Starting phenix.real_space_refine on Wed Jul 30 22:37:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihm_35449/07_2025/8ihm_35449.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihm_35449/07_2025/8ihm_35449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihm_35449/07_2025/8ihm_35449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihm_35449/07_2025/8ihm_35449.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihm_35449/07_2025/8ihm_35449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihm_35449/07_2025/8ihm_35449.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 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: {'PHE:plan': 1, 'ARG: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: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS: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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ML3:plan-1': 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 9.34, per 1000 atoms: 0.71 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: 3.48 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 6.07 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: 5.67 Time building geometry restraints manager: 4.10 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=" 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=" SG ML3 E 36 " pdb=" CD ML3 E 36 " ideal model delta sigma weight residual 1.815 1.757 0.058 2.00e-02 2.50e+03 8.55e+00 bond pdb=" CA ALA D 74 " pdb=" C ALA D 74 " ideal model delta sigma weight residual 1.524 1.458 0.066 2.25e-02 1.98e+03 8.52e+00 bond pdb=" CA TYR A 99 " pdb=" C TYR A 99 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.35e-02 5.49e+03 7.10e+00 bond pdb=" CB ML3 E 36 " pdb=" SG ML3 E 36 " ideal model delta sigma weight residual 1.817 1.765 0.052 2.00e-02 2.50e+03 6.66e+00 ... (remaining 14031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 19972 2.30 - 4.60: 323 4.60 - 6.89: 29 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=" N ILE N 72 " pdb=" CA ILE N 72 " pdb=" C ILE N 72 " ideal model delta sigma weight residual 112.50 119.83 -7.33 1.39e+00 5.18e-01 2.78e+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 - 0.032: 1368 0.032 - 0.064: 678 0.064 - 0.096: 185 0.096 - 0.128: 61 0.128 - 0.160: 9 Chirality restraints: 2301 Sorted by residual: 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 chirality pdb=" CA PRO G 80 " pdb=" N PRO G 80 " pdb=" C PRO G 80 " pdb=" CB PRO G 80 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ALA D 74 " pdb=" N ALA D 74 " pdb=" C ALA D 74 " pdb=" CB ALA D 74 " both_signs ideal model delta sigma weight residual False 2.48 2.34 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2298 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 63 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" C GLU F 63 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU F 63 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN F 64 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 66 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 8 " -0.027 2.00e-02 2.50e+03 1.23e-02 4.57e+00 pdb=" N9 DG J 8 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG J 8 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DG J 8 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG J 8 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG J 8 " -0.010 2.00e-02 2.50e+03 pdb=" O6 DG J 8 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DG J 8 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG J 8 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG J 8 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DG J 8 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG J 8 " 0.001 2.00e-02 2.50e+03 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3530 2.82 - 3.34: 13386 3.34 - 3.86: 25816 3.86 - 4.38: 29084 4.38 - 4.90: 39690 Nonbonded interactions: 111506 Sorted by model distance: nonbonded pdb=" O ILE M 54 " pdb=" OG1 THR M 55 " model vdw 2.297 3.040 nonbonded pdb=" C3' DT I 71 " pdb=" C1' DT I 71 " model vdw 2.319 3.120 nonbonded pdb=" OP1 DT I 12 " pdb=" N GLY N 83 " model vdw 2.365 3.120 nonbonded pdb=" N3 DC I -73 " pdb=" N2 DG J 74 " model vdw 2.372 3.200 nonbonded pdb=" O SER M 62 " pdb=" OG SER M 62 " model vdw 2.399 3.040 ... (remaining 111501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 45 or (resid 46 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 through 62 or (r \ esid 63 and (name N or name CA or name C or name O or name CB )) or resid 64 thr \ ough 70 or (resid 71 through 72 and (name N or name CA or name C or name O or na \ me CB )) or resid 73 through 81 or (resid 82 and (name N or name CA or name C or \ name O or name CB )) or resid 83 through 89 or (resid 90 through 91 and (name N \ or name CA or name C or name O or name CB )) or resid 92 through 96 or (resid 9 \ 7 through 98 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 9 or (resid 100 through 102 and (name N or name CA or name C or name O or name C \ B )) or resid 103 or (resid 104 through 108 and (name N or name CA or name C or \ name O or name CB )) or resid 109 through 134)) selection = (chain 'E' and (resid 38 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 74 or (r \ esid 75 and (name N or name CA or name C or name O )) or resid 76 through 87 or \ (resid 88 and (name N or name CA or name C or name O )) or resid 89 through 104 \ or (resid 105 through 108 and (name N or name CA or name C or name O or name CB \ )) or resid 109 through 114 or (resid 115 through 116 and (name N or name CA or \ name C or name O or name CB )) or resid 117 or (resid 118 and (name N or name CA \ or name C or name O or name CB )) or resid 119 or (resid 120 and (name N or nam \ e CA or name C or name O or name CB )) or resid 121 through 134)) } ncs_group { reference = (chain 'B' and (resid 22 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 29 or (resid 30 through 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 35 or (res \ id 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 50 or (resid 51 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 52 th \ rough 61 or (resid 62 and (name N or name CA or name C or name O or name CB )) o \ r resid 63 through 64 or (resid 65 through 67 and (name N or name CA or name C o \ r name O or name CB )) or resid 68 through 77 or (resid 78 through 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 or (resid 82 through \ 83 and (name N or name CA or name C or name O or name CB )) or resid 84 or (resi \ d 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 101)) selection = (chain 'F' and (resid 22 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 34 or (resid 35 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1)) or resid 36 through 44 or (resid 45 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 70 or (resid 71 and (n \ ame N or name CA or name C or name O or name CB )) or resid 72 or (resid 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 through 90 or ( \ resid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 th \ rough 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) o \ r resid 98 through 99 or (resid 100 and (name N or name CA or name C or name O o \ r name CB )) or resid 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 15 or (resid 16 and (name N or name CA or name \ C or name O )) or resid 17 through 24 or (resid 25 and (name N or name CA or nam \ e C or name O or name CB )) or resid 26 through 35 or (resid 36 and (name N or n \ ame CA or name C or name O or name CB )) or resid 37 through 40 or (resid 41 and \ (name N or name CA or name C or name O or name CB )) or resid 42 through 55 or \ (resid 56 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1)) or resid 57 or (resid 58 through 60 and (name N or name CA o \ r name C or name O or name CB )) or resid 61 through 62 or (resid 63 and (name N \ or name CA or name C or name O or name CB )) or resid 64 through 76 or (resid 7 \ 7 through 78 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 9 through 80 or (resid 81 and (name N or name CA or name C or name O or name CB \ )) or resid 82 through 84 or (resid 85 through 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 89 or (resid 90 and (name N or na \ me CA or name C or name O or name CB )) or resid 91 through 94 or (resid 95 and \ (name N or name CA or name C or name O or name CB )) or resid 96 through 114 or \ (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 116 \ through 117)) selection = (chain 'G' and (resid 12 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 48 or (resid 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 58 or (res \ id 59 through 60 and (name N or name CA or name C or name O or name CB )) or res \ id 61 through 77 or (resid 78 and (name N or name CA or name C or name O or name \ CB )) or resid 79 through 86 or (resid 87 and (name N or name CA or name C or n \ ame O or name CB )) or resid 88 through 100 or (resid 101 and (name N or name CA \ or name C or name O or name CB )) or resid 102 through 117)) } ncs_group { reference = (chain 'D' and ((resid 33 through 40 and (name N or name CA or name C or name O \ or name CB )) or resid 41 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 or (resid 57 through 61 and (n \ ame N or name CA or name C or name O or name CB )) or resid 62 through 84 or (re \ sid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 or ( \ resid 87 through 90 and (name N or name CA or name C or name O or name CB )) or \ resid 91 through 121)) selection = (chain 'H' and (resid 33 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 59 or (resid 60 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 64 or (res \ id 65 and (name N or name CA or name C or name O or name CB )) or resid 66 throu \ gh 83 or (resid 84 through 85 and (name N or name CA or name C or name O or name \ CB )) or resid 86 through 87 or (resid 88 through 90 and (name N or name CA or \ name C or name O or name CB )) or resid 91 through 111 or (resid 112 and (name N \ or name CA or name C or name O or name CB )) or resid 113 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 38.980 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.007 0.066 14036 Z= 0.343 Angle : 0.752 11.488 20332 Z= 0.469 Chirality : 0.041 0.160 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.002 TRP N 91 HIS 0.003 0.001 HIS N 18 PHE 0.023 0.002 PHE C 25 TYR 0.014 0.002 TYR D 37 ARG 0.006 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.20027 ( 751) hydrogen bonds : angle 8.02285 ( 1850) covalent geometry : bond 0.00726 (14036) covalent geometry : angle 0.75250 (20332) *********************** 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 : 0.916 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: 0.3131 time to fit residues: 77.8290 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 : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 79 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.120181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085564 restraints weight = 34092.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087619 restraints weight = 18045.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088910 restraints weight = 12703.179| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14036 Z= 0.222 Angle : 0.659 7.158 20332 Z= 0.384 Chirality : 0.038 0.136 2301 Planarity : 0.005 0.051 1495 Dihedral : 32.084 174.540 4413 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.77 % Allowed : 13.64 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.27), residues: 861 helix: -0.54 (0.21), residues: 581 sheet: -1.97 (1.01), residues: 19 loop : -1.26 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 31 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.002 PHE C 25 TYR 0.015 0.002 TYR F 88 ARG 0.004 0.000 ARG F 23 Details of bonding type rmsd hydrogen bonds : bond 0.05692 ( 751) hydrogen bonds : angle 4.01443 ( 1850) covalent geometry : bond 0.00493 (14036) covalent geometry : angle 0.65889 (20332) *********************** 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 167 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 1.040 Fit side-chains REVERT: B 53 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 77 LYS cc_start: 0.9010 (mttm) cc_final: 0.8501 (mmtt) REVERT: B 98 TYR cc_start: 0.8750 (m-10) cc_final: 0.8539 (m-10) REVERT: D 73 GLU cc_start: 0.8103 (tp30) cc_final: 0.7893 (tp30) REVERT: D 120 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8627 (m) REVERT: E 81 ASP cc_start: 0.7927 (t0) cc_final: 0.7667 (t0) REVERT: H 106 HIS cc_start: 0.8033 (m-70) cc_final: 0.7587 (m-70) REVERT: N 37 MET cc_start: 0.7811 (ppp) cc_final: 0.7555 (ppp) REVERT: N 65 GLU cc_start: 0.4908 (tt0) cc_final: 0.4481 (tt0) REVERT: N 110 ARG cc_start: 0.8355 (mmp80) cc_final: 0.7883 (mmp80) REVERT: N 114 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8162 (tm-30) outliers start: 11 outliers final: 7 residues processed: 161 average time/residue: 0.2830 time to fit residues: 64.3748 Evaluate side-chains 152 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 54 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.121373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.086729 restraints weight = 33921.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.088777 restraints weight = 17890.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.090041 restraints weight = 12599.861| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14036 Z= 0.168 Angle : 0.607 9.878 20332 Z= 0.354 Chirality : 0.036 0.173 2301 Planarity : 0.004 0.038 1495 Dihedral : 31.825 172.653 4413 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.41 % Allowed : 16.05 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.28), residues: 861 helix: 0.65 (0.22), residues: 574 sheet: -1.14 (1.15), residues: 19 loop : -0.95 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 31 HIS 0.006 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.012 0.001 TYR C 57 ARG 0.003 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.04921 ( 751) hydrogen bonds : angle 3.31209 ( 1850) covalent geometry : bond 0.00367 (14036) covalent geometry : angle 0.60665 (20332) *********************** 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 172 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 1.030 Fit side-chains REVERT: A 81 ASP cc_start: 0.8129 (m-30) cc_final: 0.7867 (p0) REVERT: B 22 LEU cc_start: 0.3625 (OUTLIER) cc_final: 0.3412 (pp) REVERT: B 53 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8095 (tm-30) REVERT: B 77 LYS cc_start: 0.8946 (mttm) cc_final: 0.8459 (mmtt) REVERT: B 98 TYR cc_start: 0.8740 (m-10) cc_final: 0.8441 (m-10) REVERT: D 73 GLU cc_start: 0.7946 (tp30) cc_final: 0.7698 (tp30) REVERT: E 81 ASP cc_start: 0.7765 (t0) cc_final: 0.7543 (t0) REVERT: G 35 ARG cc_start: 0.9156 (mtm-85) cc_final: 0.8257 (mtm-85) REVERT: G 97 LEU cc_start: 0.8162 (mp) cc_final: 0.7801 (mt) REVERT: H 106 HIS cc_start: 0.7453 (m90) cc_final: 0.7077 (m-70) REVERT: N 110 ARG cc_start: 0.8385 (mmp80) cc_final: 0.8021 (mmp80) REVERT: N 114 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8258 (tm-30) outliers start: 15 outliers final: 8 residues processed: 165 average time/residue: 0.2930 time to fit residues: 67.2030 Evaluate side-chains 149 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 G residue 100 VAL Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 65 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 0.0020 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.120779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085926 restraints weight = 33693.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087946 restraints weight = 18116.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.089193 restraints weight = 12881.996| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14036 Z= 0.183 Angle : 0.603 6.265 20332 Z= 0.352 Chirality : 0.036 0.142 2301 Planarity : 0.004 0.040 1495 Dihedral : 31.767 174.305 4413 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.89 % Allowed : 16.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.29), residues: 861 helix: 1.03 (0.22), residues: 575 sheet: -1.18 (1.08), residues: 19 loop : -0.83 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 91 HIS 0.007 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.012 0.001 TYR C 57 ARG 0.003 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 751) hydrogen bonds : angle 3.19992 ( 1850) covalent geometry : bond 0.00407 (14036) covalent geometry : angle 0.60305 (20332) *********************** 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 164 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8084 (m-30) cc_final: 0.7805 (p0) REVERT: B 22 LEU cc_start: 0.3477 (OUTLIER) cc_final: 0.3222 (pp) REVERT: B 53 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 77 LYS cc_start: 0.8898 (mttm) cc_final: 0.8405 (mmtt) REVERT: B 98 TYR cc_start: 0.8784 (m-10) cc_final: 0.8460 (m-10) REVERT: C 38 ASN cc_start: 0.8313 (m110) cc_final: 0.8093 (m110) REVERT: E 81 ASP cc_start: 0.7823 (t0) cc_final: 0.7577 (t0) REVERT: G 35 ARG cc_start: 0.9144 (mtm-85) cc_final: 0.8232 (mtm-85) REVERT: H 81 ASN cc_start: 0.8083 (m-40) cc_final: 0.7832 (m-40) REVERT: H 106 HIS cc_start: 0.7591 (m90) cc_final: 0.7203 (m-70) REVERT: N 114 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8171 (tm-30) outliers start: 18 outliers final: 14 residues processed: 157 average time/residue: 0.3266 time to fit residues: 70.3472 Evaluate side-chains 153 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 84 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.122966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088408 restraints weight = 33670.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090465 restraints weight = 17743.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091721 restraints weight = 12493.248| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14036 Z= 0.157 Angle : 0.580 7.339 20332 Z= 0.340 Chirality : 0.035 0.172 2301 Planarity : 0.004 0.041 1495 Dihedral : 31.488 178.924 4413 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.53 % Allowed : 17.34 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.29), residues: 861 helix: 1.40 (0.22), residues: 575 sheet: -0.79 (1.11), residues: 19 loop : -0.68 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 88 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.009 0.001 TYR N 81 ARG 0.004 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 751) hydrogen bonds : angle 2.91372 ( 1850) covalent geometry : bond 0.00342 (14036) covalent geometry : angle 0.57995 (20332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.3127 (OUTLIER) cc_final: 0.2832 (pp) REVERT: B 77 LYS cc_start: 0.8845 (mttm) cc_final: 0.8347 (mmtt) REVERT: D 73 GLU cc_start: 0.7995 (tp30) cc_final: 0.7677 (tp30) REVERT: E 81 ASP cc_start: 0.7784 (t0) cc_final: 0.7550 (t0) REVERT: E 94 GLU cc_start: 0.8228 (tp30) cc_final: 0.7892 (tp30) REVERT: F 88 TYR cc_start: 0.8379 (m-80) cc_final: 0.8162 (m-80) REVERT: G 35 ARG cc_start: 0.9108 (mtm-85) cc_final: 0.8207 (mtm-85) REVERT: G 38 ASN cc_start: 0.7171 (t0) cc_final: 0.6954 (t0) REVERT: H 106 HIS cc_start: 0.7464 (m90) cc_final: 0.7099 (m-70) REVERT: H 112 THR cc_start: 0.9051 (m) cc_final: 0.8845 (p) REVERT: M 54 ILE cc_start: 0.4878 (OUTLIER) cc_final: 0.4613 (tt) REVERT: N 13 ARG cc_start: 0.7428 (mtm110) cc_final: 0.7120 (mtm110) REVERT: N 90 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6913 (mm-30) REVERT: N 114 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8171 (tm-30) outliers start: 22 outliers final: 13 residues processed: 164 average time/residue: 0.3051 time to fit residues: 68.3279 Evaluate side-chains 158 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 65 GLU 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 54 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 44 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.122709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088171 restraints weight = 34058.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.090155 restraints weight = 18283.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091365 restraints weight = 12979.205| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14036 Z= 0.176 Angle : 0.596 6.922 20332 Z= 0.347 Chirality : 0.035 0.174 2301 Planarity : 0.004 0.041 1495 Dihedral : 31.497 173.863 4413 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.53 % Allowed : 18.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.29), residues: 861 helix: 1.51 (0.22), residues: 576 sheet: -0.55 (1.16), residues: 19 loop : -0.64 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 88 HIS 0.005 0.001 HIS B 75 PHE 0.007 0.001 PHE E 67 TYR 0.015 0.001 TYR N 81 ARG 0.006 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 751) hydrogen bonds : angle 2.95206 ( 1850) covalent geometry : bond 0.00389 (14036) covalent geometry : angle 0.59588 (20332) *********************** 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 166 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.969 Fit side-chains REVERT: B 22 LEU cc_start: 0.2921 (OUTLIER) cc_final: 0.2624 (pp) REVERT: B 77 LYS cc_start: 0.8868 (mttm) cc_final: 0.8372 (mmtt) REVERT: B 98 TYR cc_start: 0.8810 (m-10) cc_final: 0.8473 (m-10) REVERT: D 73 GLU cc_start: 0.8036 (tp30) cc_final: 0.7737 (tp30) REVERT: E 81 ASP cc_start: 0.7878 (t0) cc_final: 0.7639 (t0) REVERT: E 94 GLU cc_start: 0.8268 (tp30) cc_final: 0.7871 (tp30) REVERT: G 35 ARG cc_start: 0.9113 (mtm-85) cc_final: 0.8194 (mtm-85) REVERT: H 106 HIS cc_start: 0.7472 (m90) cc_final: 0.7101 (m-70) REVERT: M 54 ILE cc_start: 0.4767 (OUTLIER) cc_final: 0.4499 (tt) REVERT: N 13 ARG cc_start: 0.7331 (mtm110) cc_final: 0.7008 (mtm110) REVERT: N 110 ARG cc_start: 0.8446 (mmp80) cc_final: 0.7996 (mmp80) REVERT: N 114 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8124 (tm-30) outliers start: 22 outliers final: 16 residues processed: 158 average time/residue: 0.3578 time to fit residues: 75.9023 Evaluate side-chains 156 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 66 VAL 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 M residue 53 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 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 = 0.3994 r_free = 0.3994 target = 0.123977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089686 restraints weight = 33544.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.091621 restraints weight = 18002.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092833 restraints weight = 12769.446| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14036 Z= 0.159 Angle : 0.585 6.699 20332 Z= 0.341 Chirality : 0.035 0.159 2301 Planarity : 0.004 0.042 1495 Dihedral : 31.391 172.772 4413 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.53 % Allowed : 18.94 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.29), residues: 861 helix: 1.68 (0.22), residues: 576 sheet: -0.21 (1.16), residues: 19 loop : -0.57 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 88 HIS 0.005 0.001 HIS B 75 PHE 0.007 0.001 PHE E 67 TYR 0.009 0.001 TYR D 80 ARG 0.007 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 751) hydrogen bonds : angle 2.83240 ( 1850) covalent geometry : bond 0.00349 (14036) covalent geometry : angle 0.58536 (20332) *********************** 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 168 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 2.179 Fit side-chains REVERT: B 22 LEU cc_start: 0.2849 (OUTLIER) cc_final: 0.2539 (pp) REVERT: B 77 LYS cc_start: 0.8817 (mttm) cc_final: 0.8355 (mmtt) REVERT: B 98 TYR cc_start: 0.8779 (m-10) cc_final: 0.8447 (m-10) REVERT: D 73 GLU cc_start: 0.7995 (tp30) cc_final: 0.7634 (tp30) REVERT: E 81 ASP cc_start: 0.7759 (t0) cc_final: 0.7539 (t0) REVERT: E 94 GLU cc_start: 0.8255 (tp30) cc_final: 0.7862 (tp30) REVERT: G 35 ARG cc_start: 0.9054 (mtm-85) cc_final: 0.8192 (mtm-85) REVERT: H 106 HIS cc_start: 0.7330 (m90) cc_final: 0.7028 (m-70) REVERT: M 54 ILE cc_start: 0.4815 (OUTLIER) cc_final: 0.4540 (tt) REVERT: N 13 ARG cc_start: 0.7321 (mtm110) cc_final: 0.6809 (mtm110) REVERT: N 90 GLU cc_start: 0.6277 (mm-30) cc_final: 0.5665 (pt0) REVERT: N 110 ARG cc_start: 0.8431 (mmp80) cc_final: 0.8017 (mmp80) REVERT: N 114 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8072 (tm-30) outliers start: 22 outliers final: 16 residues processed: 159 average time/residue: 0.4650 time to fit residues: 102.0627 Evaluate side-chains 158 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 77 LEU 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 M residue 53 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.124388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090211 restraints weight = 33636.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.092175 restraints weight = 17888.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093407 restraints weight = 12640.696| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14036 Z= 0.154 Angle : 0.593 11.458 20332 Z= 0.342 Chirality : 0.035 0.160 2301 Planarity : 0.004 0.042 1495 Dihedral : 31.344 171.425 4413 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.05 % Allowed : 19.26 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.29), residues: 861 helix: 1.81 (0.22), residues: 575 sheet: -1.23 (1.55), residues: 10 loop : -0.52 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 88 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.036 0.001 TYR D 80 ARG 0.007 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 751) hydrogen bonds : angle 2.80228 ( 1850) covalent geometry : bond 0.00337 (14036) covalent geometry : angle 0.59337 (20332) *********************** 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 167 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.208 Fit side-chains REVERT: B 22 LEU cc_start: 0.2838 (OUTLIER) cc_final: 0.2379 (pp) REVERT: B 77 LYS cc_start: 0.8836 (mttm) cc_final: 0.8360 (mmtt) REVERT: B 98 TYR cc_start: 0.8758 (m-10) cc_final: 0.8441 (m-10) REVERT: D 73 GLU cc_start: 0.7983 (tp30) cc_final: 0.7670 (tp30) REVERT: D 122 LYS cc_start: 0.6390 (tppt) cc_final: 0.6107 (tppt) REVERT: E 81 ASP cc_start: 0.7714 (t0) cc_final: 0.7500 (t0) REVERT: E 94 GLU cc_start: 0.8210 (tp30) cc_final: 0.7813 (tp30) REVERT: G 35 ARG cc_start: 0.9047 (mtm-85) cc_final: 0.8178 (mtm-85) REVERT: H 81 ASN cc_start: 0.8455 (m110) cc_final: 0.8123 (m110) REVERT: M 54 ILE cc_start: 0.4770 (OUTLIER) cc_final: 0.4514 (tt) REVERT: N 13 ARG cc_start: 0.7207 (mtm110) cc_final: 0.6623 (mtm110) REVERT: N 90 GLU cc_start: 0.6023 (mm-30) cc_final: 0.5371 (pt0) REVERT: N 110 ARG cc_start: 0.8382 (mmp80) cc_final: 0.7963 (mmp80) REVERT: N 114 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8262 (tm-30) outliers start: 19 outliers final: 16 residues processed: 158 average time/residue: 0.2963 time to fit residues: 64.1767 Evaluate side-chains 157 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 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 = 0.3974 r_free = 0.3974 target = 0.122704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088109 restraints weight = 33541.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.090047 restraints weight = 18138.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.091229 restraints weight = 12916.384| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14036 Z= 0.197 Angle : 0.626 9.839 20332 Z= 0.357 Chirality : 0.036 0.172 2301 Planarity : 0.004 0.043 1495 Dihedral : 31.422 171.360 4413 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.37 % Allowed : 20.06 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 861 helix: 1.75 (0.22), residues: 575 sheet: -1.26 (1.54), residues: 10 loop : -0.63 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 91 HIS 0.005 0.001 HIS B 75 PHE 0.007 0.001 PHE M 63 TYR 0.011 0.001 TYR C 57 ARG 0.008 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04562 ( 751) hydrogen bonds : angle 2.98224 ( 1850) covalent geometry : bond 0.00442 (14036) covalent geometry : angle 0.62586 (20332) *********************** 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 164 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.969 Fit side-chains REVERT: B 22 LEU cc_start: 0.2782 (OUTLIER) cc_final: 0.2431 (pp) REVERT: B 77 LYS cc_start: 0.8880 (mttm) cc_final: 0.8390 (mmtt) REVERT: B 98 TYR cc_start: 0.8788 (m-10) cc_final: 0.8439 (m-10) REVERT: D 73 GLU cc_start: 0.8048 (tp30) cc_final: 0.7669 (tp30) REVERT: D 122 LYS cc_start: 0.6457 (tppt) cc_final: 0.6153 (tppt) REVERT: E 81 ASP cc_start: 0.7887 (t0) cc_final: 0.7648 (t0) REVERT: G 35 ARG cc_start: 0.9076 (mtm-85) cc_final: 0.8141 (mtm-85) REVERT: H 81 ASN cc_start: 0.8549 (m110) cc_final: 0.8264 (m110) REVERT: H 106 HIS cc_start: 0.7424 (m-70) cc_final: 0.7094 (m-70) REVERT: M 54 ILE cc_start: 0.4735 (OUTLIER) cc_final: 0.4469 (tt) REVERT: N 13 ARG cc_start: 0.7273 (mtm110) cc_final: 0.6681 (mtm110) REVERT: N 90 GLU cc_start: 0.6015 (mm-30) cc_final: 0.5412 (pt0) REVERT: N 110 ARG cc_start: 0.8516 (mmp80) cc_final: 0.8155 (mmp80) REVERT: N 114 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8244 (tm-30) outliers start: 21 outliers final: 18 residues processed: 156 average time/residue: 0.3186 time to fit residues: 67.4707 Evaluate side-chains 162 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 66 VAL 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 G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.123384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088966 restraints weight = 33459.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.090877 restraints weight = 18006.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.092077 restraints weight = 12800.460| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14036 Z= 0.183 Angle : 0.620 8.497 20332 Z= 0.355 Chirality : 0.036 0.166 2301 Planarity : 0.004 0.042 1495 Dihedral : 31.423 172.107 4413 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.21 % Allowed : 19.74 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.29), residues: 861 helix: 1.78 (0.22), residues: 575 sheet: 0.00 (1.15), residues: 19 loop : -0.60 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 91 HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.026 0.002 TYR D 80 ARG 0.008 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 751) hydrogen bonds : angle 2.93723 ( 1850) covalent geometry : bond 0.00409 (14036) covalent geometry : angle 0.61993 (20332) ********************** 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 159 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.989 Fit side-chains REVERT: B 22 LEU cc_start: 0.3034 (OUTLIER) cc_final: 0.2669 (pp) REVERT: B 77 LYS cc_start: 0.8860 (mttm) cc_final: 0.8421 (mmtt) REVERT: B 98 TYR cc_start: 0.8793 (m-10) cc_final: 0.8456 (m-10) REVERT: D 73 GLU cc_start: 0.8021 (tp30) cc_final: 0.7641 (tp30) REVERT: E 81 ASP cc_start: 0.7816 (t0) cc_final: 0.7580 (t0) REVERT: E 94 GLU cc_start: 0.8103 (tp30) cc_final: 0.7898 (tp30) REVERT: G 35 ARG cc_start: 0.9084 (mtm-85) cc_final: 0.8167 (mtm-85) REVERT: H 81 ASN cc_start: 0.8522 (m110) cc_final: 0.8198 (m-40) REVERT: H 106 HIS cc_start: 0.7464 (m-70) cc_final: 0.7126 (m-70) REVERT: M 54 ILE cc_start: 0.4724 (OUTLIER) cc_final: 0.4454 (tt) REVERT: N 13 ARG cc_start: 0.7212 (mtm110) cc_final: 0.6763 (mtm110) REVERT: N 24 GLU cc_start: 0.6060 (tp30) cc_final: 0.5408 (tp30) REVERT: N 90 GLU cc_start: 0.5841 (mm-30) cc_final: 0.5321 (pt0) REVERT: N 110 ARG cc_start: 0.8444 (mmp80) cc_final: 0.8056 (mmp80) REVERT: N 114 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8258 (tm-30) outliers start: 20 outliers final: 18 residues processed: 151 average time/residue: 0.3091 time to fit residues: 63.2831 Evaluate side-chains 158 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 66 VAL 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 G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 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 = 0.3967 r_free = 0.3967 target = 0.122163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.087409 restraints weight = 33561.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089308 restraints weight = 18214.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090474 restraints weight = 13029.229| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14036 Z= 0.224 Angle : 0.642 9.947 20332 Z= 0.366 Chirality : 0.037 0.169 2301 Planarity : 0.004 0.044 1495 Dihedral : 31.483 172.108 4413 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.53 % Allowed : 19.90 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.29), residues: 861 helix: 1.66 (0.22), residues: 576 sheet: 0.03 (1.16), residues: 19 loop : -0.68 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 91 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE M 63 TYR 0.029 0.002 TYR F 88 ARG 0.008 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 751) hydrogen bonds : angle 3.09916 ( 1850) covalent geometry : bond 0.00506 (14036) covalent geometry : angle 0.64226 (20332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4365.81 seconds wall clock time: 76 minutes 41.82 seconds (4601.82 seconds total)