Starting phenix.real_space_refine on Mon Aug 25 05:47:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9azm_44016/08_2025/9azm_44016.cif Found real_map, /net/cci-nas-00/data/ceres_data/9azm_44016/08_2025/9azm_44016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9azm_44016/08_2025/9azm_44016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9azm_44016/08_2025/9azm_44016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9azm_44016/08_2025/9azm_44016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9azm_44016/08_2025/9azm_44016.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 483 5.49 5 S 77 5.16 5 C 14362 2.51 5 N 4693 2.21 5 O 6167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25782 Number of models: 1 Model: "" Number of chains: 16 Chain: "CD" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 667 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 77} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "SD" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "SF" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "SK" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 827 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "SP" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "SQ" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1142 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "SS" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1198 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "ST" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 137} Chain: "SU" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 821 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Sc" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "Sd" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 52} Chain: "Sg" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "SM" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "SZ" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Sf" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "S2" Number of atoms: 10283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 10283 Classifications: {'RNA': 483} Modifications used: {'rna2p_pur': 43, 'rna2p_pyr': 41, 'rna3p_pur': 198, 'rna3p_pyr': 201} Link IDs: {'rna2p': 84, 'rna3p': 398} Time building chain proxies: 6.17, per 1000 atoms: 0.24 Number of scatterers: 25782 At special positions: 0 Unit cell: (158.064, 138.84, 154.86, 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 77 16.00 P 483 15.00 O 6167 8.00 N 4693 7.00 C 14362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 963.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 27 sheets defined 36.2% alpha, 13.5% beta 148 base pairs and 235 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'CD' and resid 283 through 295 Processing helix chain 'SD' and resid 6 through 29 Processing helix chain 'SD' and resid 54 through 59 removed outlier: 3.658A pdb=" N VALSD 58 " --> pdb=" O ARGSD 54 " (cutoff:3.500A) Processing helix chain 'SD' and resid 63 through 77 Processing helix chain 'SD' and resid 93 through 96 Processing helix chain 'SD' and resid 97 through 112 Processing helix chain 'SD' and resid 114 through 130 Processing helix chain 'SD' and resid 163 through 167 Processing helix chain 'SF' and resid 18 through 22 Processing helix chain 'SF' and resid 32 through 36 removed outlier: 3.674A pdb=" N GLNSF 36 " --> pdb=" O ILESF 33 " (cutoff:3.500A) Processing helix chain 'SF' and resid 67 through 77 removed outlier: 3.566A pdb=" N METSF 77 " --> pdb=" O THRSF 73 " (cutoff:3.500A) Processing helix chain 'SF' and resid 85 through 105 removed outlier: 3.528A pdb=" N ARGSF 91 " --> pdb=" O LEUSF 87 " (cutoff:3.500A) Processing helix chain 'SF' and resid 107 through 120 Processing helix chain 'SF' and resid 144 through 162 Processing helix chain 'SF' and resid 168 through 183 Processing helix chain 'SF' and resid 187 through 203 removed outlier: 3.582A pdb=" N GLUSF 195 " --> pdb=" O LYSSF 191 " (cutoff:3.500A) Processing helix chain 'SK' and resid 4 through 18 removed outlier: 3.681A pdb=" N GLUSK 13 " --> pdb=" O ILESK 9 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEUSK 14 " --> pdb=" O ALASK 10 " (cutoff:3.500A) Processing helix chain 'SK' and resid 35 through 39 Processing helix chain 'SK' and resid 41 through 55 removed outlier: 3.570A pdb=" N GLNSK 50 " --> pdb=" O METSK 46 " (cutoff:3.500A) Processing helix chain 'SK' and resid 72 through 83 removed outlier: 4.005A pdb=" N GLNSK 77 " --> pdb=" O ASNSK 73 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYRSK 78 " --> pdb=" O GLUSK 74 " (cutoff:3.500A) Processing helix chain 'SK' and resid 91 through 96 removed outlier: 3.973A pdb=" N ARGSK 95 " --> pdb=" O PROSK 91 " (cutoff:3.500A) Processing helix chain 'SP' and resid 21 through 28 removed outlier: 3.572A pdb=" N ASPSP 27 " --> pdb=" O ASPSP 23 " (cutoff:3.500A) Processing helix chain 'SP' and resid 29 through 37 removed outlier: 4.513A pdb=" N GLNSP 35 " --> pdb=" O GLUSP 31 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEUSP 36 " --> pdb=" O GLNSP 32 " (cutoff:3.500A) Processing helix chain 'SP' and resid 38 through 47 Processing helix chain 'SP' and resid 50 through 67 Processing helix chain 'SP' and resid 86 through 90 Processing helix chain 'SP' and resid 115 through 119 Processing helix chain 'SQ' and resid 47 through 52 Processing helix chain 'SQ' and resid 52 through 59 Processing helix chain 'SQ' and resid 60 through 63 Processing helix chain 'SQ' and resid 76 through 100 Processing helix chain 'SQ' and resid 101 through 114 removed outlier: 3.692A pdb=" N LYSSQ 105 " --> pdb=" O ASPSQ 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILESQ 111 " --> pdb=" O GLUSQ 107 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 116 through 120 Processing helix chain 'SS' and resid 25 through 30 Processing helix chain 'SS' and resid 31 through 33 No H-bonds generated for 'chain 'SS' and resid 31 through 33' Processing helix chain 'SS' and resid 37 through 48 Processing helix chain 'SS' and resid 55 through 59 Processing helix chain 'SS' and resid 60 through 73 removed outlier: 3.703A pdb=" N ARGSS 66 " --> pdb=" O ASPSS 62 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASNSS 73 " --> pdb=" O THRSS 69 " (cutoff:3.500A) Processing helix chain 'SS' and resid 74 through 78 removed outlier: 3.543A pdb=" N LYSSS 78 " --> pdb=" O ARGSS 75 " (cutoff:3.500A) Processing helix chain 'SS' and resid 80 through 84 removed outlier: 3.614A pdb=" N LEUSS 84 " --> pdb=" O ASPSS 81 " (cutoff:3.500A) Processing helix chain 'SS' and resid 100 through 117 Processing helix chain 'SS' and resid 119 through 128 Processing helix chain 'SS' and resid 140 through 144 removed outlier: 3.612A pdb=" N GLYSS 143 " --> pdb=" O GLYSS 140 " (cutoff:3.500A) Processing helix chain 'ST' and resid 10 through 25 Processing helix chain 'ST' and resid 31 through 36 removed outlier: 4.480A pdb=" N ASPST 35 " --> pdb=" O GLUST 32 " (cutoff:3.500A) Processing helix chain 'ST' and resid 51 through 67 removed outlier: 3.678A pdb=" N THRST 55 " --> pdb=" O ASNST 51 " (cutoff:3.500A) Processing helix chain 'ST' and resid 71 through 79 Processing helix chain 'ST' and resid 96 through 110 removed outlier: 3.657A pdb=" N ALAST 100 " --> pdb=" O SERST 96 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEUST 110 " --> pdb=" O ALAST 106 " (cutoff:3.500A) Processing helix chain 'ST' and resid 124 through 144 Processing helix chain 'SU' and resid 28 through 45 removed outlier: 3.641A pdb=" N ALASU 37 " --> pdb=" O GLUSU 33 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASPSU 38 " --> pdb=" O LYSSU 34 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEUSU 39 " --> pdb=" O VALSU 35 " (cutoff:3.500A) Processing helix chain 'SU' and resid 94 through 99 removed outlier: 3.505A pdb=" N VALSU 98 " --> pdb=" O PROSU 94 " (cutoff:3.500A) Processing helix chain 'SU' and resid 100 through 105 removed outlier: 3.782A pdb=" N ILESU 104 " --> pdb=" O ILESU 101 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SERSU 105 " --> pdb=" O THRSU 102 " (cutoff:3.500A) Processing helix chain 'Sd' and resid 32 through 36 Processing helix chain 'Sd' and resid 40 through 51 removed outlier: 5.269A pdb=" N LYSSd 48 " --> pdb=" O ARGSd 44 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASPSd 49 " --> pdb=" O GLNSd 45 " (cutoff:3.500A) Processing helix chain 'SM' and resid 12 through 28 removed outlier: 4.493A pdb=" N ALASM 17 " --> pdb=" O ASPSM 13 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEUSM 18 " --> pdb=" O VALSM 14 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VALSM 21 " --> pdb=" O ALASM 17 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEUSM 22 " --> pdb=" O LEUSM 18 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HISSM 28 " --> pdb=" O THRSM 24 " (cutoff:3.500A) Processing helix chain 'SM' and resid 34 through 44 Processing helix chain 'SM' and resid 58 through 72 removed outlier: 3.522A pdb=" N VALSM 62 " --> pdb=" O GLUSM 58 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLUSM 66 " --> pdb=" O VALSM 62 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALASM 67 " --> pdb=" O LYSSM 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEUSM 68 " --> pdb=" O LEUSM 64 " (cutoff:3.500A) Processing helix chain 'SM' and resid 81 through 89 removed outlier: 3.545A pdb=" N LEUSM 85 " --> pdb=" O ASPSM 81 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUSM 87 " --> pdb=" O LYSSM 83 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRPSM 88 " --> pdb=" O LYSSM 84 " (cutoff:3.500A) Processing helix chain 'SM' and resid 99 through 103 removed outlier: 3.977A pdb=" N LYSSM 102 " --> pdb=" O LYSSM 99 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VALSM 103 " --> pdb=" O PROSM 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'SM' and resid 99 through 103' Processing helix chain 'SM' and resid 119 through 132 removed outlier: 4.131A pdb=" N VALSM 123 " --> pdb=" O GLNSM 119 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 51 through 60 Processing helix chain 'SZ' and resid 61 through 65 removed outlier: 3.508A pdb=" N TYRSZ 65 " --> pdb=" O VALSZ 62 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 69 through 77 Processing helix chain 'SZ' and resid 81 through 95 Processing helix chain 'Sf' and resid 123 through 127 removed outlier: 3.556A pdb=" N GLYSf 127 " --> pdb=" O ASPSf 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'CD' and resid 318 through 320 removed outlier: 6.411A pdb=" N THRSf 147 " --> pdb=" O LEUCD 319 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'SD' and resid 37 through 40 removed outlier: 3.770A pdb=" N GLUSD 85 " --> pdb=" O THRSD 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'SD' and resid 150 through 155 removed outlier: 3.742A pdb=" N GLYSD 133 " --> pdb=" O METSD 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'SD' and resid 224 through 226 Processing sheet with id=AA5, first strand: chain 'SF' and resid 123 through 125 removed outlier: 8.239A pdb=" N ALASF 138 " --> pdb=" O ASNSc 45 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N LYSSc 47 " --> pdb=" O ALASF 138 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASPSF 140 " --> pdb=" O LYSSc 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'SK' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'SK' and resid 58 through 59 Processing sheet with id=AA8, first strand: chain 'SP' and resid 76 through 78 removed outlier: 6.476A pdb=" N VALSP 76 " --> pdb=" O GLYSP 95 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N TYRSP 97 " --> pdb=" O VALSP 76 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N THRSP 78 " --> pdb=" O TYRSP 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'SQ' and resid 9 through 16 removed outlier: 7.029A pdb=" N LYSSQ 33 " --> pdb=" O VALSQ 70 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N VALSQ 72 " --> pdb=" O LYSSQ 33 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'SS' and resid 12 through 13 removed outlier: 3.625A pdb=" N LEUSS 13 " --> pdb=" O ILESS 20 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'ST' and resid 81 through 83 Processing sheet with id=AB3, first strand: chain 'ST' and resid 113 through 115 Processing sheet with id=AB4, first strand: chain 'SU' and resid 54 through 55 Processing sheet with id=AB5, first strand: chain 'SU' and resid 54 through 55 Processing sheet with id=AB6, first strand: chain 'SU' and resid 64 through 65 Processing sheet with id=AB7, first strand: chain 'Sc' and resid 41 through 42 Processing sheet with id=AB8, first strand: chain 'Sd' and resid 30 through 31 Processing sheet with id=AB9, first strand: chain 'Sg' and resid 4 through 10 removed outlier: 4.983A pdb=" N VALSg 309 " --> pdb=" O ARGSg 8 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARGSg 308 " --> pdb=" O ALASg 300 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALASg 300 " --> pdb=" O ARGSg 308 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Sg' and resid 20 through 23 removed outlier: 3.594A pdb=" N GLNSg 20 " --> pdb=" O ALASg 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYSSg 44 " --> pdb=" O PROSg 55 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Sg' and resid 66 through 71 removed outlier: 6.588A pdb=" N GLYSg 81 " --> pdb=" O SERSg 67 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VALSg 69 " --> pdb=" O LEUSg 79 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEUSg 79 " --> pdb=" O VALSg 69 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILESg 71 " --> pdb=" O PHESg 77 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N PHESg 77 " --> pdb=" O ILESg 71 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARGSg 99 " --> pdb=" O LEUSg 89 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASPSg 91 " --> pdb=" O THRSg 97 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N THRSg 97 " --> pdb=" O ASPSg 91 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Sg' and resid 108 through 113 removed outlier: 6.768A pdb=" N GLYSg 123 " --> pdb=" O LEUSg 109 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VALSg 111 " --> pdb=" O VALSg 121 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VALSg 121 " --> pdb=" O VALSg 111 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEUSg 131 " --> pdb=" O LYSSg 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Sg' and resid 154 through 156 Processing sheet with id=AC5, first strand: chain 'Sg' and resid 195 through 200 removed outlier: 6.931A pdb=" N GLYSg 210 " --> pdb=" O ASNSg 196 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VALSg 198 " --> pdb=" O ALASg 208 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALASg 208 " --> pdb=" O VALSg 198 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VALSg 200 " --> pdb=" O LEUSg 206 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEUSg 206 " --> pdb=" O VALSg 200 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASPSg 220 " --> pdb=" O HISSg 226 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HISSg 226 " --> pdb=" O ASPSg 220 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Sg' and resid 236 through 240 removed outlier: 6.583A pdb=" N ALASg 251 " --> pdb=" O ASNSg 237 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEUSg 239 " --> pdb=" O CYSSg 249 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N CYSSg 249 " --> pdb=" O LEUSg 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'SM' and resid 76 through 79 Processing sheet with id=AC8, first strand: chain 'SZ' and resid 98 through 99 Processing sheet with id=AC9, first strand: chain 'Sf' and resid 106 through 108 585 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 369 hydrogen bonds 562 hydrogen bond angles 0 basepair planarities 148 basepair parallelities 235 stacking parallelities Total time for adding SS restraints: 6.91 Time building geometry restraints manager: 2.75 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: 5555 1.33 - 1.45: 8423 1.45 - 1.58: 12188 1.58 - 1.70: 971 1.70 - 1.82: 117 Bond restraints: 27254 Sorted by residual: bond pdb=" CB PROSD 222 " pdb=" CG PROSD 222 " ideal model delta sigma weight residual 1.492 1.632 -0.140 5.00e-02 4.00e+02 7.83e+00 bond pdb=" CA ASNSZ 46 " pdb=" CB ASNSZ 46 " ideal model delta sigma weight residual 1.527 1.592 -0.065 2.48e-02 1.63e+03 6.89e+00 bond pdb=" CB PROSD 194 " pdb=" CG PROSD 194 " ideal model delta sigma weight residual 1.492 1.610 -0.118 5.00e-02 4.00e+02 5.54e+00 bond pdb=" CB PROSg 283 " pdb=" CG PROSg 283 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.91e+00 bond pdb=" CB METSP 70 " pdb=" CG METSP 70 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.77e+00 ... (remaining 27249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 38719 3.43 - 6.85: 323 6.85 - 10.28: 46 10.28 - 13.70: 11 13.70 - 17.13: 3 Bond angle restraints: 39102 Sorted by residual: angle pdb=" CA PROSD 194 " pdb=" N PROSD 194 " pdb=" CD PROSD 194 " ideal model delta sigma weight residual 112.00 97.33 14.67 1.40e+00 5.10e-01 1.10e+02 angle pdb=" CA PROSD 222 " pdb=" N PROSD 222 " pdb=" CD PROSD 222 " ideal model delta sigma weight residual 112.00 98.58 13.42 1.40e+00 5.10e-01 9.19e+01 angle pdb=" N PHESF 61 " pdb=" CA PHESF 61 " pdb=" CB PHESF 61 " ideal model delta sigma weight residual 114.17 107.33 6.84 1.14e+00 7.69e-01 3.61e+01 angle pdb=" CA GLUSf 110 " pdb=" CB GLUSf 110 " pdb=" CG GLUSf 110 " ideal model delta sigma weight residual 114.10 126.05 -11.95 2.00e+00 2.50e-01 3.57e+01 angle pdb=" CB METSP 70 " pdb=" CG METSP 70 " pdb=" SD METSP 70 " ideal model delta sigma weight residual 112.70 129.83 -17.13 3.00e+00 1.11e-01 3.26e+01 ... (remaining 39097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.96: 15421 33.96 - 67.92: 1676 67.92 - 101.87: 193 101.87 - 135.83: 3 135.83 - 169.79: 4 Dihedral angle restraints: 17297 sinusoidal: 11693 harmonic: 5604 Sorted by residual: dihedral pdb=" CA GLUSQ 43 " pdb=" C GLUSQ 43 " pdb=" N PROSQ 44 " pdb=" CA PROSQ 44 " ideal model delta harmonic sigma weight residual -180.00 -110.98 -69.02 0 5.00e+00 4.00e-02 1.91e+02 dihedral pdb=" CA ASNSZ 46 " pdb=" C ASNSZ 46 " pdb=" N LEUSZ 47 " pdb=" CA LEUSZ 47 " ideal model delta harmonic sigma weight residual 180.00 123.71 56.29 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" O4' CS21660 " pdb=" C1' CS21660 " pdb=" N1 CS21660 " pdb=" C2 CS21660 " ideal model delta sinusoidal sigma weight residual 200.00 43.01 156.99 1 1.50e+01 4.44e-03 8.19e+01 ... (remaining 17294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4066 0.056 - 0.112: 593 0.112 - 0.167: 92 0.167 - 0.223: 14 0.223 - 0.279: 2 Chirality restraints: 4767 Sorted by residual: chirality pdb=" CA PROSD 194 " pdb=" N PROSD 194 " pdb=" C PROSD 194 " pdb=" CB PROSD 194 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C1' GS21604 " pdb=" O4' GS21604 " pdb=" C2' GS21604 " pdb=" N9 GS21604 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA GLUSf 110 " pdb=" N GLUSf 110 " pdb=" C GLUSf 110 " pdb=" CB GLUSf 110 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 4764 not shown) Planarity restraints: 3185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLUSQ 43 " -0.097 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PROSQ 44 " 0.254 5.00e-02 4.00e+02 pdb=" CA PROSQ 44 " -0.082 5.00e-02 4.00e+02 pdb=" CD PROSQ 44 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASPSD 193 " -0.096 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PROSD 194 " 0.229 5.00e-02 4.00e+02 pdb=" CA PROSD 194 " -0.062 5.00e-02 4.00e+02 pdb=" CD PROSD 194 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THRSD 221 " -0.094 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PROSD 222 " 0.224 5.00e-02 4.00e+02 pdb=" CA PROSD 222 " -0.063 5.00e-02 4.00e+02 pdb=" CD PROSD 222 " -0.068 5.00e-02 4.00e+02 ... (remaining 3182 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 309 2.55 - 3.14: 20218 3.14 - 3.73: 48306 3.73 - 4.31: 66217 4.31 - 4.90: 95727 Nonbonded interactions: 230777 Sorted by model distance: nonbonded pdb=" O2' CS21488 " pdb=" OP2 GS21490 " model vdw 1.968 3.040 nonbonded pdb=" O ARGSZ 80 " pdb=" O2' GS21598 " model vdw 2.124 3.040 nonbonded pdb=" OD1 ASNSF 83 " pdb=" O2' AS21651 " model vdw 2.131 3.040 nonbonded pdb=" O VALSg 18 " pdb=" OG1 THRSg 287 " model vdw 2.146 3.040 nonbonded pdb=" O LYSSZ 52 " pdb=" NZ LYSSZ 52 " model vdw 2.151 3.120 ... (remaining 230772 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.070 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 29.310 Find NCS groups from input model: 0.150 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 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 : 0.004 0.140 27254 Z= 0.175 Angle : 0.850 17.129 39102 Z= 0.445 Chirality : 0.042 0.279 4767 Planarity : 0.007 0.147 3185 Dihedral : 22.706 169.792 13685 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.66 % Favored : 90.03 % Rotamer: Outliers : 4.61 % Allowed : 42.73 % Favored : 52.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.55 (0.18), residues: 1916 helix: -1.07 (0.20), residues: 565 sheet: -1.40 (0.29), residues: 308 loop : -2.18 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGSc 31 TYR 0.023 0.002 TYRSQ 115 PHE 0.023 0.002 PHESg 241 TRP 0.052 0.002 TRPCD 287 HIS 0.017 0.001 HISSg 188 Details of bonding type rmsd covalent geometry : bond 0.00388 (27254) covalent geometry : angle 0.85005 (39102) hydrogen bonds : bond 0.21296 ( 952) hydrogen bonds : angle 7.58177 ( 2152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 364 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SK 89 ILE cc_start: 0.8994 (mp) cc_final: 0.8696 (mp) REVERT: SP 111 MET cc_start: 0.9190 (mtt) cc_final: 0.8936 (mtt) REVERT: ST 130 ASP cc_start: 0.8637 (m-30) cc_final: 0.8361 (m-30) REVERT: Sc 41 SER cc_start: 0.8460 (p) cc_final: 0.8240 (t) REVERT: Sg 223 GLU cc_start: 0.6403 (pp20) cc_final: 0.5565 (pp20) REVERT: Sg 225 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8228 (ptpp) REVERT: SM 24 THR cc_start: 0.9360 (p) cc_final: 0.9050 (t) outliers start: 77 outliers final: 48 residues processed: 421 average time/residue: 0.6203 time to fit residues: 305.9362 Evaluate side-chains 377 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 329 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CD residue 277 GLU Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 46 THR Chi-restraints excluded: chain SD residue 168 VAL Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SD residue 223 ILE Chi-restraints excluded: chain SF residue 26 ASP Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 196 LEU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 74 GLU Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 26 LYS Chi-restraints excluded: chain SQ residue 27 ARG Chi-restraints excluded: chain SQ residue 41 MET Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SS residue 79 ILE Chi-restraints excluded: chain SS residue 116 LYS Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 25 SER Chi-restraints excluded: chain ST residue 28 LEU Chi-restraints excluded: chain ST residue 34 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 115 THR Chi-restraints excluded: chain Sc residue 6 VAL Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sc residue 61 SER Chi-restraints excluded: chain Sg residue 63 SER Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 160 SER Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 236 ILE Chi-restraints excluded: chain Sg residue 271 LYS Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 312 VAL Chi-restraints excluded: chain SM residue 11 VAL Chi-restraints excluded: chain SM residue 22 LEU Chi-restraints excluded: chain SM residue 31 LEU Chi-restraints excluded: chain SM residue 64 LEU Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain Sf residue 108 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SF 82 ASN SP 32 GLN SP 35 GLN SP 46 ASN SQ 97 GLN SU 92 HIS ** Sg 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sg 285 GLN SM 19 GLN ** SM 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.071788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.053195 restraints weight = 77315.363| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.13 r_work: 0.2827 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27254 Z= 0.260 Angle : 0.764 12.895 39102 Z= 0.389 Chirality : 0.044 0.214 4767 Planarity : 0.006 0.142 3185 Dihedral : 22.572 163.727 9839 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.97 % Favored : 89.72 % Rotamer: Outliers : 9.75 % Allowed : 33.51 % Favored : 56.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.18), residues: 1916 helix: -0.22 (0.21), residues: 582 sheet: -1.49 (0.28), residues: 322 loop : -2.07 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGSf 138 TYR 0.018 0.002 TYRSZ 65 PHE 0.043 0.002 PHESF 61 TRP 0.027 0.002 TRPSg 219 HIS 0.010 0.001 HISST 42 Details of bonding type rmsd covalent geometry : bond 0.00540 (27254) covalent geometry : angle 0.76362 (39102) hydrogen bonds : bond 0.07290 ( 952) hydrogen bonds : angle 4.86228 ( 2152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 341 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CD 287 TRP cc_start: 0.9045 (t-100) cc_final: 0.8655 (t-100) REVERT: SD 50 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8887 (mm) REVERT: SD 56 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8963 (tp-100) REVERT: SD 67 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8470 (mtm110) REVERT: SD 74 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8937 (tm-30) REVERT: SD 94 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8713 (mtm-85) REVERT: SF 29 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8481 (mm-40) REVERT: SF 36 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: SF 45 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8120 (p90) REVERT: SF 106 GLU cc_start: 0.8384 (pp20) cc_final: 0.7897 (pp20) REVERT: SF 127 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.6343 (tpp-160) REVERT: SF 136 ARG cc_start: 0.7101 (mtp180) cc_final: 0.6729 (mtp85) REVERT: SK 29 MET cc_start: 0.9324 (ttm) cc_final: 0.8978 (ttp) REVERT: SK 31 LYS cc_start: 0.9358 (mptp) cc_final: 0.8973 (mptp) REVERT: SK 89 ILE cc_start: 0.9068 (mp) cc_final: 0.8561 (mp) REVERT: SP 32 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8867 (pm20) REVERT: SP 34 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8145 (mtm) REVERT: SP 65 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8879 (tptp) REVERT: SP 111 MET cc_start: 0.9252 (mtt) cc_final: 0.9026 (mtt) REVERT: SQ 10 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.8913 (m) REVERT: SQ 84 ILE cc_start: 0.9721 (OUTLIER) cc_final: 0.9518 (mp) REVERT: SQ 107 GLU cc_start: 0.8785 (pp20) cc_final: 0.8524 (pp20) REVERT: SQ 114 GLN cc_start: 0.8921 (pt0) cc_final: 0.8710 (pp30) REVERT: SQ 116 ASP cc_start: 0.8141 (t0) cc_final: 0.7760 (t0) REVERT: SS 63 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.7511 (mm-30) REVERT: SS 73 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8659 (p0) REVERT: SS 92 ASP cc_start: 0.8531 (t0) cc_final: 0.8066 (t0) REVERT: ST 114 GLU cc_start: 0.8518 (pm20) cc_final: 0.8132 (pm20) REVERT: SU 111 GLU cc_start: 0.8437 (tt0) cc_final: 0.8189 (tt0) REVERT: SU 113 GLU cc_start: 0.8012 (mp0) cc_final: 0.7691 (mp0) REVERT: Sc 18 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9251 (mt) REVERT: Sc 60 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6642 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5047 (OUTLIER) cc_final: 0.4690 (tt0) REVERT: Sc 66 ARG cc_start: 0.7480 (mpp80) cc_final: 0.7222 (mtm-85) REVERT: Sg 14 HIS cc_start: 0.8559 (OUTLIER) cc_final: 0.7537 (p90) REVERT: Sg 195 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8449 (mm) REVERT: Sg 228 TYR cc_start: 0.7411 (t80) cc_final: 0.7188 (t80) REVERT: SM 88 TRP cc_start: 0.9288 (m-10) cc_final: 0.9081 (m-10) REVERT: Sf 103 LEU cc_start: 0.6921 (pt) cc_final: 0.6675 (pp) REVERT: Sf 113 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8365 (mmtt) outliers start: 163 outliers final: 69 residues processed: 454 average time/residue: 0.6943 time to fit residues: 364.3131 Evaluate side-chains 410 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 324 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CD residue 347 THR Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 46 THR Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 67 ARG Chi-restraints excluded: chain SD residue 94 ARG Chi-restraints excluded: chain SD residue 168 VAL Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 26 ASP Chi-restraints excluded: chain SF residue 36 GLN Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 79 HIS Chi-restraints excluded: chain SF residue 127 ARG Chi-restraints excluded: chain SF residue 141 VAL Chi-restraints excluded: chain SF residue 177 LEU Chi-restraints excluded: chain SF residue 185 SER Chi-restraints excluded: chain SF residue 196 LEU Chi-restraints excluded: chain SF residue 204 ARG Chi-restraints excluded: chain SK residue 20 VAL Chi-restraints excluded: chain SK residue 35 LEU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 85 LEU Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SK residue 96 ARG Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 32 GLN Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 52 LYS Chi-restraints excluded: chain SP residue 65 LYS Chi-restraints excluded: chain SP residue 84 ILE Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 26 LYS Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 67 ASP Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 84 ILE Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SS residue 12 ILE Chi-restraints excluded: chain SS residue 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 45 LEU Chi-restraints excluded: chain SS residue 63 GLU Chi-restraints excluded: chain SS residue 73 ASN Chi-restraints excluded: chain SS residue 79 ILE Chi-restraints excluded: chain SS residue 83 PHE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 34 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 121 ARG Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 115 THR Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 36 ASP Chi-restraints excluded: chain Sc residue 37 ASP Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 62 GLU Chi-restraints excluded: chain Sg residue 14 HIS Chi-restraints excluded: chain Sg residue 62 HIS Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 144 ASP Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 195 LEU Chi-restraints excluded: chain Sg residue 219 TRP Chi-restraints excluded: chain Sg residue 236 ILE Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 312 VAL Chi-restraints excluded: chain Sg residue 313 THR Chi-restraints excluded: chain SM residue 14 VAL Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain SZ residue 47 LEU Chi-restraints excluded: chain SZ residue 58 LEU Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 94 LYS Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain Sf residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 194 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SF 82 ASN SF 137 GLN SK 66 HIS SP 46 ASN SQ 86 GLN SQ 97 GLN ST 137 GLN SU 92 HIS Sc 29 GLN ** Sg 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 48 HIS SZ 45 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.071294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.052751 restraints weight = 77660.283| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.21 r_work: 0.2817 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27254 Z= 0.227 Angle : 0.724 13.995 39102 Z= 0.367 Chirality : 0.043 0.220 4767 Planarity : 0.006 0.132 3185 Dihedral : 22.523 164.191 9799 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.97 % Favored : 89.77 % Rotamer: Outliers : 9.46 % Allowed : 32.38 % Favored : 58.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.19), residues: 1916 helix: -0.01 (0.21), residues: 583 sheet: -1.35 (0.29), residues: 316 loop : -2.05 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGST 121 TYR 0.018 0.002 TYRSZ 65 PHE 0.035 0.002 PHESF 61 TRP 0.024 0.002 TRPSg 219 HIS 0.009 0.001 HISSg 188 Details of bonding type rmsd covalent geometry : bond 0.00470 (27254) covalent geometry : angle 0.72447 (39102) hydrogen bonds : bond 0.06709 ( 952) hydrogen bonds : angle 4.47448 ( 2152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 349 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CD 282 MET cc_start: 0.7601 (tpt) cc_final: 0.7272 (tpt) REVERT: CD 287 TRP cc_start: 0.9070 (t-100) cc_final: 0.8657 (t-100) REVERT: SD 56 GLN cc_start: 0.9188 (tp-100) cc_final: 0.8926 (tp-100) REVERT: SD 74 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8807 (tm-30) REVERT: SD 94 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8675 (ptp90) REVERT: SF 29 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8517 (mm-40) REVERT: SF 127 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.6284 (tpp-160) REVERT: SK 29 MET cc_start: 0.9297 (ttm) cc_final: 0.8911 (ttp) REVERT: SK 89 ILE cc_start: 0.9157 (mp) cc_final: 0.8532 (mp) REVERT: SP 34 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8167 (mtt) REVERT: SP 65 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8904 (tptp) REVERT: SP 69 PRO cc_start: 0.9232 (Cg_exo) cc_final: 0.8968 (Cg_endo) REVERT: SQ 41 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7503 (mpp) REVERT: SQ 84 ILE cc_start: 0.9715 (OUTLIER) cc_final: 0.9499 (mp) REVERT: SQ 107 GLU cc_start: 0.8893 (pp20) cc_final: 0.8611 (pp20) REVERT: SQ 116 ASP cc_start: 0.8398 (t0) cc_final: 0.7902 (t0) REVERT: SS 73 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8554 (p0) REVERT: ST 114 GLU cc_start: 0.8430 (pm20) cc_final: 0.8094 (pm20) REVERT: SU 48 LEU cc_start: 0.8538 (mt) cc_final: 0.8319 (mp) REVERT: SU 113 GLU cc_start: 0.7971 (mp0) cc_final: 0.7435 (mp0) REVERT: Sc 18 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9279 (mt) REVERT: Sc 29 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: Sc 33 GLU cc_start: 0.8198 (pp20) cc_final: 0.7796 (pp20) REVERT: Sc 41 SER cc_start: 0.8667 (p) cc_final: 0.8444 (t) REVERT: Sc 60 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6413 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5207 (OUTLIER) cc_final: 0.4981 (tt0) REVERT: Sc 66 ARG cc_start: 0.7388 (mpp80) cc_final: 0.7054 (mtm-85) REVERT: Sd 5 GLN cc_start: 0.8736 (mp10) cc_final: 0.8346 (mp10) REVERT: Sd 13 LYS cc_start: 0.8589 (mmmm) cc_final: 0.8384 (mmmt) REVERT: Sg 14 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.7334 (p90) REVERT: Sg 195 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8493 (mm) REVERT: Sg 228 TYR cc_start: 0.7423 (t80) cc_final: 0.7165 (t80) REVERT: Sg 282 GLU cc_start: 0.9024 (mp0) cc_final: 0.8674 (pm20) REVERT: SM 58 GLU cc_start: 0.9034 (tp30) cc_final: 0.8612 (tp30) REVERT: SM 84 LYS cc_start: 0.9182 (tppt) cc_final: 0.8841 (tptp) REVERT: SZ 50 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8410 (p90) REVERT: Sf 103 LEU cc_start: 0.6951 (pt) cc_final: 0.6712 (pp) REVERT: Sf 107 LYS cc_start: 0.8706 (tptp) cc_final: 0.8469 (tptp) outliers start: 158 outliers final: 71 residues processed: 464 average time/residue: 0.6837 time to fit residues: 366.8247 Evaluate side-chains 416 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 332 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CD residue 286 GLU Chi-restraints excluded: chain CD residue 347 THR Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 46 THR Chi-restraints excluded: chain SD residue 94 ARG Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 26 ASP Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 79 HIS Chi-restraints excluded: chain SF residue 127 ARG Chi-restraints excluded: chain SF residue 141 VAL Chi-restraints excluded: chain SF residue 177 LEU Chi-restraints excluded: chain SK residue 35 LEU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SK residue 96 ARG Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 33 LEU Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 57 LEU Chi-restraints excluded: chain SP residue 65 LYS Chi-restraints excluded: chain SP residue 84 ILE Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SQ residue 26 LYS Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 41 MET Chi-restraints excluded: chain SQ residue 67 ASP Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 78 VAL Chi-restraints excluded: chain SQ residue 84 ILE Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SS residue 12 ILE Chi-restraints excluded: chain SS residue 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 45 LEU Chi-restraints excluded: chain SS residue 59 LEU Chi-restraints excluded: chain SS residue 73 ASN Chi-restraints excluded: chain SS residue 83 PHE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain SS residue 99 LEU Chi-restraints excluded: chain SS residue 115 LYS Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 28 LEU Chi-restraints excluded: chain ST residue 30 VAL Chi-restraints excluded: chain ST residue 41 LYS Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 29 GLN Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 62 GLU Chi-restraints excluded: chain Sg residue 14 HIS Chi-restraints excluded: chain Sg residue 62 HIS Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 144 ASP Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 195 LEU Chi-restraints excluded: chain Sg residue 287 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 312 VAL Chi-restraints excluded: chain SM residue 14 VAL Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain SZ residue 47 LEU Chi-restraints excluded: chain SZ residue 50 PHE Chi-restraints excluded: chain SZ residue 58 LEU Chi-restraints excluded: chain SZ residue 59 CYS Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 94 LYS Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 130 VAL Chi-restraints excluded: chain Sf residue 136 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 12 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SF 82 ASN SF 137 GLN SP 46 ASN ** SQ 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 97 GLN ST 137 GLN SU 92 HIS Sc 29 GLN ** Sg 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sg 305 ASN ** SM 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.072630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.054299 restraints weight = 77191.061| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.21 r_work: 0.2865 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27254 Z= 0.156 Angle : 0.685 13.499 39102 Z= 0.345 Chirality : 0.040 0.226 4767 Planarity : 0.005 0.122 3185 Dihedral : 22.467 168.554 9788 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.18 % Favored : 89.61 % Rotamer: Outliers : 8.68 % Allowed : 33.45 % Favored : 57.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.19), residues: 1916 helix: 0.17 (0.21), residues: 588 sheet: -1.35 (0.29), residues: 316 loop : -2.03 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGSc 31 TYR 0.015 0.001 TYRSD 34 PHE 0.025 0.002 PHESf 136 TRP 0.019 0.002 TRPSg 219 HIS 0.009 0.001 HISSg 188 Details of bonding type rmsd covalent geometry : bond 0.00328 (27254) covalent geometry : angle 0.68498 (39102) hydrogen bonds : bond 0.06131 ( 952) hydrogen bonds : angle 4.28304 ( 2152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 354 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CD 282 MET cc_start: 0.7642 (tpt) cc_final: 0.7235 (tpt) REVERT: CD 283 THR cc_start: 0.7936 (OUTLIER) cc_final: 0.7079 (t) REVERT: CD 287 TRP cc_start: 0.9075 (t-100) cc_final: 0.8649 (t-100) REVERT: SD 50 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8744 (mm) REVERT: SD 56 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8891 (tp-100) REVERT: SD 74 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8816 (tm-30) REVERT: SD 94 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8684 (ptp90) REVERT: SD 106 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8293 (ttp80) REVERT: SD 117 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8097 (ttm-80) REVERT: SF 25 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8607 (t) REVERT: SF 29 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8404 (mm-40) REVERT: SF 36 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: SF 83 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8540 (m110) REVERT: SK 29 MET cc_start: 0.9255 (ttm) cc_final: 0.8908 (ttp) REVERT: SK 89 ILE cc_start: 0.9150 (mp) cc_final: 0.8390 (mp) REVERT: SP 57 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9193 (mp) REVERT: SP 66 GLU cc_start: 0.8552 (mp0) cc_final: 0.8299 (mp0) REVERT: SQ 10 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.8887 (m) REVERT: SQ 107 GLU cc_start: 0.8906 (pp20) cc_final: 0.8638 (pp20) REVERT: SQ 116 ASP cc_start: 0.8481 (t0) cc_final: 0.8011 (t0) REVERT: SS 63 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8568 (mm-30) REVERT: SS 73 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8417 (p0) REVERT: ST 114 GLU cc_start: 0.8376 (pm20) cc_final: 0.8035 (pm20) REVERT: SU 113 GLU cc_start: 0.7925 (mp0) cc_final: 0.7605 (mp0) REVERT: Sc 18 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9169 (mt) REVERT: Sc 33 GLU cc_start: 0.8280 (pp20) cc_final: 0.7939 (pp20) REVERT: Sc 60 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6423 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5132 (OUTLIER) cc_final: 0.4921 (tt0) REVERT: Sg 14 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.7283 (p90) REVERT: Sg 140 TYR cc_start: 0.8232 (t80) cc_final: 0.7905 (t80) REVERT: Sg 195 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8434 (mm) REVERT: Sg 228 TYR cc_start: 0.7495 (t80) cc_final: 0.7255 (t80) REVERT: Sg 282 GLU cc_start: 0.9005 (mp0) cc_final: 0.8664 (pm20) REVERT: SM 88 TRP cc_start: 0.9243 (m-10) cc_final: 0.8871 (m-10) REVERT: Sf 103 LEU cc_start: 0.6881 (pt) cc_final: 0.6636 (pp) REVERT: Sf 107 LYS cc_start: 0.8726 (tptp) cc_final: 0.8521 (tptp) outliers start: 145 outliers final: 62 residues processed: 463 average time/residue: 0.6693 time to fit residues: 358.2476 Evaluate side-chains 412 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 334 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CD residue 283 THR Chi-restraints excluded: chain CD residue 286 GLU Chi-restraints excluded: chain CD residue 347 THR Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 46 THR Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 94 ARG Chi-restraints excluded: chain SD residue 106 ARG Chi-restraints excluded: chain SD residue 117 ARG Chi-restraints excluded: chain SD residue 153 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SF residue 17 ILE Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 26 ASP Chi-restraints excluded: chain SF residue 36 GLN Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 83 ASN Chi-restraints excluded: chain SF residue 141 VAL Chi-restraints excluded: chain SK residue 13 GLU Chi-restraints excluded: chain SK residue 35 LEU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 85 LEU Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 57 LEU Chi-restraints excluded: chain SP residue 84 ILE Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 26 LYS Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 67 ASP Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SS residue 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 59 LEU Chi-restraints excluded: chain SS residue 63 GLU Chi-restraints excluded: chain SS residue 73 ASN Chi-restraints excluded: chain SS residue 83 PHE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain SS residue 99 LEU Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 62 GLU Chi-restraints excluded: chain Sg residue 14 HIS Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 144 ASP Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 195 LEU Chi-restraints excluded: chain Sg residue 287 THR Chi-restraints excluded: chain Sg residue 306 LEU Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 312 VAL Chi-restraints excluded: chain Sg residue 313 THR Chi-restraints excluded: chain SM residue 14 VAL Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain SZ residue 47 LEU Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 94 LYS Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 130 VAL Chi-restraints excluded: chain Sf residue 143 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 225 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 226 GLN SF 82 ASN SP 46 ASN SP 54 HIS SQ 48 GLN SQ 97 GLN SU 92 HIS Sc 29 GLN ** Sg 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sg 64 HIS ** Sg 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 48 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.072462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.054069 restraints weight = 76950.483| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.26 r_work: 0.2859 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27254 Z= 0.160 Angle : 0.686 13.799 39102 Z= 0.345 Chirality : 0.040 0.219 4767 Planarity : 0.005 0.132 3185 Dihedral : 22.399 169.765 9788 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.23 % Favored : 89.61 % Rotamer: Outliers : 8.50 % Allowed : 33.39 % Favored : 58.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.19), residues: 1916 helix: 0.31 (0.22), residues: 586 sheet: -1.33 (0.29), residues: 318 loop : -1.97 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGSf 95 TYR 0.014 0.001 TYRSZ 65 PHE 0.019 0.002 PHESP 119 TRP 0.020 0.001 TRPSg 219 HIS 0.012 0.001 HISSg 188 Details of bonding type rmsd covalent geometry : bond 0.00335 (27254) covalent geometry : angle 0.68637 (39102) hydrogen bonds : bond 0.06052 ( 952) hydrogen bonds : angle 4.13936 ( 2152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 348 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CD 283 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7544 (t) REVERT: CD 287 TRP cc_start: 0.9045 (t-100) cc_final: 0.8705 (t-100) REVERT: SD 50 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8677 (mm) REVERT: SD 56 GLN cc_start: 0.9161 (tp-100) cc_final: 0.8869 (tp-100) REVERT: SD 74 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8844 (tm-30) REVERT: SD 94 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8745 (ptp90) REVERT: SD 106 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8258 (ttp80) REVERT: SD 117 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8088 (ttm-80) REVERT: SD 157 MET cc_start: 0.9052 (tpp) cc_final: 0.8845 (tpp) REVERT: SF 25 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8664 (t) REVERT: SF 83 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8415 (m110) REVERT: SF 136 ARG cc_start: 0.7397 (mtp180) cc_final: 0.7057 (mtp85) REVERT: SK 29 MET cc_start: 0.9316 (ttm) cc_final: 0.8965 (ttp) REVERT: SK 31 LYS cc_start: 0.9367 (mptp) cc_final: 0.9026 (mptp) REVERT: SK 89 ILE cc_start: 0.9145 (mp) cc_final: 0.8611 (mp) REVERT: SP 23 ASP cc_start: 0.9099 (m-30) cc_final: 0.8822 (m-30) REVERT: SP 27 ASP cc_start: 0.8889 (m-30) cc_final: 0.8632 (m-30) REVERT: SP 66 GLU cc_start: 0.8632 (mp0) cc_final: 0.8421 (mp0) REVERT: SQ 107 GLU cc_start: 0.8953 (pp20) cc_final: 0.8666 (pp20) REVERT: SQ 116 ASP cc_start: 0.8528 (t0) cc_final: 0.8073 (t0) REVERT: SS 63 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8611 (mm-30) REVERT: ST 111 LYS cc_start: 0.9413 (mmmm) cc_final: 0.9158 (mppt) REVERT: ST 114 GLU cc_start: 0.8380 (pm20) cc_final: 0.7917 (pm20) REVERT: SU 113 GLU cc_start: 0.7912 (mp0) cc_final: 0.7458 (mp0) REVERT: Sc 28 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8648 (p) REVERT: Sc 33 GLU cc_start: 0.8309 (pp20) cc_final: 0.7729 (pp20) REVERT: Sc 60 GLU cc_start: 0.6896 (tm-30) cc_final: 0.6339 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5157 (OUTLIER) cc_final: 0.4937 (tt0) REVERT: Sd 5 GLN cc_start: 0.8812 (mp10) cc_final: 0.8322 (mp10) REVERT: Sd 13 LYS cc_start: 0.8520 (mmmm) cc_final: 0.8320 (mmmt) REVERT: Sg 14 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.7115 (p90) REVERT: Sg 42 MET cc_start: 0.8733 (ttm) cc_final: 0.8253 (ptm) REVERT: Sg 79 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8877 (pt) REVERT: Sg 113 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8889 (m-80) REVERT: Sg 140 TYR cc_start: 0.8349 (t80) cc_final: 0.8028 (t80) REVERT: Sg 195 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8348 (mm) REVERT: Sg 228 TYR cc_start: 0.7543 (t80) cc_final: 0.7310 (t80) REVERT: Sg 282 GLU cc_start: 0.8954 (mp0) cc_final: 0.8642 (pm20) REVERT: SM 37 GLU cc_start: 0.8239 (mp0) cc_final: 0.7908 (mp0) REVERT: SM 88 TRP cc_start: 0.9253 (m-10) cc_final: 0.8898 (m-10) outliers start: 142 outliers final: 70 residues processed: 454 average time/residue: 0.6358 time to fit residues: 335.2004 Evaluate side-chains 416 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 332 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CD residue 283 THR Chi-restraints excluded: chain CD residue 286 GLU Chi-restraints excluded: chain CD residue 346 ILE Chi-restraints excluded: chain CD residue 347 THR Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 46 THR Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 94 ARG Chi-restraints excluded: chain SD residue 104 SER Chi-restraints excluded: chain SD residue 106 ARG Chi-restraints excluded: chain SD residue 117 ARG Chi-restraints excluded: chain SD residue 153 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 26 ASP Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 83 ASN Chi-restraints excluded: chain SF residue 141 VAL Chi-restraints excluded: chain SK residue 13 GLU Chi-restraints excluded: chain SK residue 35 LEU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 85 LEU Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 57 LEU Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SQ residue 26 LYS Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 42 ILE Chi-restraints excluded: chain SQ residue 48 GLN Chi-restraints excluded: chain SQ residue 67 ASP Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SQ residue 110 ASP Chi-restraints excluded: chain SQ residue 127 CYS Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SS residue 12 ILE Chi-restraints excluded: chain SS residue 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 63 GLU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 83 PHE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain SS residue 99 LEU Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 62 GLU Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 14 HIS Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 64 HIS Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 79 LEU Chi-restraints excluded: chain Sg residue 113 PHE Chi-restraints excluded: chain Sg residue 144 ASP Chi-restraints excluded: chain Sg residue 147 HIS Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 168 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 195 LEU Chi-restraints excluded: chain Sg residue 287 THR Chi-restraints excluded: chain Sg residue 306 LEU Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 312 VAL Chi-restraints excluded: chain Sg residue 313 THR Chi-restraints excluded: chain SM residue 14 VAL Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain SZ residue 58 LEU Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 130 VAL Chi-restraints excluded: chain Sf residue 136 PHE Chi-restraints excluded: chain Sf residue 143 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 178 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CD 349 GLN SF 82 ASN SP 46 ASN SQ 97 GLN SU 92 HIS Sc 29 GLN ** Sg 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sg 64 HIS Sg 143 GLN ** Sg 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 19 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.069236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.050609 restraints weight = 77624.483| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.21 r_work: 0.2759 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 27254 Z= 0.292 Angle : 0.753 15.235 39102 Z= 0.380 Chirality : 0.044 0.262 4767 Planarity : 0.006 0.124 3185 Dihedral : 22.412 165.219 9788 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.59 % Favored : 89.09 % Rotamer: Outliers : 8.86 % Allowed : 33.87 % Favored : 57.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.19), residues: 1916 helix: 0.30 (0.22), residues: 580 sheet: -1.37 (0.28), residues: 320 loop : -1.99 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGSc 66 TYR 0.022 0.002 TYRSZ 65 PHE 0.025 0.002 PHESf 136 TRP 0.021 0.002 TRPSg 219 HIS 0.024 0.002 HISSg 64 Details of bonding type rmsd covalent geometry : bond 0.00601 (27254) covalent geometry : angle 0.75315 (39102) hydrogen bonds : bond 0.06733 ( 952) hydrogen bonds : angle 4.15068 ( 2152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 347 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CD 283 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.6685 (t) REVERT: CD 287 TRP cc_start: 0.9025 (t-100) cc_final: 0.8561 (t-100) REVERT: CD 349 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8669 (pm20) REVERT: SD 50 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8802 (mm) REVERT: SD 56 GLN cc_start: 0.9172 (tp-100) cc_final: 0.8807 (tp-100) REVERT: SD 74 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8762 (tm-30) REVERT: SD 94 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8717 (ptp90) REVERT: SD 106 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8352 (ttp80) REVERT: SD 117 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8325 (ttt90) REVERT: SF 45 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8014 (p90) REVERT: SF 146 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8301 (ttt90) REVERT: SK 29 MET cc_start: 0.9296 (ttm) cc_final: 0.8968 (ttp) REVERT: SK 31 LYS cc_start: 0.9426 (mptp) cc_final: 0.9086 (mptp) REVERT: SK 80 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8419 (tpp-160) REVERT: SK 89 ILE cc_start: 0.9241 (mp) cc_final: 0.8398 (mp) REVERT: SP 27 ASP cc_start: 0.8873 (m-30) cc_final: 0.8598 (m-30) REVERT: SP 31 GLU cc_start: 0.8966 (mp0) cc_final: 0.8686 (mp0) REVERT: SP 34 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: SQ 107 GLU cc_start: 0.8985 (pp20) cc_final: 0.8768 (pp20) REVERT: SQ 116 ASP cc_start: 0.8555 (t0) cc_final: 0.8055 (t0) REVERT: ST 111 LYS cc_start: 0.9395 (mmmm) cc_final: 0.9147 (mppt) REVERT: ST 114 GLU cc_start: 0.8394 (pm20) cc_final: 0.7920 (pm20) REVERT: SU 21 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7726 (ttm170) REVERT: SU 92 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.7260 (t-90) REVERT: SU 113 GLU cc_start: 0.7883 (mp0) cc_final: 0.7615 (mp0) REVERT: Sc 18 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9323 (mt) REVERT: Sc 33 GLU cc_start: 0.8326 (pp20) cc_final: 0.7676 (pp20) REVERT: Sc 60 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6371 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5310 (OUTLIER) cc_final: 0.5103 (tt0) REVERT: Sg 14 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.7342 (p90) REVERT: Sg 27 PHE cc_start: 0.9402 (m-80) cc_final: 0.9175 (m-80) REVERT: Sg 79 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8893 (pt) REVERT: Sg 113 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.9023 (m-80) REVERT: Sg 140 TYR cc_start: 0.8335 (t80) cc_final: 0.8123 (t80) REVERT: Sg 195 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8413 (mm) REVERT: Sg 217 MET cc_start: 0.7285 (pmm) cc_final: 0.7080 (pmt) REVERT: Sg 228 TYR cc_start: 0.7575 (t80) cc_final: 0.7285 (t80) REVERT: Sg 282 GLU cc_start: 0.8890 (mp0) cc_final: 0.8642 (pm20) REVERT: SM 37 GLU cc_start: 0.8343 (mp0) cc_final: 0.8081 (mp0) REVERT: SM 58 GLU cc_start: 0.8858 (tp30) cc_final: 0.8120 (tp30) REVERT: SM 88 TRP cc_start: 0.9244 (m-10) cc_final: 0.8893 (m-10) REVERT: Sf 107 LYS cc_start: 0.8941 (tppt) cc_final: 0.8617 (ttpp) REVERT: Sf 113 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8402 (mmtp) REVERT: Sf 117 LEU cc_start: 0.9215 (mp) cc_final: 0.8986 (mp) outliers start: 148 outliers final: 79 residues processed: 455 average time/residue: 0.5757 time to fit residues: 304.7179 Evaluate side-chains 436 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 339 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CD residue 283 THR Chi-restraints excluded: chain CD residue 346 ILE Chi-restraints excluded: chain CD residue 347 THR Chi-restraints excluded: chain CD residue 349 GLN Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 46 THR Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 94 ARG Chi-restraints excluded: chain SD residue 106 ARG Chi-restraints excluded: chain SD residue 117 ARG Chi-restraints excluded: chain SD residue 169 ASP Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SD residue 204 LEU Chi-restraints excluded: chain SD residue 218 LEU Chi-restraints excluded: chain SF residue 17 ILE Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 26 ASP Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 79 HIS Chi-restraints excluded: chain SF residue 141 VAL Chi-restraints excluded: chain SF residue 146 ARG Chi-restraints excluded: chain SK residue 13 GLU Chi-restraints excluded: chain SK residue 35 LEU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 80 ARG Chi-restraints excluded: chain SK residue 85 LEU Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 57 LEU Chi-restraints excluded: chain SP residue 74 GLU Chi-restraints excluded: chain SP residue 76 VAL Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SQ residue 26 LYS Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 78 VAL Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 111 ILE Chi-restraints excluded: chain SQ residue 127 CYS Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SS residue 12 ILE Chi-restraints excluded: chain SS residue 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 59 LEU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain SS residue 99 LEU Chi-restraints excluded: chain SS residue 116 LYS Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 28 LEU Chi-restraints excluded: chain ST residue 36 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 121 ARG Chi-restraints excluded: chain SU residue 21 ARG Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 92 HIS Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 112 VAL Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 62 GLU Chi-restraints excluded: chain Sc residue 64 GLU Chi-restraints excluded: chain Sd residue 25 SER Chi-restraints excluded: chain Sg residue 14 HIS Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 52 TYR Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 79 LEU Chi-restraints excluded: chain Sg residue 113 PHE Chi-restraints excluded: chain Sg residue 144 ASP Chi-restraints excluded: chain Sg residue 147 HIS Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 168 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 195 LEU Chi-restraints excluded: chain Sg residue 287 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 312 VAL Chi-restraints excluded: chain Sg residue 313 THR Chi-restraints excluded: chain SM residue 14 VAL Chi-restraints excluded: chain SM residue 31 LEU Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 94 LYS Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 130 VAL Chi-restraints excluded: chain Sf residue 143 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 111 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 216 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CD 349 GLN SF 82 ASN SP 46 ASN SQ 48 GLN SQ 97 GLN SU 92 HIS Sc 29 GLN Sg 62 HIS Sg 64 HIS ** Sg 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.072255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053960 restraints weight = 77912.318| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.24 r_work: 0.2862 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27254 Z= 0.140 Angle : 0.707 13.738 39102 Z= 0.354 Chirality : 0.040 0.268 4767 Planarity : 0.005 0.130 3185 Dihedral : 22.379 170.876 9788 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.02 % Favored : 89.82 % Rotamer: Outliers : 7.78 % Allowed : 35.25 % Favored : 56.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.19), residues: 1916 helix: 0.37 (0.22), residues: 587 sheet: -1.31 (0.28), residues: 318 loop : -1.92 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGSc 31 TYR 0.020 0.001 TYRSM 61 PHE 0.023 0.002 PHESf 136 TRP 0.017 0.001 TRPSg 219 HIS 0.015 0.001 HISSU 92 Details of bonding type rmsd covalent geometry : bond 0.00297 (27254) covalent geometry : angle 0.70652 (39102) hydrogen bonds : bond 0.05835 ( 952) hydrogen bonds : angle 4.05713 ( 2152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 363 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SD 56 GLN cc_start: 0.9221 (tp-100) cc_final: 0.8920 (tp-100) REVERT: SD 74 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8522 (tm-30) REVERT: SD 106 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8234 (ttp80) REVERT: SD 117 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8109 (ttt90) REVERT: SF 25 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8732 (t) REVERT: SF 27 ASP cc_start: 0.8279 (p0) cc_final: 0.8058 (p0) REVERT: SK 29 MET cc_start: 0.9276 (ttm) cc_final: 0.8919 (ttp) REVERT: SK 31 LYS cc_start: 0.9427 (mptp) cc_final: 0.9030 (mptp) REVERT: SK 80 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8507 (tpp-160) REVERT: SK 89 ILE cc_start: 0.9073 (mp) cc_final: 0.8739 (mp) REVERT: SP 23 ASP cc_start: 0.9124 (m-30) cc_final: 0.8665 (m-30) REVERT: SP 27 ASP cc_start: 0.8934 (m-30) cc_final: 0.8637 (m-30) REVERT: SP 31 GLU cc_start: 0.9075 (mp0) cc_final: 0.8769 (mp0) REVERT: SP 34 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8335 (mtm) REVERT: SP 66 GLU cc_start: 0.8550 (mp0) cc_final: 0.8270 (mp0) REVERT: SQ 107 GLU cc_start: 0.8977 (pp20) cc_final: 0.8709 (pp20) REVERT: SQ 116 ASP cc_start: 0.8537 (t0) cc_final: 0.8043 (t0) REVERT: ST 35 ASP cc_start: 0.9107 (p0) cc_final: 0.8880 (p0) REVERT: ST 111 LYS cc_start: 0.9441 (mmmm) cc_final: 0.9166 (mppt) REVERT: ST 114 GLU cc_start: 0.8316 (pm20) cc_final: 0.7921 (pm20) REVERT: SU 21 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7689 (ttm170) REVERT: SU 113 GLU cc_start: 0.7943 (mp0) cc_final: 0.7423 (mp0) REVERT: Sc 18 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9256 (mt) REVERT: Sc 33 GLU cc_start: 0.8342 (pp20) cc_final: 0.7835 (pp20) REVERT: Sc 60 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6493 (tm-30) REVERT: Sd 5 GLN cc_start: 0.8851 (mp10) cc_final: 0.8313 (mp10) REVERT: Sg 14 HIS cc_start: 0.8645 (OUTLIER) cc_final: 0.7107 (p90) REVERT: Sg 42 MET cc_start: 0.8679 (ttm) cc_final: 0.8318 (ptm) REVERT: Sg 140 TYR cc_start: 0.8330 (t80) cc_final: 0.8007 (t80) REVERT: Sg 150 TRP cc_start: 0.8037 (m100) cc_final: 0.7580 (m-10) REVERT: Sg 195 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8408 (mm) REVERT: Sg 228 TYR cc_start: 0.7549 (t80) cc_final: 0.7278 (t80) REVERT: Sg 282 GLU cc_start: 0.8949 (mp0) cc_final: 0.8677 (pm20) REVERT: SM 37 GLU cc_start: 0.8236 (mp0) cc_final: 0.7952 (mp0) REVERT: SM 58 GLU cc_start: 0.8766 (tp30) cc_final: 0.8494 (tp30) REVERT: SM 60 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8853 (pmm) REVERT: SM 84 LYS cc_start: 0.9214 (tppt) cc_final: 0.8966 (tppp) REVERT: Sf 107 LYS cc_start: 0.8933 (tppt) cc_final: 0.8651 (ttpp) REVERT: Sf 113 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8247 (mmtp) outliers start: 130 outliers final: 54 residues processed: 453 average time/residue: 0.6089 time to fit residues: 320.4571 Evaluate side-chains 419 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 355 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CD residue 346 ILE Chi-restraints excluded: chain CD residue 347 THR Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 46 THR Chi-restraints excluded: chain SD residue 106 ARG Chi-restraints excluded: chain SD residue 117 ARG Chi-restraints excluded: chain SD residue 153 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SF residue 17 ILE Chi-restraints excluded: chain SF residue 19 LEU Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 26 ASP Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SK residue 13 GLU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 80 ARG Chi-restraints excluded: chain SK residue 85 LEU Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 67 ASP Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SS residue 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 99 LEU Chi-restraints excluded: chain SS residue 116 LYS Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain SU residue 21 ARG Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 64 GLU Chi-restraints excluded: chain Sg residue 14 HIS Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 52 TYR Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 168 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 195 LEU Chi-restraints excluded: chain Sg residue 287 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 312 VAL Chi-restraints excluded: chain Sg residue 313 THR Chi-restraints excluded: chain SM residue 14 VAL Chi-restraints excluded: chain SM residue 60 MET Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 94 LYS Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain Sf residue 98 VAL Chi-restraints excluded: chain Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 130 VAL Chi-restraints excluded: chain Sf residue 143 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 174 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 189 optimal weight: 5.9990 chunk 6 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SF 82 ASN SP 24 GLN SP 46 ASN SQ 97 GLN Sc 29 GLN Sg 62 HIS Sg 64 HIS ** Sg 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 19 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.070807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.052428 restraints weight = 77763.079| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.22 r_work: 0.2816 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27254 Z= 0.185 Angle : 0.719 13.819 39102 Z= 0.362 Chirality : 0.041 0.236 4767 Planarity : 0.005 0.127 3185 Dihedral : 22.326 168.773 9782 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.28 % Favored : 89.56 % Rotamer: Outliers : 6.16 % Allowed : 37.46 % Favored : 56.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.19), residues: 1916 helix: 0.50 (0.22), residues: 576 sheet: -1.28 (0.28), residues: 322 loop : -1.92 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGSc 51 TYR 0.026 0.002 TYRSF 188 PHE 0.025 0.002 PHESF 61 TRP 0.020 0.001 TRPCD 287 HIS 0.013 0.001 HISSg 188 Details of bonding type rmsd covalent geometry : bond 0.00389 (27254) covalent geometry : angle 0.71928 (39102) hydrogen bonds : bond 0.06052 ( 952) hydrogen bonds : angle 4.05978 ( 2152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 352 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SD 50 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8639 (mm) REVERT: SD 56 GLN cc_start: 0.9176 (tp-100) cc_final: 0.8827 (tp-100) REVERT: SD 74 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8629 (tm-30) REVERT: SD 106 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8254 (ttp80) REVERT: SD 117 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8163 (ttm-80) REVERT: SF 25 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8814 (t) REVERT: SK 29 MET cc_start: 0.9275 (ttm) cc_final: 0.8915 (ttp) REVERT: SK 31 LYS cc_start: 0.9401 (mptp) cc_final: 0.9052 (mptp) REVERT: SK 80 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8520 (tpp-160) REVERT: SK 89 ILE cc_start: 0.8999 (mp) cc_final: 0.8717 (mp) REVERT: SP 23 ASP cc_start: 0.8987 (m-30) cc_final: 0.8563 (m-30) REVERT: SP 27 ASP cc_start: 0.8832 (m-30) cc_final: 0.8562 (m-30) REVERT: SP 31 GLU cc_start: 0.8912 (mp0) cc_final: 0.8649 (mp0) REVERT: SP 34 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8391 (mtm) REVERT: SP 66 GLU cc_start: 0.8448 (mp0) cc_final: 0.8225 (mp0) REVERT: SQ 107 GLU cc_start: 0.8990 (pp20) cc_final: 0.8730 (pp20) REVERT: SQ 116 ASP cc_start: 0.8548 (t0) cc_final: 0.8061 (t0) REVERT: ST 35 ASP cc_start: 0.9092 (p0) cc_final: 0.8880 (p0) REVERT: ST 114 GLU cc_start: 0.8364 (pm20) cc_final: 0.7941 (pm20) REVERT: SU 92 HIS cc_start: 0.7585 (m90) cc_final: 0.7099 (t70) REVERT: SU 113 GLU cc_start: 0.7841 (mp0) cc_final: 0.7531 (mp0) REVERT: Sc 18 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9285 (mt) REVERT: Sc 31 ARG cc_start: 0.8591 (tpp80) cc_final: 0.8248 (tpp80) REVERT: Sc 33 GLU cc_start: 0.8342 (pp20) cc_final: 0.7629 (pp20) REVERT: Sc 60 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6705 (tm-30) REVERT: Sd 5 GLN cc_start: 0.8967 (mp10) cc_final: 0.8442 (mp10) REVERT: Sg 14 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.7278 (p90) REVERT: Sg 140 TYR cc_start: 0.8382 (t80) cc_final: 0.8089 (t80) REVERT: Sg 150 TRP cc_start: 0.7991 (m100) cc_final: 0.7628 (m-10) REVERT: Sg 195 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8378 (mm) REVERT: Sg 228 TYR cc_start: 0.7548 (t80) cc_final: 0.7208 (t80) REVERT: Sg 282 GLU cc_start: 0.8865 (mp0) cc_final: 0.8642 (pm20) REVERT: SM 23 LYS cc_start: 0.8895 (mppt) cc_final: 0.8574 (mptt) REVERT: SM 37 GLU cc_start: 0.8279 (mp0) cc_final: 0.7967 (mp0) REVERT: SM 63 LYS cc_start: 0.9235 (ptmt) cc_final: 0.8886 (pptt) REVERT: SM 78 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8857 (mmmm) REVERT: SM 83 LYS cc_start: 0.9152 (mmmt) cc_final: 0.8893 (mmmt) REVERT: SM 84 LYS cc_start: 0.9204 (tppt) cc_final: 0.8934 (tppp) REVERT: Sf 107 LYS cc_start: 0.8974 (tppt) cc_final: 0.8725 (ttpp) REVERT: Sf 113 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8319 (mmtp) REVERT: Sf 117 LEU cc_start: 0.9284 (mp) cc_final: 0.9038 (mp) REVERT: Sf 119 ARG cc_start: 0.8342 (mtm180) cc_final: 0.8074 (mmm-85) outliers start: 103 outliers final: 69 residues processed: 421 average time/residue: 0.6162 time to fit residues: 300.2256 Evaluate side-chains 423 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 345 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CD residue 347 THR Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 46 THR Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 106 ARG Chi-restraints excluded: chain SD residue 117 ARG Chi-restraints excluded: chain SD residue 153 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SD residue 218 LEU Chi-restraints excluded: chain SF residue 17 ILE Chi-restraints excluded: chain SF residue 19 LEU Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 26 ASP Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 141 VAL Chi-restraints excluded: chain SK residue 13 GLU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 80 ARG Chi-restraints excluded: chain SK residue 85 LEU Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 67 ASP Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 111 ILE Chi-restraints excluded: chain SQ residue 127 CYS Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SS residue 12 ILE Chi-restraints excluded: chain SS residue 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain SS residue 99 LEU Chi-restraints excluded: chain SS residue 116 LYS Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 28 LEU Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 50 VAL Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 64 GLU Chi-restraints excluded: chain Sd residue 25 SER Chi-restraints excluded: chain Sg residue 14 HIS Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 52 TYR Chi-restraints excluded: chain Sg residue 64 HIS Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 147 HIS Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 168 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 195 LEU Chi-restraints excluded: chain Sg residue 287 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 312 VAL Chi-restraints excluded: chain Sg residue 313 THR Chi-restraints excluded: chain SM residue 14 VAL Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain SM residue 123 VAL Chi-restraints excluded: chain SZ residue 47 LEU Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 94 LYS Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 130 VAL Chi-restraints excluded: chain Sf residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 203 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SF 82 ASN SP 24 GLN SP 46 ASN SQ 97 GLN Sc 29 GLN ** Sg 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sg 64 HIS ** Sg 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.069081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.050458 restraints weight = 78190.425| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.20 r_work: 0.2760 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27254 Z= 0.257 Angle : 0.771 15.050 39102 Z= 0.389 Chirality : 0.043 0.229 4767 Planarity : 0.005 0.125 3185 Dihedral : 22.346 165.210 9782 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.07 % Favored : 89.67 % Rotamer: Outliers : 6.10 % Allowed : 37.40 % Favored : 56.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.19), residues: 1916 helix: 0.41 (0.22), residues: 585 sheet: -1.28 (0.28), residues: 319 loop : -1.93 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGSU 41 TYR 0.021 0.002 TYRSZ 65 PHE 0.050 0.003 PHESg 65 TRP 0.035 0.002 TRPCD 287 HIS 0.010 0.002 HISSg 188 Details of bonding type rmsd covalent geometry : bond 0.00534 (27254) covalent geometry : angle 0.77089 (39102) hydrogen bonds : bond 0.06522 ( 952) hydrogen bonds : angle 4.10325 ( 2152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 355 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CD 287 TRP cc_start: 0.9001 (t-100) cc_final: 0.8418 (t-100) REVERT: SD 50 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8734 (mm) REVERT: SD 56 GLN cc_start: 0.9232 (tp-100) cc_final: 0.8899 (tp-100) REVERT: SD 74 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8680 (tm-30) REVERT: SD 117 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8289 (ttm-80) REVERT: SD 157 MET cc_start: 0.9067 (tpp) cc_final: 0.8840 (tpp) REVERT: SF 25 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8915 (t) REVERT: SF 60 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8551 (mtp180) REVERT: SF 204 ARG cc_start: 0.5589 (OUTLIER) cc_final: 0.3580 (ttp80) REVERT: SK 5 LYS cc_start: 0.8800 (ttpm) cc_final: 0.8595 (ttmm) REVERT: SK 29 MET cc_start: 0.9329 (ttm) cc_final: 0.8946 (ttp) REVERT: SK 31 LYS cc_start: 0.9427 (mptp) cc_final: 0.9001 (mptp) REVERT: SK 80 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8368 (tpp-160) REVERT: SK 89 ILE cc_start: 0.9023 (mp) cc_final: 0.8692 (mp) REVERT: SP 23 ASP cc_start: 0.9087 (m-30) cc_final: 0.8782 (m-30) REVERT: SP 27 ASP cc_start: 0.8970 (m-30) cc_final: 0.8706 (m-30) REVERT: SP 31 GLU cc_start: 0.9042 (mp0) cc_final: 0.8819 (mp0) REVERT: SP 34 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8395 (mtm) REVERT: SQ 107 GLU cc_start: 0.9011 (pp20) cc_final: 0.8745 (pp20) REVERT: SQ 116 ASP cc_start: 0.8547 (t0) cc_final: 0.8051 (t0) REVERT: ST 35 ASP cc_start: 0.9166 (p0) cc_final: 0.8943 (p0) REVERT: ST 114 GLU cc_start: 0.8380 (pm20) cc_final: 0.7980 (pm20) REVERT: SU 44 LYS cc_start: 0.9440 (mmmm) cc_final: 0.9235 (mmtm) REVERT: SU 92 HIS cc_start: 0.7575 (m90) cc_final: 0.7182 (t70) REVERT: SU 113 GLU cc_start: 0.7935 (mp0) cc_final: 0.7637 (mp0) REVERT: Sc 18 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9347 (mt) REVERT: Sc 33 GLU cc_start: 0.8424 (pp20) cc_final: 0.7771 (pp20) REVERT: Sd 5 GLN cc_start: 0.9030 (mp10) cc_final: 0.8520 (mp10) REVERT: Sg 14 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.7366 (p90) REVERT: Sg 27 PHE cc_start: 0.9419 (m-80) cc_final: 0.9200 (m-80) REVERT: Sg 42 MET cc_start: 0.8707 (ttm) cc_final: 0.8285 (ptm) REVERT: Sg 150 TRP cc_start: 0.8126 (m100) cc_final: 0.7621 (m-10) REVERT: Sg 195 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8446 (mm) REVERT: Sg 228 TYR cc_start: 0.7613 (t80) cc_final: 0.7252 (t80) REVERT: Sg 282 GLU cc_start: 0.8984 (mp0) cc_final: 0.8697 (pm20) REVERT: SM 37 GLU cc_start: 0.8417 (mp0) cc_final: 0.8160 (mp0) REVERT: SM 63 LYS cc_start: 0.9269 (ptmt) cc_final: 0.8955 (pptt) REVERT: SM 78 LYS cc_start: 0.9138 (mmmm) cc_final: 0.8868 (mmmm) REVERT: SM 84 LYS cc_start: 0.9227 (tppt) cc_final: 0.8966 (tppp) REVERT: SZ 50 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8334 (p90) REVERT: Sf 117 LEU cc_start: 0.9196 (mp) cc_final: 0.8948 (mp) REVERT: Sf 119 ARG cc_start: 0.8540 (mtm180) cc_final: 0.8306 (mmm-85) outliers start: 102 outliers final: 70 residues processed: 426 average time/residue: 0.5770 time to fit residues: 285.1530 Evaluate side-chains 429 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 348 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CD residue 347 THR Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 46 THR Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 117 ARG Chi-restraints excluded: chain SD residue 153 VAL Chi-restraints excluded: chain SD residue 169 ASP Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SF residue 17 ILE Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 26 ASP Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 60 ARG Chi-restraints excluded: chain SF residue 204 ARG Chi-restraints excluded: chain SK residue 13 GLU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 80 ARG Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 76 VAL Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 67 ASP Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 110 ASP Chi-restraints excluded: chain SQ residue 111 ILE Chi-restraints excluded: chain SQ residue 127 CYS Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SS residue 12 ILE Chi-restraints excluded: chain SS residue 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 59 LEU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain SS residue 99 LEU Chi-restraints excluded: chain SS residue 116 LYS Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 28 LEU Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 121 ARG Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 50 VAL Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 37 ASP Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 64 GLU Chi-restraints excluded: chain Sd residue 25 SER Chi-restraints excluded: chain Sg residue 14 HIS Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 52 TYR Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 168 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 195 LEU Chi-restraints excluded: chain Sg residue 261 LEU Chi-restraints excluded: chain Sg residue 287 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 312 VAL Chi-restraints excluded: chain SM residue 14 VAL Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain SM residue 123 VAL Chi-restraints excluded: chain SZ residue 47 LEU Chi-restraints excluded: chain SZ residue 50 PHE Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 94 LYS Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sf residue 98 VAL Chi-restraints excluded: chain Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 130 VAL Chi-restraints excluded: chain Sf residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 233 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SF 82 ASN SP 24 GLN SP 46 ASN SQ 48 GLN SQ 97 GLN SU 92 HIS Sc 29 GLN Sg 62 HIS ** Sg 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.069016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.050456 restraints weight = 77998.269| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.20 r_work: 0.2761 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27254 Z= 0.244 Angle : 0.777 14.910 39102 Z= 0.391 Chirality : 0.043 0.215 4767 Planarity : 0.006 0.143 3185 Dihedral : 22.357 165.905 9782 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.33 % Favored : 89.46 % Rotamer: Outliers : 5.86 % Allowed : 38.24 % Favored : 55.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.19), residues: 1916 helix: 0.43 (0.22), residues: 585 sheet: -1.29 (0.28), residues: 319 loop : -1.94 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGSc 66 TYR 0.020 0.002 TYRSZ 65 PHE 0.028 0.002 PHESF 61 TRP 0.032 0.002 TRPCD 287 HIS 0.012 0.001 HISSg 188 Details of bonding type rmsd covalent geometry : bond 0.00509 (27254) covalent geometry : angle 0.77734 (39102) hydrogen bonds : bond 0.06346 ( 952) hydrogen bonds : angle 4.12294 ( 2152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 350 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SD 50 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8772 (mm) REVERT: SD 56 GLN cc_start: 0.9231 (tp-100) cc_final: 0.8786 (tp-100) REVERT: SD 74 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8662 (tm-30) REVERT: SD 117 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8243 (ttm-80) REVERT: SF 25 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8894 (t) REVERT: SF 45 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.8007 (p90) REVERT: SF 60 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8472 (mtp180) REVERT: SF 204 ARG cc_start: 0.5563 (OUTLIER) cc_final: 0.3557 (ttp80) REVERT: SK 5 LYS cc_start: 0.8803 (ttpm) cc_final: 0.8603 (ttmm) REVERT: SK 29 MET cc_start: 0.9320 (ttm) cc_final: 0.8930 (ttp) REVERT: SK 31 LYS cc_start: 0.9422 (mptp) cc_final: 0.9017 (mptp) REVERT: SK 80 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8382 (tpp-160) REVERT: SK 89 ILE cc_start: 0.9087 (mp) cc_final: 0.8787 (mp) REVERT: SP 23 ASP cc_start: 0.9027 (m-30) cc_final: 0.8556 (m-30) REVERT: SP 27 ASP cc_start: 0.8961 (m-30) cc_final: 0.8671 (m-30) REVERT: SP 31 GLU cc_start: 0.9038 (mp0) cc_final: 0.8790 (mp0) REVERT: SP 34 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8364 (mtm) REVERT: SQ 107 GLU cc_start: 0.9005 (pp20) cc_final: 0.8763 (pp20) REVERT: SQ 116 ASP cc_start: 0.8515 (t0) cc_final: 0.8035 (t0) REVERT: ST 35 ASP cc_start: 0.9172 (p0) cc_final: 0.8934 (p0) REVERT: ST 114 GLU cc_start: 0.8379 (pm20) cc_final: 0.7979 (pm20) REVERT: ST 143 LYS cc_start: 0.9031 (tppt) cc_final: 0.8794 (tppt) REVERT: SU 44 LYS cc_start: 0.9447 (mmmm) cc_final: 0.9231 (mmtm) REVERT: SU 92 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.7247 (t70) REVERT: SU 113 GLU cc_start: 0.7919 (mp0) cc_final: 0.7623 (mp0) REVERT: Sc 18 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9342 (mt) REVERT: Sc 33 GLU cc_start: 0.8410 (pp20) cc_final: 0.7890 (pp20) REVERT: Sd 5 GLN cc_start: 0.9031 (mp10) cc_final: 0.8505 (mp10) REVERT: Sg 14 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.7407 (p90) REVERT: Sg 27 PHE cc_start: 0.9451 (m-80) cc_final: 0.9235 (m-80) REVERT: Sg 42 MET cc_start: 0.8725 (ttm) cc_final: 0.8245 (ptm) REVERT: Sg 150 TRP cc_start: 0.8125 (m100) cc_final: 0.7633 (m-10) REVERT: Sg 195 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8452 (mm) REVERT: Sg 228 TYR cc_start: 0.7623 (t80) cc_final: 0.7255 (t80) REVERT: Sg 282 GLU cc_start: 0.8956 (mp0) cc_final: 0.8681 (pm20) REVERT: SM 23 LYS cc_start: 0.9553 (mmmm) cc_final: 0.9203 (mppt) REVERT: SM 37 GLU cc_start: 0.8378 (mp0) cc_final: 0.8126 (mp0) REVERT: SM 63 LYS cc_start: 0.9215 (ptmt) cc_final: 0.8853 (pptt) REVERT: SM 78 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8866 (mmmm) REVERT: SM 83 LYS cc_start: 0.9339 (mmmm) cc_final: 0.9123 (mmmt) REVERT: SM 84 LYS cc_start: 0.9206 (tppt) cc_final: 0.8912 (tppp) REVERT: Sf 117 LEU cc_start: 0.9184 (mp) cc_final: 0.8907 (mp) REVERT: Sf 118 ARG cc_start: 0.8618 (mpt-90) cc_final: 0.8034 (mpt-90) REVERT: Sf 119 ARG cc_start: 0.8597 (mtm180) cc_final: 0.8339 (mmm-85) outliers start: 98 outliers final: 67 residues processed: 416 average time/residue: 0.5589 time to fit residues: 269.4775 Evaluate side-chains 425 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 346 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CD residue 347 THR Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 46 THR Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 117 ARG Chi-restraints excluded: chain SD residue 153 VAL Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SF residue 17 ILE Chi-restraints excluded: chain SF residue 19 LEU Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 60 ARG Chi-restraints excluded: chain SF residue 79 HIS Chi-restraints excluded: chain SF residue 204 ARG Chi-restraints excluded: chain SK residue 13 GLU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 80 ARG Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 76 VAL Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 67 ASP Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 111 ILE Chi-restraints excluded: chain SQ residue 127 CYS Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SS residue 12 ILE Chi-restraints excluded: chain SS residue 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 59 LEU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain SS residue 99 LEU Chi-restraints excluded: chain SS residue 116 LYS Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 28 LEU Chi-restraints excluded: chain ST residue 36 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 50 VAL Chi-restraints excluded: chain SU residue 92 HIS Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 64 GLU Chi-restraints excluded: chain Sd residue 25 SER Chi-restraints excluded: chain Sg residue 14 HIS Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 52 TYR Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 168 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 195 LEU Chi-restraints excluded: chain Sg residue 249 CYS Chi-restraints excluded: chain Sg residue 261 LEU Chi-restraints excluded: chain Sg residue 287 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 312 VAL Chi-restraints excluded: chain SM residue 14 VAL Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain SM residue 123 VAL Chi-restraints excluded: chain SZ residue 47 LEU Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 94 LYS Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sf residue 98 VAL Chi-restraints excluded: chain Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 130 VAL Chi-restraints excluded: chain Sf residue 136 PHE Chi-restraints excluded: chain Sf residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 155 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SF 82 ASN SP 24 GLN SP 46 ASN SQ 48 GLN SQ 97 GLN Sc 29 GLN Sg 62 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.068059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.049401 restraints weight = 77712.278| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.19 r_work: 0.2730 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 27254 Z= 0.314 Angle : 0.810 16.196 39102 Z= 0.407 Chirality : 0.045 0.227 4767 Planarity : 0.006 0.150 3185 Dihedral : 22.326 164.055 9780 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.39 % Favored : 89.35 % Rotamer: Outliers : 5.86 % Allowed : 38.00 % Favored : 56.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.19), residues: 1916 helix: 0.36 (0.22), residues: 585 sheet: -1.31 (0.28), residues: 328 loop : -1.97 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGSU 41 TYR 0.024 0.002 TYRSZ 65 PHE 0.047 0.003 PHESf 136 TRP 0.048 0.002 TRPCD 287 HIS 0.018 0.002 HISSU 92 Details of bonding type rmsd covalent geometry : bond 0.00649 (27254) covalent geometry : angle 0.80993 (39102) hydrogen bonds : bond 0.06664 ( 952) hydrogen bonds : angle 4.14811 ( 2152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11813.36 seconds wall clock time: 201 minutes 41.62 seconds (12101.62 seconds total)