Starting phenix.real_space_refine on Fri Jul 3 07:18:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihm_35449/07_2026/8ihm_35449.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihm_35449/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ihm_35449/07_2026/8ihm_35449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihm_35449/07_2026/8ihm_35449.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ihm_35449/07_2026/8ihm_35449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihm_35449/07_2026/8ihm_35449.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.04, per 1000 atoms: 0.23 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: 1.15 Conformation dependent library (CDL) restraints added in 415.9 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: 1.81 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: 2.28 Time building geometry restraints manager: 1.52 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: 19706 2.30 - 4.60: 587 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.090 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- 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= 0.670 Angle : 0.889 11.488 20332 Z= 0.759 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 0.88936 / 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 : 0.347 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: 0.1488 time to fit residues: 37.4920 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 : 0.378 ------------------------------------------------------------------------------- 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 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 = 0.3928 r_free = 0.3928 target = 0.119640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.085214 restraints weight = 34005.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087235 restraints weight = 17915.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088481 restraints weight = 12616.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089234 restraints weight = 10527.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089569 restraints weight = 9572.777| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1279 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= 0.182 Angle : 0.730 8.568 20332 Z= 0.426 Chirality : 0.048 0.328 2301 Planarity : 0.005 0.051 1495 Dihedral : 32.292 170.033 4413 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.77 % Allowed : 13.48 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.27), residues: 861 helix: -0.77 (0.21), residues: 577 sheet: -2.08 (1.08), residues: 19 loop : -1.28 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 23 TYR 0.014 0.002 TYR D 37 PHE 0.011 0.002 PHE N 78 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 0.00307 / 0.18 (14036) covalent geometry : angle 0.73028 / 0.43 (20332) hydrogen bonds : bond 0.06884 / 4.55 ( 751) hydrogen bonds : angle 4.33616 / 3.05 ( 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 163 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.343 Fit side-chains REVERT: B 77 LYS cc_start: 0.9084 (mttm) cc_final: 0.8534 (mmtt) REVERT: H 91 ILE cc_start: 0.8947 (mm) cc_final: 0.8733 (mm) REVERT: H 106 HIS cc_start: 0.8068 (m-70) cc_final: 0.7633 (m-70) REVERT: N 81 TYR cc_start: 0.7689 (m-80) cc_final: 0.7480 (m-80) REVERT: N 110 ARG cc_start: 0.8506 (mmp80) cc_final: 0.8087 (mmp80) REVERT: N 114 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8197 (tm-30) outliers start: 11 outliers final: 8 residues processed: 159 average time/residue: 0.1257 time to fit residues: 28.4604 Evaluate side-chains 148 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 62 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 105 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 90 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3960 r_free = 0.3960 target = 0.121519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.087080 restraints weight = 34241.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089177 restraints weight = 17805.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090475 restraints weight = 12429.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.091223 restraints weight = 10340.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.091584 restraints weight = 9413.446| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14036 Z= 0.160 Angle : 0.675 9.228 20332 Z= 0.394 Chirality : 0.046 0.305 2301 Planarity : 0.004 0.042 1495 Dihedral : 32.258 169.067 4413 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.41 % Allowed : 15.25 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.28), residues: 861 helix: 0.26 (0.22), residues: 579 sheet: -1.30 (1.20), residues: 19 loop : -0.96 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.026 0.002 TYR F 88 PHE 0.010 0.001 PHE N 78 TRP 0.009 0.001 TRP N 31 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.16 (14036) covalent geometry : angle 0.67456 / 0.39 (20332) hydrogen bonds : bond 0.06008 / 3.92 ( 751) hydrogen bonds : angle 3.64700 / 2.57 ( 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 174 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.304 Fit side-chains REVERT: B 22 LEU cc_start: 0.3785 (OUTLIER) cc_final: 0.3548 (pp) REVERT: B 53 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8278 (tm-30) REVERT: B 77 LYS cc_start: 0.8964 (mttm) cc_final: 0.8484 (mmtt) REVERT: B 98 TYR cc_start: 0.8751 (m-10) cc_final: 0.8507 (m-80) REVERT: D 120 SER cc_start: 0.8828 (p) cc_final: 0.8584 (m) REVERT: H 81 ASN cc_start: 0.8538 (m-40) cc_final: 0.8051 (m-40) REVERT: H 106 HIS cc_start: 0.7723 (m90) cc_final: 0.7455 (m-70) REVERT: M 54 ILE cc_start: 0.4684 (OUTLIER) cc_final: 0.4382 (tt) REVERT: N 110 ARG cc_start: 0.8283 (mmp80) cc_final: 0.7921 (mmp80) REVERT: N 114 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8367 (tm-30) outliers start: 15 outliers final: 10 residues processed: 166 average time/residue: 0.1350 time to fit residues: 31.1869 Evaluate side-chains 162 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 62 ILE 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 G residue 56 GLU Chi-restraints excluded: chain G residue 100 VAL 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: 2.9990 chunk 86 optimal weight: 30.0000 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 109 optimal weight: 0.0370 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 ** 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 = 0.3962 r_free = 0.3962 target = 0.121827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087653 restraints weight = 34084.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089634 restraints weight = 18188.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.090854 restraints weight = 12883.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091544 restraints weight = 10752.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091921 restraints weight = 9816.659| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14036 Z= 0.152 Angle : 0.658 7.008 20332 Z= 0.383 Chirality : 0.045 0.305 2301 Planarity : 0.004 0.045 1495 Dihedral : 32.152 170.211 4413 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.85 % Allowed : 15.89 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.29), residues: 861 helix: 0.77 (0.22), residues: 578 sheet: -1.44 (1.17), residues: 19 loop : -0.91 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 20 TYR 0.013 0.001 TYR F 88 PHE 0.008 0.001 PHE E 67 TRP 0.010 0.001 TRP N 31 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.15 (14036) covalent geometry : angle 0.65822 / 0.38 (20332) hydrogen bonds : bond 0.05619 / 3.65 ( 751) hydrogen bonds : angle 3.38279 / 2.38 ( 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 181 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.380 Fit side-chains REVERT: B 22 LEU cc_start: 0.3655 (OUTLIER) cc_final: 0.3410 (pp) REVERT: B 52 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8118 (tm-30) REVERT: B 53 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8170 (tm-30) REVERT: B 77 LYS cc_start: 0.8944 (mttm) cc_final: 0.8441 (mmtt) REVERT: G 35 ARG cc_start: 0.9233 (mtm-85) cc_final: 0.8449 (mtm-85) REVERT: H 81 ASN cc_start: 0.8539 (m-40) cc_final: 0.8053 (m-40) REVERT: H 106 HIS cc_start: 0.7566 (m90) cc_final: 0.7205 (m-70) REVERT: M 54 ILE cc_start: 0.4634 (OUTLIER) cc_final: 0.4193 (tt) REVERT: N 110 ARG cc_start: 0.8307 (mmp80) cc_final: 0.7951 (mmp80) REVERT: N 114 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8200 (tm-30) outliers start: 24 outliers final: 13 residues processed: 168 average time/residue: 0.1317 time to fit residues: 31.0052 Evaluate side-chains 163 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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 G residue 111 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 chunk 95 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** F 75 HIS ** 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 = 0.3963 r_free = 0.3963 target = 0.122049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.087609 restraints weight = 34011.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089588 restraints weight = 18243.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090813 restraints weight = 12918.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091510 restraints weight = 10817.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.091828 restraints weight = 9881.517| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14036 Z= 0.153 Angle : 0.646 6.990 20332 Z= 0.375 Chirality : 0.044 0.295 2301 Planarity : 0.004 0.039 1495 Dihedral : 32.087 170.721 4413 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.85 % Allowed : 17.17 % 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: 0.48 (0.28), residues: 861 helix: 0.97 (0.22), residues: 579 sheet: -1.58 (1.12), residues: 19 loop : -0.87 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 20 TYR 0.009 0.001 TYR F 88 PHE 0.008 0.001 PHE B 61 TRP 0.005 0.001 TRP N 31 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (14036) covalent geometry : angle 0.64558 / 0.38 (20332) hydrogen bonds : bond 0.05435 / 3.54 ( 751) hydrogen bonds : angle 3.24863 / 2.29 ( 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 171 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.348 Fit side-chains REVERT: A 74 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9113 (mm) REVERT: B 22 LEU cc_start: 0.3784 (OUTLIER) cc_final: 0.3583 (pp) REVERT: B 53 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8075 (tm-30) REVERT: B 77 LYS cc_start: 0.8937 (mttm) cc_final: 0.8465 (mmtt) REVERT: B 98 TYR cc_start: 0.8818 (m-10) cc_final: 0.8493 (m-10) REVERT: F 23 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7816 (mtm-85) REVERT: G 35 ARG cc_start: 0.9212 (mtm-85) cc_final: 0.8223 (mtm-85) REVERT: H 81 ASN cc_start: 0.8531 (m-40) cc_final: 0.8051 (m-40) REVERT: H 106 HIS cc_start: 0.7503 (m90) cc_final: 0.7145 (m-70) REVERT: M 54 ILE cc_start: 0.4635 (OUTLIER) cc_final: 0.4435 (tt) REVERT: N 110 ARG cc_start: 0.8297 (mmp80) cc_final: 0.7942 (mmp80) outliers start: 24 outliers final: 15 residues processed: 159 average time/residue: 0.1380 time to fit residues: 30.2810 Evaluate side-chains 162 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE 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 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 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: 2.9990 chunk 75 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 72 optimal weight: 40.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** 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 = 0.3922 r_free = 0.3922 target = 0.119458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084724 restraints weight = 34000.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086611 restraints weight = 18603.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.087771 restraints weight = 13312.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.088436 restraints weight = 11200.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088738 restraints weight = 10237.491| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14036 Z= 0.251 Angle : 0.726 7.122 20332 Z= 0.408 Chirality : 0.047 0.305 2301 Planarity : 0.005 0.041 1495 Dihedral : 32.221 171.237 4413 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.01 % Allowed : 17.50 % 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: 0.28 (0.29), residues: 861 helix: 0.84 (0.22), residues: 580 sheet: -1.59 (1.08), residues: 19 loop : -1.02 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 20 TYR 0.015 0.002 TYR C 57 PHE 0.009 0.002 PHE N 78 TRP 0.006 0.002 TRP N 91 HIS 0.005 0.001 HIS N 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.25 (14036) covalent geometry : angle 0.72551 / 0.41 (20332) hydrogen bonds : bond 0.05975 / 3.92 ( 751) hydrogen bonds : angle 3.54831 / 2.48 ( 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 168 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.354 Fit side-chains REVERT: A 74 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9189 (mm) REVERT: B 53 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8234 (tm-30) REVERT: B 77 LYS cc_start: 0.8971 (mttm) cc_final: 0.8477 (mmtt) REVERT: B 98 TYR cc_start: 0.8863 (m-10) cc_final: 0.8544 (m-10) REVERT: G 35 ARG cc_start: 0.9243 (mtm-85) cc_final: 0.8284 (mtm-85) REVERT: H 81 ASN cc_start: 0.8581 (m-40) cc_final: 0.8138 (m-40) REVERT: H 106 HIS cc_start: 0.7645 (m90) cc_final: 0.7226 (m-70) REVERT: M 54 ILE cc_start: 0.4471 (OUTLIER) cc_final: 0.4196 (tt) REVERT: N 110 ARG cc_start: 0.8202 (mmp80) cc_final: 0.7996 (mmp80) outliers start: 25 outliers final: 19 residues processed: 157 average time/residue: 0.1398 time to fit residues: 30.4462 Evaluate side-chains 159 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE 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 D residue 77 LEU 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 79 ILE 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: 0.7980 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** F 75 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.121445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086841 restraints weight = 33730.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088781 restraints weight = 18201.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090024 restraints weight = 12974.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090711 restraints weight = 10873.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.091028 restraints weight = 9946.457| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14036 Z= 0.149 Angle : 0.647 7.200 20332 Z= 0.376 Chirality : 0.044 0.310 2301 Planarity : 0.004 0.040 1495 Dihedral : 32.058 171.966 4413 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.17 % Allowed : 17.82 % 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: 0.67 (0.29), residues: 861 helix: 1.11 (0.22), residues: 580 sheet: -1.52 (1.07), residues: 19 loop : -0.80 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.012 0.001 TYR N 81 PHE 0.008 0.001 PHE B 61 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 0.00246 / 0.15 (14036) covalent geometry : angle 0.64732 / 0.38 (20332) hydrogen bonds : bond 0.05321 / 3.47 ( 751) hydrogen bonds : angle 3.17999 / 2.24 ( 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 175 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.358 Fit side-chains REVERT: A 74 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9159 (mm) REVERT: B 53 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8070 (tm-30) REVERT: B 77 LYS cc_start: 0.8933 (mttm) cc_final: 0.8459 (mmtt) REVERT: B 98 TYR cc_start: 0.8837 (m-10) cc_final: 0.8529 (m-10) REVERT: F 23 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7890 (mtm-85) REVERT: G 35 ARG cc_start: 0.9245 (mtm-85) cc_final: 0.8445 (mtm-85) REVERT: H 81 ASN cc_start: 0.8514 (m-40) cc_final: 0.8088 (m-40) REVERT: H 106 HIS cc_start: 0.7560 (m90) cc_final: 0.7208 (m-70) REVERT: M 54 ILE cc_start: 0.4280 (OUTLIER) cc_final: 0.4040 (tt) REVERT: N 59 GLN cc_start: 0.6366 (OUTLIER) cc_final: 0.5961 (pm20) outliers start: 26 outliers final: 18 residues processed: 163 average time/residue: 0.1399 time to fit residues: 31.4854 Evaluate side-chains 165 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE 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 E residue 51 ILE Chi-restraints excluded: chain F residue 22 LEU 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 M residue 54 ILE Chi-restraints excluded: chain N residue 59 GLN Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 79 ILE 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: 10.0000 chunk 67 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.0170 chunk 44 optimal weight: 0.1980 chunk 102 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.122415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.087743 restraints weight = 33349.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.089775 restraints weight = 17640.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.091048 restraints weight = 12444.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.091780 restraints weight = 10389.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.092108 restraints weight = 9483.162| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 14036 Z= 0.143 Angle : 0.647 8.817 20332 Z= 0.374 Chirality : 0.043 0.299 2301 Planarity : 0.004 0.055 1495 Dihedral : 31.961 171.912 4413 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.69 % Allowed : 18.30 % 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: 1.02 (0.29), residues: 861 helix: 1.39 (0.22), residues: 575 sheet: -1.06 (1.10), residues: 19 loop : -0.69 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 92 TYR 0.012 0.001 TYR D 80 PHE 0.010 0.001 PHE D 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 0.00240 / 0.14 (14036) covalent geometry : angle 0.64673 / 0.37 (20332) hydrogen bonds : bond 0.05141 / 3.36 ( 751) hydrogen bonds : angle 3.01889 / 2.14 ( 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 178 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9081 (mm) REVERT: B 53 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7903 (tm-30) REVERT: B 77 LYS cc_start: 0.8885 (mttm) cc_final: 0.8394 (mmtt) REVERT: B 98 TYR cc_start: 0.8860 (m-10) cc_final: 0.8539 (m-10) REVERT: F 23 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7908 (mtm-85) REVERT: G 35 ARG cc_start: 0.9225 (mtm-85) cc_final: 0.8425 (mtm-85) REVERT: H 81 ASN cc_start: 0.8513 (m110) cc_final: 0.8084 (m110) REVERT: H 106 HIS cc_start: 0.7508 (m90) cc_final: 0.7100 (m-70) REVERT: N 59 GLN cc_start: 0.6373 (OUTLIER) cc_final: 0.5911 (pm20) outliers start: 23 outliers final: 18 residues processed: 167 average time/residue: 0.1353 time to fit residues: 31.4739 Evaluate side-chains 169 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 62 ILE 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 22 LEU 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 79 ILE Chi-restraints excluded: chain N residue 94 TYR 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: 9.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.0270 chunk 106 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 20 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.122188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.087571 restraints weight = 33902.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.089592 restraints weight = 18227.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.090826 restraints weight = 12941.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.091580 restraints weight = 10847.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091879 restraints weight = 9898.070| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14036 Z= 0.141 Angle : 0.644 10.072 20332 Z= 0.371 Chirality : 0.043 0.301 2301 Planarity : 0.004 0.043 1495 Dihedral : 31.922 171.996 4413 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.37 % Allowed : 19.74 % Favored : 76.89 % 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: 1.22 (0.29), residues: 861 helix: 1.54 (0.22), residues: 576 sheet: -0.89 (1.14), residues: 19 loop : -0.63 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 20 TYR 0.023 0.002 TYR D 80 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 0.00236 / 0.14 (14036) covalent geometry : angle 0.64447 / 0.37 (20332) hydrogen bonds : bond 0.05071 / 3.31 ( 751) hydrogen bonds : angle 2.99889 / 2.13 ( 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 167 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.351 Fit side-chains REVERT: A 74 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9042 (mm) REVERT: B 77 LYS cc_start: 0.8859 (mttm) cc_final: 0.8355 (mmtt) REVERT: B 98 TYR cc_start: 0.8848 (m-10) cc_final: 0.8530 (m-10) REVERT: E 94 GLU cc_start: 0.8088 (tp30) cc_final: 0.7862 (tp30) REVERT: G 35 ARG cc_start: 0.9212 (mtm-85) cc_final: 0.8396 (mtm-85) REVERT: H 81 ASN cc_start: 0.8518 (m110) cc_final: 0.8076 (m110) REVERT: H 106 HIS cc_start: 0.7475 (m90) cc_final: 0.7075 (m-70) outliers start: 21 outliers final: 18 residues processed: 156 average time/residue: 0.1187 time to fit residues: 26.1126 Evaluate side-chains 162 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE 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 22 LEU Chi-restraints excluded: chain F residue 49 LEU 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 65 GLU Chi-restraints excluded: chain N residue 79 ILE Chi-restraints excluded: chain N residue 94 TYR 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: 0.0010 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3920 r_free = 0.3920 target = 0.119319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.084071 restraints weight = 33957.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.085971 restraints weight = 18335.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.087148 restraints weight = 13106.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087825 restraints weight = 11031.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.088149 restraints weight = 10099.440| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 14036 Z= 0.269 Angle : 0.763 9.658 20332 Z= 0.420 Chirality : 0.047 0.331 2301 Planarity : 0.005 0.044 1495 Dihedral : 32.182 172.142 4413 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.37 % Allowed : 19.42 % Favored : 77.21 % 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: 0.71 (0.29), residues: 861 helix: 1.13 (0.22), residues: 578 sheet: -1.28 (1.06), residues: 19 loop : -0.75 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 20 TYR 0.028 0.002 TYR D 80 PHE 0.011 0.002 PHE M 63 TRP 0.011 0.002 TRP N 91 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.27 (14036) covalent geometry : angle 0.76267 / 0.42 (20332) hydrogen bonds : bond 0.05935 / 3.92 ( 751) hydrogen bonds : angle 3.49660 / 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 157 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.218 Fit side-chains REVERT: B 77 LYS cc_start: 0.8985 (mttm) cc_final: 0.8464 (mmtt) REVERT: B 98 TYR cc_start: 0.8878 (m-10) cc_final: 0.8554 (m-10) REVERT: G 35 ARG cc_start: 0.9250 (mtm-85) cc_final: 0.8418 (mtm-85) REVERT: H 81 ASN cc_start: 0.8603 (m110) cc_final: 0.8199 (m110) REVERT: H 106 HIS cc_start: 0.7682 (m90) cc_final: 0.7292 (m-70) outliers start: 21 outliers final: 18 residues processed: 147 average time/residue: 0.1335 time to fit residues: 26.7350 Evaluate side-chains 153 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 D residue 66 VAL Chi-restraints excluded: chain E residue 51 ILE 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 N residue 65 GLU Chi-restraints excluded: chain N residue 79 ILE 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: 0.8980 chunk 45 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 10.9990 chunk 54 optimal weight: 9.9990 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** 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 = 0.3873 r_free = 0.3873 target = 0.116568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081299 restraints weight = 34341.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.083082 restraints weight = 18933.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.084199 restraints weight = 13655.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.084793 restraints weight = 11506.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.085151 restraints weight = 10579.912| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.086 14036 Z= 0.449 Angle : 0.938 13.027 20332 Z= 0.498 Chirality : 0.055 0.370 2301 Planarity : 0.006 0.049 1495 Dihedral : 32.496 174.200 4413 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.37 % Allowed : 19.42 % Favored : 77.21 % 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: -0.40 (0.28), residues: 861 helix: 0.31 (0.21), residues: 582 sheet: -1.65 (1.06), residues: 19 loop : -1.29 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 20 TYR 0.027 0.003 TYR F 88 PHE 0.018 0.003 PHE M 63 TRP 0.015 0.003 TRP N 91 HIS 0.006 0.002 HIS N 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00964 / 0.45 (14036) covalent geometry : angle 0.93795 / 0.50 (20332) hydrogen bonds : bond 0.07154 / 4.77 ( 751) hydrogen bonds : angle 4.17219 / 2.94 ( 1850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2336.71 seconds wall clock time: 40 minutes 59.28 seconds (2459.28 seconds total)