name O or name CB )) or resid 91 through 111 or (resid 112 and (name N \ or name CA or name C or name O or name CB )) or resid 113 through 121)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 12.050 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 14036 Z= 0.671 Angle : 0.895 11.488 20332 Z= 0.764 Chirality : 0.050 0.185 2301 Planarity : 0.004 0.054 1495 Dihedral : 29.269 177.526 5929 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.23), residues: 861 helix: -2.84 (0.17), residues: 548 sheet: -2.63 (1.01), residues: 19 loop : -1.68 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 23 TYR 0.014 0.002 TYR D 37 PHE 0.023 0.002 PHE C 25 TRP 0.008 0.002 TRP N 91 HIS 0.003 0.001 HIS N 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.67 (14036) covalent geometry : angle 0.89537 / 0.76 (20332) hydrogen bonds : bond 0.20027 / 13.66 ( 751) hydrogen bonds : angle 8.02285 / 5.67 ( 1850) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.327 Fit side-chains REVERT: B 77 LYS cc_start: 0.8833 (mttm) cc_final: 0.8613 (mmtt) REVERT: C 38 ASN cc_start: 0.8345 (m110) cc_final: 0.7689 (m110) REVERT: E 94 GLU cc_start: 0.8384 (tp30) cc_final: 0.8150 (tp30) REVERT: F 84 MET cc_start: 0.8148 (tpp) cc_final: 0.7889 (tpp) REVERT: H 106 HIS cc_start: 0.8097 (m-70) cc_final: 0.7801 (m-70) REVERT: N 114 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8389 (tm-30) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1262 time to fit residues: 31.9527 Evaluate side-chains 153 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN E 108 ASN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 79 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.119816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.085488 restraints weight = 33961.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087541 restraints weight = 17827.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088802 restraints weight = 12509.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.089491 restraints weight = 10411.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089883 restraints weight = 9497.861| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14036 Z= 0.178 Angle : 0.753 9.346 20332 Z= 0.431 Chirality : 0.050 0.360 2301 Planarity : 0.005 0.052 1495 Dihedral : 32.234 170.854 4413 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.93 % Allowed : 13.64 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.27), residues: 861 helix: -0.75 (0.21), residues: 577 sheet: -2.00 (1.09), residues: 19 loop : -1.26 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 110 TYR 0.016 0.002 TYR A 41 PHE 0.011 0.002 PHE C 25 TRP 0.012 0.002 TRP N 31 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.18 (14036) covalent geometry : angle 0.75319 / 0.43 (20332) hydrogen bonds : bond 0.06792 / 4.49 ( 751) hydrogen bonds : angle 4.27953 / 3.01 ( 1850) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.352 Fit side-chains REVERT: B 77 LYS cc_start: 0.9083 (mttm) cc_final: 0.8527 (mmtt) REVERT: H 91 ILE cc_start: 0.8951 (mm) cc_final: 0.8738 (mm) REVERT: H 106 HIS cc_start: 0.8057 (m-70) cc_final: 0.7605 (m-70) REVERT: N 110 ARG cc_start: 0.8365 (mmp80) cc_final: 0.7823 (mmp80) REVERT: N 114 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8173 (tm-30) outliers start: 12 outliers final: 8 residues processed: 161 average time/residue: 0.1231 time to fit residues: 28.2873 Evaluate side-chains 150 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 105 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN E 125 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.120947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086337 restraints weight = 34218.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.088382 restraints weight = 17956.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089674 restraints weight = 12611.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090409 restraints weight = 10498.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090736 restraints weight = 9547.615| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14036 Z= 0.177 Angle : 0.704 9.360 20332 Z= 0.404 Chirality : 0.047 0.340 2301 Planarity : 0.004 0.043 1495 Dihedral : 32.234 168.577 4413 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.57 % Allowed : 15.41 % Favored : 82.02 % 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: -0.43 (0.28), residues: 861 helix: 0.16 (0.22), residues: 582 sheet: -1.47 (1.16), residues: 19 loop : -0.97 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 110 TYR 0.016 0.002 TYR B 98 PHE 0.011 0.001 PHE N 78 TRP 0.010 0.001 TRP N 31 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.18 (14036) covalent geometry : angle 0.70412 / 0.40 (20332) hydrogen bonds : bond 0.06135 / 4.01 ( 751) hydrogen bonds : angle 3.73219 / 2.63 ( 1850) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.368 Fit side-chains REVERT: B 22 LEU cc_start: 0.3879 (OUTLIER) cc_final: 0.3640 (pp) REVERT: B 77 LYS cc_start: 0.8970 (mttm) cc_final: 0.8483 (mmtt) REVERT: B 98 TYR cc_start: 0.8780 (m-10) cc_final: 0.8524 (m-10) REVERT: D 120 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8598 (m) REVERT: H 81 ASN cc_start: 0.8580 (m-40) cc_final: 0.8107 (m-40) REVERT: H 106 HIS cc_start: 0.7701 (m90) cc_final: 0.7421 (m-70) REVERT: M 54 ILE cc_start: 0.4682 (OUTLIER) cc_final: 0.4372 (tt) REVERT: N 110 ARG cc_start: 0.8342 (mmp80) cc_final: 0.7937 (mmp80) REVERT: N 114 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8238 (tm-30) outliers start: 16 outliers final: 11 residues processed: 165 average time/residue: 0.1373 time to fit residues: 31.4919 Evaluate side-chains 164 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 54 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 30.0000 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 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 = 0.3955 r_free = 0.3955 target = 0.121429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.087171 restraints weight = 34082.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.089151 restraints weight = 18283.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.090369 restraints weight = 12927.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.090966 restraints weight = 10800.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091392 restraints weight = 9898.245| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14036 Z= 0.156 Angle : 0.677 7.568 20332 Z= 0.390 Chirality : 0.046 0.342 2301 Planarity : 0.004 0.039 1495 Dihedral : 32.101 169.594 4413 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.37 % Allowed : 16.05 % Favored : 80.58 % 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: 0.06 (0.28), residues: 861 helix: 0.60 (0.22), residues: 578 sheet: -1.42 (1.15), residues: 19 loop : -0.92 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 20 TYR 0.016 0.001 TYR F 88 PHE 0.009 0.001 PHE B 61 TRP 0.009 0.001 TRP N 31 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.16 (14036) covalent geometry : angle 0.67749 / 0.39 (20332) hydrogen bonds : bond 0.05676 / 3.69 ( 751) hydrogen bonds : angle 3.44140 / 2.43 ( 1850) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.367 Fit side-chains REVERT: B 22 LEU cc_start: 0.3885 (OUTLIER) cc_final: 0.3648 (pp) REVERT: B 52 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8189 (tm-30) REVERT: B 77 LYS cc_start: 0.8959 (mttm) cc_final: 0.8450 (mmtt) REVERT: B 98 TYR cc_start: 0.8768 (m-10) cc_final: 0.8440 (m-10) REVERT: G 35 ARG cc_start: 0.9251 (mtm-85) cc_final: 0.8230 (mtm-85) REVERT: H 81 ASN cc_start: 0.8554 (m-40) cc_final: 0.8065 (m-40) REVERT: H 106 HIS cc_start: 0.7589 (m90) cc_final: 0.7249 (m-70) REVERT: M 54 ILE cc_start: 0.4539 (OUTLIER) cc_final: 0.4059 (tt) REVERT: N 110 ARG cc_start: 0.8364 (mmp80) cc_final: 0.7998 (mmp80) REVERT: N 114 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8170 (tm-30) outliers start: 21 outliers final: 12 residues processed: 167 average time/residue: 0.1339 time to fit residues: 31.1874 Evaluate side-chains 164 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 94 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 84 optimal weight: 30.0000 chunk 95 optimal weight: 8.9990 chunk 108 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.122223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087812 restraints weight = 33927.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089786 restraints weight = 18230.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.091017 restraints weight = 12940.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091726 restraints weight = 10818.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.092064 restraints weight = 9887.076| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14036 Z= 0.147 Angle : 0.658 7.569 20332 Z= 0.379 Chirality : 0.045 0.333 2301 Planarity : 0.004 0.038 1495 Dihedral : 31.993 170.177 4413 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.53 % Allowed : 16.69 % Favored : 79.78 % 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: 0.45 (0.28), residues: 861 helix: 0.94 (0.22), residues: 579 sheet: -1.37 (1.09), residues: 19 loop : -0.88 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 20 TYR 0.012 0.001 TYR N 81 PHE 0.008 0.001 PHE E 78 TRP 0.007 0.001 TRP N 31 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.15 (14036) covalent geometry : angle 0.65789 / 0.38 (20332) hydrogen bonds : bond 0.05415 / 3.52 ( 751) hydrogen bonds : angle 3.23449 / 2.28 ( 1850) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.275 Fit side-chains REVERT: B 22 LEU cc_start: 0.3806 (OUTLIER) cc_final: 0.3452 (pp) REVERT: B 52 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8116 (tm-30) REVERT: B 77 LYS cc_start: 0.8932 (mttm) cc_final: 0.8461 (mmtt) REVERT: B 98 TYR cc_start: 0.8801 (m-10) cc_final: 0.8476 (m-10) REVERT: F 23 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7820 (mtm-85) REVERT: G 35 ARG cc_start: 0.9242 (mtm-85) cc_final: 0.8237 (mtm-85) REVERT: H 81 ASN cc_start: 0.8547 (m-40) cc_final: 0.8064 (m-40) REVERT: H 106 HIS cc_start: 0.7476 (m90) cc_final: 0.7094 (m-70) REVERT: M 54 ILE cc_start: 0.4638 (OUTLIER) cc_final: 0.4378 (tt) REVERT: N 37 MET cc_start: 0.7724 (ppp) cc_final: 0.7467 (ppp) REVERT: N 110 ARG cc_start: 0.8302 (mmp80) cc_final: 0.7892 (mmp80) REVERT: N 114 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8318 (tm-30) outliers start: 22 outliers final: 15 residues processed: 164 average time/residue: 0.1197 time to fit residues: 27.4877 Evaluate side-chains 162 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 0.0470 chunk 59 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 40.0000 overall best weight: 2.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.119775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085059 restraints weight = 33985.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086951 restraints weight = 18570.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088127 restraints weight = 13277.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088824 restraints weight = 11140.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089193 restraints weight = 10164.498| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14036 Z= 0.230 Angle : 0.723 7.672 20332 Z= 0.404 Chirality : 0.047 0.342 2301 Planarity : 0.004 0.043 1495 Dihedral : 32.104 170.510 4413 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.69 % Allowed : 17.34 % Favored : 78.97 % 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: 0.39 (0.29), residues: 861 helix: 0.91 (0.22), residues: 580 sheet: -1.49 (1.06), residues: 19 loop : -0.95 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 20 TYR 0.021 0.002 TYR N 81 PHE 0.008 0.001 PHE E 67 TRP 0.006 0.001 TRP N 91 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 (14036) covalent geometry : angle 0.72280 / 0.40 (20332) hydrogen bonds : bond 0.05829 / 3.82 ( 751) hydrogen bonds : angle 3.48824 / 2.44 ( 1850) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: B 52 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8100 (tm-30) REVERT: B 77 LYS cc_start: 0.8954 (mttm) cc_final: 0.8469 (mmtt) REVERT: B 98 TYR cc_start: 0.8848 (m-10) cc_final: 0.8534 (m-10) REVERT: G 35 ARG cc_start: 0.9238 (mtm-85) cc_final: 0.8269 (mtm-85) REVERT: H 81 ASN cc_start: 0.8585 (m-40) cc_final: 0.8133 (m-40) REVERT: H 106 HIS cc_start: 0.7620 (m90) cc_final: 0.7217 (m-70) REVERT: M 54 ILE cc_start: 0.4357 (OUTLIER) cc_final: 0.4128 (tt) REVERT: N 37 MET cc_start: 0.7943 (ppp) cc_final: 0.7677 (ppp) REVERT: N 114 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8260 (tm-30) outliers start: 23 outliers final: 16 residues processed: 153 average time/residue: 0.1180 time to fit residues: 25.2678 Evaluate side-chains 155 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 0.3980 chunk 73 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 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 = 0.3964 r_free = 0.3964 target = 0.122105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087563 restraints weight = 33804.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089517 restraints weight = 18231.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090774 restraints weight = 12998.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.091397 restraints weight = 10877.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091819 restraints weight = 9969.907| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14036 Z= 0.145 Angle : 0.650 7.776 20332 Z= 0.376 Chirality : 0.044 0.351 2301 Planarity : 0.004 0.040 1495 Dihedral : 31.940 171.301 4413 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.53 % Allowed : 17.66 % Favored : 78.81 % 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: 0.76 (0.29), residues: 861 helix: 1.22 (0.22), residues: 574 sheet: -1.15 (1.08), residues: 19 loop : -0.84 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 20 TYR 0.011 0.001 TYR N 81 PHE 0.008 0.001 PHE E 78 TRP 0.007 0.001 TRP N 91 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.15 (14036) covalent geometry : angle 0.65007 / 0.38 (20332) hydrogen bonds : bond 0.05271 / 3.44 ( 751) hydrogen bonds : angle 3.14670 / 2.22 ( 1850) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.324 Fit side-chains REVERT: B 77 LYS cc_start: 0.8927 (mttm) cc_final: 0.8450 (mmtt) REVERT: B 98 TYR cc_start: 0.8846 (m-10) cc_final: 0.8543 (m-10) REVERT: F 23 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7882 (mtm-85) REVERT: G 35 ARG cc_start: 0.9259 (mtm-85) cc_final: 0.8443 (mtm-85) REVERT: H 81 ASN cc_start: 0.8530 (m-40) cc_final: 0.8102 (m-40) REVERT: H 106 HIS cc_start: 0.7507 (m90) cc_final: 0.7168 (m-70) REVERT: N 37 MET cc_start: 0.7996 (ppp) cc_final: 0.7786 (ppp) REVERT: N 59 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6496 (pm20) REVERT: N 110 ARG cc_start: 0.8376 (mmp80) cc_final: 0.8023 (mmp80) REVERT: N 114 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8168 (tm-30) outliers start: 22 outliers final: 17 residues processed: 164 average time/residue: 0.1388 time to fit residues: 31.4869 Evaluate side-chains 166 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 59 GLN Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.0270 chunk 102 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 81 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 = 0.3947 r_free = 0.3947 target = 0.121087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.086042 restraints weight = 33468.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087972 restraints weight = 18071.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089224 restraints weight = 12935.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.089932 restraints weight = 10830.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090068 restraints weight = 9904.646| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14036 Z= 0.169 Angle : 0.674 7.707 20332 Z= 0.383 Chirality : 0.045 0.352 2301 Planarity : 0.004 0.041 1495 Dihedral : 31.974 171.201 4413 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.85 % Allowed : 17.50 % Favored : 78.65 % 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: 0.81 (0.29), residues: 861 helix: 1.22 (0.22), residues: 581 sheet: -0.99 (1.08), residues: 19 loop : -0.80 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.013 0.001 TYR F 88 PHE 0.008 0.001 PHE E 67 TRP 0.006 0.001 TRP N 91 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.17 (14036) covalent geometry : angle 0.67396 / 0.38 (20332) hydrogen bonds : bond 0.05335 / 3.49 ( 751) hydrogen bonds : angle 3.18378 / 2.25 ( 1850) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: B 77 LYS cc_start: 0.8916 (mttm) cc_final: 0.8417 (mmtt) REVERT: B 98 TYR cc_start: 0.8851 (m-10) cc_final: 0.8532 (m-10) REVERT: G 35 ARG cc_start: 0.9235 (mtm-85) cc_final: 0.8423 (mtm-85) REVERT: H 81 ASN cc_start: 0.8524 (m-40) cc_final: 0.8090 (m-40) REVERT: H 106 HIS cc_start: 0.7519 (m90) cc_final: 0.7135 (m-70) REVERT: N 37 MET cc_start: 0.8015 (ppp) cc_final: 0.7785 (ppp) REVERT: N 59 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6506 (pm20) REVERT: N 114 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8192 (tm-30) outliers start: 24 outliers final: 17 residues processed: 161 average time/residue: 0.1179 time to fit residues: 26.6874 Evaluate side-chains 163 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 59 GLN Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 106 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN F 75 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.121990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.087327 restraints weight = 33690.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089296 restraints weight = 18217.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.090525 restraints weight = 12973.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091216 restraints weight = 10876.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.091533 restraints weight = 9950.829| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14036 Z= 0.151 Angle : 0.662 7.737 20332 Z= 0.378 Chirality : 0.044 0.360 2301 Planarity : 0.004 0.041 1495 Dihedral : 31.921 171.537 4413 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.21 % Allowed : 18.62 % Favored : 78.17 % 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: 0.99 (0.29), residues: 861 helix: 1.33 (0.22), residues: 582 sheet: -0.91 (1.08), residues: 19 loop : -0.68 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.011 0.001 TYR F 88 PHE 0.007 0.001 PHE B 61 TRP 0.007 0.001 TRP N 91 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (14036) covalent geometry : angle 0.66184 / 0.38 (20332) hydrogen bonds : bond 0.05181 / 3.38 ( 751) hydrogen bonds : angle 3.11599 / 2.21 ( 1850) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: B 77 LYS cc_start: 0.8897 (mttm) cc_final: 0.8415 (mmtt) REVERT: B 98 TYR cc_start: 0.8864 (m-10) cc_final: 0.8562 (m-10) REVERT: G 35 ARG cc_start: 0.9255 (mtm-85) cc_final: 0.8446 (mtm-85) REVERT: H 81 ASN cc_start: 0.8531 (m110) cc_final: 0.8067 (m110) REVERT: H 106 HIS cc_start: 0.7527 (m90) cc_final: 0.7123 (m-70) REVERT: N 37 MET cc_start: 0.8011 (ppp) cc_final: 0.7763 (ppp) REVERT: N 114 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8162 (tm-30) outliers start: 20 outliers final: 17 residues processed: 163 average time/residue: 0.1087 time to fit residues: 24.5315 Evaluate side-chains 166 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 62 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.118931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083826 restraints weight = 34254.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.085727 restraints weight = 18775.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.086916 restraints weight = 13479.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087570 restraints weight = 11347.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.087873 restraints weight = 10416.557| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14036 Z= 0.245 Angle : 0.749 8.912 20332 Z= 0.413 Chirality : 0.047 0.376 2301 Planarity : 0.005 0.043 1495 Dihedral : 32.107 171.619 4413 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.89 % Allowed : 18.62 % Favored : 78.49 % 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: 0.63 (0.29), residues: 861 helix: 1.11 (0.22), residues: 576 sheet: -1.24 (1.08), residues: 19 loop : -0.90 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 20 TYR 0.016 0.002 TYR C 57 PHE 0.012 0.002 PHE M 63 TRP 0.010 0.002 TRP N 91 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.25 (14036) covalent geometry : angle 0.74855 / 0.41 (20332) hydrogen bonds : bond 0.05817 / 3.83 ( 751) hydrogen bonds : angle 3.47129 / 2.46 ( 1850) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: B 77 LYS cc_start: 0.8967 (mttm) cc_final: 0.8471 (mmtt) REVERT: B 98 TYR cc_start: 0.8872 (m-10) cc_final: 0.8567 (m-10) REVERT: G 35 ARG cc_start: 0.9255 (mtm-85) cc_final: 0.8427 (mtm-85) REVERT: H 81 ASN cc_start: 0.8596 (m110) cc_final: 0.8233 (m110) REVERT: H 106 HIS cc_start: 0.7659 (m90) cc_final: 0.7285 (m-70) REVERT: N 37 MET cc_start: 0.8154 (ppp) cc_final: 0.7925 (ppp) REVERT: N 114 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8177 (tm-30) outliers start: 18 outliers final: 15 residues processed: 154 average time/residue: 0.1058 time to fit residues: 22.2278 Evaluate side-chains 155 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 63 optimal weight: 0.0370 chunk 94 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 54 optimal weight: 0.0030 overall best weight: 2.2670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 89 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 = 0.3922 r_free = 0.3922 target = 0.119568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.084735 restraints weight = 33884.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.086623 restraints weight = 18605.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087809 restraints weight = 13342.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.088487 restraints weight = 11223.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.088845 restraints weight = 10272.690| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14036 Z= 0.232 Angle : 0.735 11.416 20332 Z= 0.407 Chirality : 0.047 0.382 2301 Planarity : 0.004 0.044 1495 Dihedral : 32.112 172.485 4413 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.73 % Allowed : 19.26 % Favored : 78.01 % 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: 0.57 (0.29), residues: 861 helix: 1.11 (0.22), residues: 576 sheet: -1.81 (1.58), residues: 10 loop : -1.05 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 20 TYR 0.013 0.002 TYR F 88 PHE 0.008 0.001 PHE N 78 TRP 0.010 0.002 TRP N 91 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.23 (14036) covalent geometry : angle 0.73483 / 0.41 (20332) hydrogen bonds : bond 0.05602 / 3.68 ( 751) hydrogen bonds : angle 3.43214 / 2.43 ( 1850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2119.29 seconds wall clock time: 37 minutes 6.74 seconds (2226.74 seconds total)