Starting phenix.real_space_refine on Sat May 24 16:21:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9azm_44016/05_2025/9azm_44016.cif Found real_map, /net/cci-nas-00/data/ceres_data/9azm_44016/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9azm_44016/05_2025/9azm_44016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9azm_44016/05_2025/9azm_44016.map" model { file = "/net/cci-nas-00/data/ceres_data/9azm_44016/05_2025/9azm_44016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9azm_44016/05_2025/9azm_44016.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.76, per 1000 atoms: 0.65 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: 5.82 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 10.05 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: 11.78 Time building geometry restraints manager: 6.73 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: 10.900 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: 0.900 Check model and map are aligned: 0.190 Set scattering table: 0.210 Process input model: 63.900 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.370 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.052 0.002 TRPCD 287 HIS 0.017 0.001 HISSg 188 PHE 0.023 0.002 PHESg 241 TYR 0.023 0.002 TYRSQ 115 ARG 0.011 0.001 ARGSc 31 Details of bonding type rmsd hydrogen bonds : bond 0.21296 ( 952) hydrogen bonds : angle 7.58177 ( 2152) covalent geometry : bond 0.00388 (27254) covalent geometry : angle 0.85005 (39102) *********************** 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 : 1.954 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: 1.1505 time to fit residues: 570.5480 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 : 1.918 ------------------------------------------------------------------------------- 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 199 optimal weight: 6.9990 chunk 178 optimal weight: 0.4980 chunk 99 optimal weight: 0.0060 chunk 61 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 184 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- 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 ** SS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Sg 285 GLN SM 48 HIS ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.074227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.055801 restraints weight = 77238.953| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.18 r_work: 0.2904 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27254 Z= 0.166 Angle : 0.718 11.607 39102 Z= 0.364 Chirality : 0.041 0.228 4767 Planarity : 0.006 0.140 3185 Dihedral : 22.545 166.485 9839 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.07 % Favored : 89.72 % Rotamer: Outliers : 9.69 % Allowed : 33.09 % Favored : 57.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.19), residues: 1916 helix: -0.27 (0.21), residues: 588 sheet: -1.44 (0.29), residues: 313 loop : -2.02 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPSg 219 HIS 0.011 0.001 HISST 42 PHE 0.038 0.002 PHESF 61 TYR 0.015 0.002 TYRSK 78 ARG 0.010 0.001 ARGSf 138 Details of bonding type rmsd hydrogen bonds : bond 0.06799 ( 952) hydrogen bonds : angle 4.79531 ( 2152) covalent geometry : bond 0.00351 (27254) covalent geometry : angle 0.71794 (39102) *********************** 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 516 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 354 time to evaluate : 2.079 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 50 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8816 (mm) REVERT: SD 56 GLN cc_start: 0.9176 (tp-100) cc_final: 0.8939 (tp-100) REVERT: SD 74 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8873 (tm-30) REVERT: SD 94 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8654 (ptp90) REVERT: SF 27 ASP cc_start: 0.8403 (p0) cc_final: 0.8188 (p0) REVERT: SF 29 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8441 (mm-40) REVERT: SF 36 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: SF 106 GLU cc_start: 0.8341 (pp20) cc_final: 0.7846 (pp20) REVERT: SF 127 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.6440 (tpp-160) REVERT: SF 136 ARG cc_start: 0.7035 (mtp180) cc_final: 0.6737 (mtp85) REVERT: SK 29 MET cc_start: 0.9301 (ttm) cc_final: 0.8933 (ttp) REVERT: SK 31 LYS cc_start: 0.9268 (mptp) cc_final: 0.8900 (mptp) REVERT: SK 89 ILE cc_start: 0.9013 (mp) cc_final: 0.8757 (mp) REVERT: SP 32 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8824 (pm20) REVERT: SP 34 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8128 (mtm) REVERT: SP 65 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8857 (tptp) REVERT: SP 69 PRO cc_start: 0.9478 (Cg_exo) cc_final: 0.8732 (Cg_endo) REVERT: SQ 107 GLU cc_start: 0.8777 (pp20) cc_final: 0.8507 (pp20) REVERT: SQ 116 ASP cc_start: 0.8183 (t0) cc_final: 0.7854 (t0) REVERT: SS 50 ILE cc_start: 0.8697 (pt) cc_final: 0.8079 (pp) REVERT: SS 63 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.7468 (mm-30) REVERT: SS 73 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8638 (p0) REVERT: SS 92 ASP cc_start: 0.8520 (t0) cc_final: 0.8132 (t0) REVERT: ST 114 GLU cc_start: 0.8504 (pm20) cc_final: 0.8106 (pm20) REVERT: ST 126 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8354 (tm-30) REVERT: ST 143 LYS cc_start: 0.9149 (tppt) cc_final: 0.8947 (tppt) REVERT: SU 111 GLU cc_start: 0.8433 (tt0) cc_final: 0.8199 (tt0) REVERT: SU 113 GLU cc_start: 0.7995 (mp0) cc_final: 0.7662 (mp0) REVERT: Sc 41 SER cc_start: 0.8493 (p) cc_final: 0.8278 (t) REVERT: Sc 60 GLU cc_start: 0.6822 (tm-30) cc_final: 0.6380 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5019 (OUTLIER) cc_final: 0.4812 (tt0) REVERT: Sc 66 ARG cc_start: 0.7448 (mpp80) cc_final: 0.7214 (mtm-85) REVERT: Sg 14 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.7416 (p90) REVERT: Sg 195 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8431 (mm) REVERT: Sg 228 TYR cc_start: 0.7495 (t80) cc_final: 0.7255 (t80) REVERT: SM 88 TRP cc_start: 0.9307 (m-10) cc_final: 0.9100 (m-10) REVERT: SZ 50 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8433 (p90) REVERT: Sf 103 LEU cc_start: 0.6794 (pt) cc_final: 0.6542 (pp) REVERT: Sf 113 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8407 (mmtt) outliers start: 162 outliers final: 61 residues processed: 464 average time/residue: 1.2987 time to fit residues: 701.6048 Evaluate side-chains 419 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 345 time to evaluate : 2.030 ------------------------------------------------------------------------------- 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 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 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 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 92 SER 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 ST residue 6 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 88 MET Chi-restraints excluded: chain ST residue 131 LEU 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 50 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 61 SER 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 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 50 PHE 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 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 109 optimal weight: 0.9990 chunk 163 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 74 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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 SQ 86 GLN SQ 97 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** ** Sg 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 48 HIS ** SZ 45 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 = 0.3437 r_free = 0.3437 target = 0.072136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.053610 restraints weight = 77000.079| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.17 r_work: 0.2843 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27254 Z= 0.216 Angle : 0.712 13.603 39102 Z= 0.360 Chirality : 0.042 0.215 4767 Planarity : 0.006 0.128 3185 Dihedral : 22.449 166.038 9788 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.86 % Favored : 89.93 % Rotamer: Outliers : 9.46 % Allowed : 32.08 % Favored : 58.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.19), residues: 1916 helix: 0.07 (0.21), residues: 581 sheet: -1.29 (0.29), residues: 310 loop : -2.04 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPSg 219 HIS 0.011 0.001 HISSg 188 PHE 0.040 0.002 PHESF 61 TYR 0.018 0.002 TYRSZ 65 ARG 0.008 0.001 ARGSg 118 Details of bonding type rmsd hydrogen bonds : bond 0.06736 ( 952) hydrogen bonds : angle 4.43723 ( 2152) covalent geometry : bond 0.00448 (27254) covalent geometry : angle 0.71218 (39102) *********************** 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 518 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 360 time to evaluate : 2.183 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: 0.7574 (tpt) cc_final: 0.7260 (tpt) REVERT: CD 287 TRP cc_start: 0.9099 (t-100) cc_final: 0.8693 (t60) REVERT: SD 56 GLN cc_start: 0.9172 (tp-100) cc_final: 0.8903 (tp-100) REVERT: SD 74 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8775 (tm-30) REVERT: SD 94 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8689 (ptp90) REVERT: SF 29 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8435 (mm-40) REVERT: SF 127 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.6333 (tpp-160) REVERT: SK 29 MET cc_start: 0.9290 (ttm) cc_final: 0.8915 (ttp) REVERT: SK 89 ILE cc_start: 0.9069 (mp) cc_final: 0.8529 (mp) REVERT: SP 65 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.8922 (tptp) REVERT: SP 69 PRO cc_start: 0.9236 (Cg_exo) cc_final: 0.9001 (Cg_endo) REVERT: SQ 10 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.8868 (m) REVERT: SQ 107 GLU cc_start: 0.8862 (pp20) cc_final: 0.8640 (pp20) REVERT: SQ 116 ASP cc_start: 0.8341 (t0) cc_final: 0.7908 (t0) REVERT: SS 73 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8524 (p0) REVERT: ST 114 GLU cc_start: 0.8410 (pm20) cc_final: 0.8013 (pm20) REVERT: ST 143 LYS cc_start: 0.9140 (tppt) cc_final: 0.8876 (tppt) REVERT: SU 111 GLU cc_start: 0.8472 (tt0) cc_final: 0.8197 (tt0) REVERT: SU 113 GLU cc_start: 0.8011 (mp0) cc_final: 0.7491 (mp0) REVERT: Sc 18 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9205 (mt) REVERT: Sc 29 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.8223 (mt0) REVERT: Sc 31 ARG cc_start: 0.8572 (tpp80) cc_final: 0.8355 (tpp80) REVERT: Sc 60 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6325 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4988 (tt0) REVERT: Sc 66 ARG cc_start: 0.7353 (mpp80) cc_final: 0.6991 (mtm-85) REVERT: Sd 5 GLN cc_start: 0.8738 (mp10) cc_final: 0.8341 (mp10) REVERT: Sg 14 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.7316 (p90) REVERT: Sg 195 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8470 (mm) REVERT: Sg 228 TYR cc_start: 0.7358 (t80) cc_final: 0.7135 (t80) REVERT: Sg 282 GLU cc_start: 0.9004 (mp0) cc_final: 0.8665 (pm20) REVERT: SM 37 GLU cc_start: 0.8362 (mp0) cc_final: 0.8138 (mp0) REVERT: SM 58 GLU cc_start: 0.9006 (tp30) cc_final: 0.8630 (tp30) REVERT: SM 88 TRP cc_start: 0.9273 (m-10) cc_final: 0.8977 (m-10) REVERT: Sf 103 LEU cc_start: 0.6789 (pt) cc_final: 0.6569 (pp) outliers start: 158 outliers final: 63 residues processed: 471 average time/residue: 1.2595 time to fit residues: 690.6468 Evaluate side-chains 408 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 335 time to evaluate : 1.938 ------------------------------------------------------------------------------- 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 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 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 10 VAL 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 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 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 73 ASN 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 87 VAL Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 47 ASN 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 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 Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 14 HIS 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 18 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 35 GLN SP 46 ASN 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 162 ASN ** 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** ** Sg 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 48 HIS ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 106 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.070051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.051463 restraints weight = 77609.627| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.18 r_work: 0.2784 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 27254 Z= 0.279 Angle : 0.743 14.907 39102 Z= 0.376 Chirality : 0.044 0.212 4767 Planarity : 0.006 0.121 3185 Dihedral : 22.452 164.886 9786 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.23 % Favored : 89.51 % Rotamer: Outliers : 9.16 % Allowed : 32.38 % Favored : 58.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.19), residues: 1916 helix: 0.18 (0.21), residues: 582 sheet: -1.22 (0.29), residues: 314 loop : -2.06 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPSg 219 HIS 0.007 0.001 HISSg 188 PHE 0.032 0.002 PHESF 61 TYR 0.022 0.002 TYRSZ 65 ARG 0.009 0.001 ARGSK 95 Details of bonding type rmsd hydrogen bonds : bond 0.06783 ( 952) hydrogen bonds : angle 4.34964 ( 2152) covalent geometry : bond 0.00575 (27254) covalent geometry : angle 0.74340 (39102) *********************** 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 500 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 347 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CD 282 MET cc_start: 0.7753 (tpt) cc_final: 0.7457 (tpp) REVERT: CD 287 TRP cc_start: 0.9122 (t-100) cc_final: 0.8636 (t-100) REVERT: SD 50 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.8880 (mm) REVERT: SD 56 GLN cc_start: 0.9227 (tp-100) cc_final: 0.8948 (tp-100) REVERT: SD 74 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8744 (tm-30) REVERT: SD 94 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8683 (ptp90) REVERT: SD 117 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8246 (ttm-80) REVERT: SF 29 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8408 (mm-40) REVERT: SF 36 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: SF 127 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6514 (tpp80) REVERT: SK 13 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: SK 29 MET cc_start: 0.9303 (ttm) cc_final: 0.8911 (ttp) REVERT: SK 80 ARG cc_start: 0.9090 (tpp80) cc_final: 0.8732 (tpp80) REVERT: SK 89 ILE cc_start: 0.9182 (mp) cc_final: 0.8602 (mp) REVERT: SK 95 ARG cc_start: 0.7669 (tmm160) cc_final: 0.7441 (tmm160) REVERT: SP 31 GLU cc_start: 0.9101 (mp0) cc_final: 0.8813 (mp0) REVERT: SP 32 GLN cc_start: 0.9103 (pm20) cc_final: 0.8859 (pm20) REVERT: SP 34 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8197 (mtm) REVERT: SP 66 GLU cc_start: 0.8521 (mp0) cc_final: 0.8294 (mp0) REVERT: SQ 10 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.8894 (m) REVERT: SQ 43 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: SQ 84 ILE cc_start: 0.9712 (OUTLIER) cc_final: 0.9445 (mp) REVERT: SQ 107 GLU cc_start: 0.8951 (pp20) cc_final: 0.8707 (pp20) REVERT: SQ 116 ASP cc_start: 0.8533 (t0) cc_final: 0.8055 (t0) REVERT: SS 55 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8817 (mmt180) REVERT: ST 114 GLU cc_start: 0.8390 (pm20) cc_final: 0.7944 (pm20) REVERT: ST 143 LYS cc_start: 0.9172 (tppt) cc_final: 0.8919 (tppt) REVERT: SU 111 GLU cc_start: 0.8433 (tt0) cc_final: 0.8208 (tt0) REVERT: SU 113 GLU cc_start: 0.8018 (mp0) cc_final: 0.7673 (mp0) REVERT: Sc 18 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9247 (mt) REVERT: Sc 31 ARG cc_start: 0.8537 (tpp80) cc_final: 0.8315 (tpp80) REVERT: Sc 60 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6546 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.5071 (tt0) REVERT: Sc 66 ARG cc_start: 0.7233 (mpp80) cc_final: 0.6961 (mtm-85) REVERT: Sd 5 GLN cc_start: 0.8782 (mp10) cc_final: 0.8278 (mp10) REVERT: Sg 14 HIS cc_start: 0.8691 (OUTLIER) cc_final: 0.7423 (p90) REVERT: Sg 195 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8457 (mm) REVERT: Sg 228 TYR cc_start: 0.7518 (t80) cc_final: 0.7306 (t80) REVERT: Sg 282 GLU cc_start: 0.9064 (mp0) cc_final: 0.8716 (pm20) REVERT: SM 48 HIS cc_start: 0.8045 (m170) cc_final: 0.7831 (m-70) REVERT: SM 88 TRP cc_start: 0.9289 (m-10) cc_final: 0.8950 (m-10) REVERT: SZ 50 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8406 (p90) REVERT: Sf 96 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8821 (mmmm) REVERT: Sf 113 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8454 (mmtt) outliers start: 153 outliers final: 75 residues processed: 454 average time/residue: 1.3052 time to fit residues: 687.9783 Evaluate side-chains 428 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 337 time to evaluate : 2.189 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain SD residue 94 ARG 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 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 SK residue 13 GLU Chi-restraints excluded: chain SK residue 17 LYS 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 34 MET Chi-restraints excluded: chain SP residue 57 LEU Chi-restraints excluded: chain SP residue 76 VAL 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 42 ILE Chi-restraints excluded: chain SQ residue 43 GLU 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 100 VAL 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 55 ARG Chi-restraints excluded: chain SS residue 59 LEU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 79 ILE Chi-restraints excluded: chain SS residue 84 LEU 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 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 43 ILE 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 66 VAL 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 SZ residue 44 LEU Chi-restraints excluded: chain SZ residue 47 LEU Chi-restraints excluded: chain SZ residue 48 VAL Chi-restraints excluded: chain SZ residue 50 PHE Chi-restraints excluded: chain SZ residue 58 LEU Chi-restraints excluded: chain SZ residue 61 GLU Chi-restraints excluded: chain SZ residue 62 VAL 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 65 optimal weight: 0.7980 chunk 209 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 SQ 97 GLN Sg 62 HIS 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** ** Sg 305 ASN ** 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 = 0.3379 r_free = 0.3379 target = 0.069459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.050883 restraints weight = 77686.904| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.17 r_work: 0.2771 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2366 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= 0.266 Angle : 0.741 14.955 39102 Z= 0.374 Chirality : 0.044 0.236 4767 Planarity : 0.005 0.117 3185 Dihedral : 22.447 164.350 9786 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.92 % Favored : 89.87 % Rotamer: Outliers : 9.58 % Allowed : 32.32 % Favored : 58.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.19), residues: 1916 helix: 0.24 (0.22), residues: 582 sheet: -1.18 (0.29), residues: 316 loop : -2.07 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPSg 219 HIS 0.007 0.001 HISSg 188 PHE 0.027 0.002 PHESF 61 TYR 0.022 0.002 TYRSZ 65 ARG 0.007 0.001 ARGSf 95 Details of bonding type rmsd hydrogen bonds : bond 0.06608 ( 952) hydrogen bonds : angle 4.23627 ( 2152) covalent geometry : bond 0.00547 (27254) covalent geometry : angle 0.74100 (39102) *********************** 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 517 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 357 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CD 283 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7732 (t) REVERT: CD 287 TRP cc_start: 0.9134 (t-100) cc_final: 0.8745 (t-100) REVERT: SD 50 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8812 (mm) REVERT: SD 56 GLN cc_start: 0.9204 (tp-100) cc_final: 0.8921 (tp-100) REVERT: SD 74 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8763 (tm-30) REVERT: SD 94 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8726 (ptp90) REVERT: SD 117 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8205 (ttm-80) REVERT: SD 169 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8558 (p0) REVERT: SF 36 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: SF 45 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8051 (p90) REVERT: SK 5 LYS cc_start: 0.8849 (ttpm) cc_final: 0.8646 (ttmm) REVERT: SK 29 MET cc_start: 0.9324 (ttm) cc_final: 0.8935 (ttp) REVERT: SK 80 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8559 (tpp80) REVERT: SK 89 ILE cc_start: 0.9234 (mp) cc_final: 0.8657 (mp) REVERT: SP 27 ASP cc_start: 0.8967 (m-30) cc_final: 0.8666 (m-30) REVERT: SP 31 GLU cc_start: 0.9036 (mp0) cc_final: 0.8751 (mp0) REVERT: SP 32 GLN cc_start: 0.9092 (pm20) cc_final: 0.8779 (pm20) REVERT: SP 34 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8203 (mtm) REVERT: SP 66 GLU cc_start: 0.8596 (mp0) cc_final: 0.8346 (mp0) REVERT: SQ 10 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.8924 (m) REVERT: SQ 43 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: SQ 84 ILE cc_start: 0.9711 (OUTLIER) cc_final: 0.9433 (mp) REVERT: SQ 107 GLU cc_start: 0.8997 (pp20) cc_final: 0.8723 (pp20) REVERT: SQ 116 ASP cc_start: 0.8557 (t0) cc_final: 0.8057 (t0) REVERT: ST 35 ASP cc_start: 0.9259 (p0) cc_final: 0.9018 (p0) REVERT: ST 114 GLU cc_start: 0.8402 (pm20) cc_final: 0.7960 (pm20) REVERT: ST 143 LYS cc_start: 0.9127 (tppt) cc_final: 0.8899 (tppt) REVERT: SU 113 GLU cc_start: 0.7985 (mp0) cc_final: 0.7623 (mp0) REVERT: Sc 18 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9317 (mt) REVERT: Sc 60 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6473 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5666 (OUTLIER) cc_final: 0.5331 (tt0) REVERT: Sc 66 ARG cc_start: 0.7245 (mpp80) cc_final: 0.7033 (mtm-85) REVERT: Sd 5 GLN cc_start: 0.8871 (mp10) cc_final: 0.8606 (mp10) REVERT: Sg 14 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.7443 (p90) REVERT: Sg 79 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8733 (pt) REVERT: Sg 113 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8902 (m-80) REVERT: Sg 145 GLU cc_start: 0.8733 (mp0) cc_final: 0.8529 (mp0) REVERT: Sg 195 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8426 (mm) REVERT: Sg 217 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7264 (pmt) REVERT: Sg 228 TYR cc_start: 0.7576 (t80) cc_final: 0.7268 (t80) REVERT: Sg 282 GLU cc_start: 0.9025 (mp0) cc_final: 0.8710 (pm20) REVERT: SM 48 HIS cc_start: 0.7966 (m170) cc_final: 0.7717 (m-70) REVERT: SM 88 TRP cc_start: 0.9281 (m-10) cc_final: 0.8934 (m-10) REVERT: SZ 50 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8430 (p90) REVERT: Sf 110 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6592 (pp20) REVERT: Sf 113 LYS cc_start: 0.8566 (mmtt) cc_final: 0.7922 (mmtm) outliers start: 160 outliers final: 75 residues processed: 473 average time/residue: 1.2515 time to fit residues: 693.3617 Evaluate side-chains 437 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 341 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 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 SF residue 17 ILE Chi-restraints excluded: chain SF residue 19 LEU 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 141 VAL Chi-restraints excluded: chain SF residue 149 GLN Chi-restraints excluded: chain SF residue 177 LEU 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 SK residue 93 THR 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 76 VAL 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 43 GLU 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 100 VAL Chi-restraints excluded: chain SQ residue 104 SER 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 79 ILE Chi-restraints excluded: chain SS residue 84 LEU 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 88 LEU Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 112 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 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 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 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 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 217 MET 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 SZ residue 47 LEU Chi-restraints excluded: chain SZ residue 48 VAL 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 Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 110 GLU Chi-restraints excluded: chain Sf residue 130 VAL 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 118 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 145 optimal weight: 0.0970 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SF 82 ASN SP 46 ASN SQ 97 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 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.069319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.050765 restraints weight = 77927.660| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.19 r_work: 0.2769 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27254 Z= 0.239 Angle : 0.729 14.925 39102 Z= 0.367 Chirality : 0.043 0.242 4767 Planarity : 0.005 0.117 3185 Dihedral : 22.413 166.515 9786 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.23 % Favored : 89.61 % Rotamer: Outliers : 9.63 % Allowed : 33.33 % Favored : 57.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.19), residues: 1916 helix: 0.24 (0.22), residues: 584 sheet: -1.12 (0.29), residues: 316 loop : -2.01 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPSg 219 HIS 0.013 0.001 HISSg 188 PHE 0.022 0.002 PHESF 61 TYR 0.020 0.002 TYRSZ 65 ARG 0.006 0.001 ARGSK 95 Details of bonding type rmsd hydrogen bonds : bond 0.06373 ( 952) hydrogen bonds : angle 4.14615 ( 2152) covalent geometry : bond 0.00496 (27254) covalent geometry : angle 0.72898 (39102) *********************** 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 509 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 348 time to evaluate : 2.137 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 283 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7717 (t) REVERT: CD 287 TRP cc_start: 0.9095 (t-100) cc_final: 0.8736 (t-100) REVERT: SD 50 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8772 (mm) REVERT: SD 56 GLN cc_start: 0.9228 (tp-100) cc_final: 0.8888 (tp-100) REVERT: SD 74 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8707 (tm-30) REVERT: SD 94 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8739 (ptp90) REVERT: SD 117 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8208 (ttm-80) REVERT: SF 45 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.8085 (p90) REVERT: SF 60 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8599 (mtp180) REVERT: SF 146 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8365 (ttt90) REVERT: SK 29 MET cc_start: 0.9339 (ttm) cc_final: 0.9013 (ttp) REVERT: SK 31 LYS cc_start: 0.9421 (mptp) cc_final: 0.9109 (mptp) REVERT: SK 89 ILE cc_start: 0.9201 (mp) cc_final: 0.8561 (mp) REVERT: SP 23 ASP cc_start: 0.9110 (m-30) cc_final: 0.8788 (m-30) REVERT: SP 27 ASP cc_start: 0.8946 (m-30) cc_final: 0.8661 (m-30) REVERT: SP 31 GLU cc_start: 0.9014 (mp0) cc_final: 0.8775 (mp0) REVERT: SP 32 GLN cc_start: 0.9112 (pm20) cc_final: 0.8706 (pm20) REVERT: SP 34 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8323 (mtm) REVERT: SP 65 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.8876 (tptp) REVERT: SQ 10 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.8954 (m) REVERT: SQ 84 ILE cc_start: 0.9698 (OUTLIER) cc_final: 0.9442 (mp) REVERT: SQ 107 GLU cc_start: 0.9026 (pp20) cc_final: 0.8735 (pp20) REVERT: SQ 116 ASP cc_start: 0.8539 (t0) cc_final: 0.8055 (t0) REVERT: ST 35 ASP cc_start: 0.9234 (p0) cc_final: 0.9023 (p0) REVERT: ST 111 LYS cc_start: 0.9414 (mmmm) cc_final: 0.9155 (mppt) REVERT: ST 114 GLU cc_start: 0.8363 (pm20) cc_final: 0.7902 (pm20) REVERT: ST 143 LYS cc_start: 0.9133 (tppt) cc_final: 0.8930 (tppt) REVERT: SU 113 GLU cc_start: 0.7948 (mp0) cc_final: 0.7632 (mp0) REVERT: Sc 18 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9305 (mt) REVERT: Sc 60 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6768 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.5233 (tt0) REVERT: Sd 5 GLN cc_start: 0.8972 (mp10) cc_final: 0.8679 (mp10) REVERT: Sg 14 HIS cc_start: 0.8757 (OUTLIER) cc_final: 0.7382 (p90) REVERT: Sg 27 PHE cc_start: 0.9435 (m-80) cc_final: 0.9196 (m-80) REVERT: Sg 42 MET cc_start: 0.8787 (ttm) cc_final: 0.8324 (ptm) REVERT: Sg 79 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8724 (pt) REVERT: Sg 113 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8895 (m-80) REVERT: Sg 140 TYR cc_start: 0.8237 (t80) cc_final: 0.7909 (t80) REVERT: Sg 195 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8451 (mm) REVERT: Sg 228 TYR cc_start: 0.7526 (t80) cc_final: 0.7275 (t80) REVERT: Sg 282 GLU cc_start: 0.8927 (mp0) cc_final: 0.8644 (pm20) REVERT: SM 48 HIS cc_start: 0.7932 (m170) cc_final: 0.7721 (m90) REVERT: SM 58 GLU cc_start: 0.8890 (tp30) cc_final: 0.8124 (tp30) REVERT: SM 84 LYS cc_start: 0.9207 (tppt) cc_final: 0.8943 (tppp) REVERT: SZ 50 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8434 (p90) REVERT: Sf 110 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6724 (pp20) REVERT: Sf 113 LYS cc_start: 0.8527 (mmtt) cc_final: 0.7973 (mmtm) outliers start: 161 outliers final: 81 residues processed: 466 average time/residue: 1.2506 time to fit residues: 680.1914 Evaluate side-chains 437 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 337 time to evaluate : 1.984 ------------------------------------------------------------------------------- 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 117 ARG Chi-restraints excluded: chain SD residue 153 VAL Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SD residue 204 LEU Chi-restraints excluded: chain SF residue 17 ILE Chi-restraints excluded: chain SF residue 19 LEU 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 79 HIS Chi-restraints excluded: chain SF residue 141 VAL Chi-restraints excluded: chain SF residue 146 ARG Chi-restraints excluded: chain SF residue 149 GLN Chi-restraints excluded: chain SF residue 177 LEU Chi-restraints excluded: chain SF residue 185 SER Chi-restraints excluded: chain SK residue 13 GLU Chi-restraints excluded: chain SK residue 17 LYS Chi-restraints excluded: chain SK residue 35 LEU Chi-restraints excluded: chain SK residue 58 VAL 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 65 LYS Chi-restraints excluded: chain SP residue 76 VAL 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 78 VAL Chi-restraints excluded: chain SQ residue 84 ILE Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 104 SER 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 84 LEU 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 88 LEU Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 112 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 43 ILE 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 Sd residue 25 SER 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 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 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 SZ residue 47 LEU Chi-restraints excluded: chain SZ residue 48 VAL Chi-restraints excluded: chain SZ residue 50 PHE Chi-restraints excluded: chain SZ residue 61 GLU 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 110 GLU 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 197 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 125 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 SP 54 HIS SQ 97 GLN Sg 62 HIS ** Sg 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sg 305 ASN ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.072053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053796 restraints weight = 78490.025| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.26 r_work: 0.2862 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27254 Z= 0.137 Angle : 0.710 13.507 39102 Z= 0.354 Chirality : 0.039 0.241 4767 Planarity : 0.005 0.117 3185 Dihedral : 22.366 171.776 9786 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.55 % Favored : 90.29 % Rotamer: Outliers : 7.36 % Allowed : 35.61 % Favored : 57.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1916 helix: 0.41 (0.22), residues: 584 sheet: -0.93 (0.29), residues: 328 loop : -1.98 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPSg 219 HIS 0.013 0.001 HISSg 188 PHE 0.019 0.002 PHESg 241 TYR 0.023 0.001 TYRSM 61 ARG 0.008 0.000 ARGSc 31 Details of bonding type rmsd hydrogen bonds : bond 0.05773 ( 952) hydrogen bonds : angle 4.03255 ( 2152) covalent geometry : bond 0.00296 (27254) covalent geometry : angle 0.70952 (39102) *********************** 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 485 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 362 time to evaluate : 1.999 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 282 MET cc_start: 0.7668 (tpt) cc_final: 0.7285 (tpt) REVERT: CD 287 TRP cc_start: 0.9027 (t-100) cc_final: 0.8718 (t-100) REVERT: SD 56 GLN cc_start: 0.9203 (tp-100) cc_final: 0.8858 (tp-100) REVERT: SD 74 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8634 (tm-30) REVERT: SF 27 ASP cc_start: 0.8299 (p0) cc_final: 0.8087 (p0) REVERT: SF 45 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8016 (p90) REVERT: SK 29 MET cc_start: 0.9310 (ttm) cc_final: 0.8968 (ttp) REVERT: SK 31 LYS cc_start: 0.9409 (mptp) cc_final: 0.9070 (mptp) REVERT: SK 80 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8787 (tpp80) REVERT: SK 89 ILE cc_start: 0.9159 (mp) cc_final: 0.8655 (mp) REVERT: SP 23 ASP cc_start: 0.9084 (m-30) cc_final: 0.8791 (m-30) REVERT: SP 27 ASP cc_start: 0.8976 (m-30) cc_final: 0.8699 (m-30) REVERT: SP 31 GLU cc_start: 0.9039 (mp0) cc_final: 0.8784 (mp0) REVERT: SP 32 GLN cc_start: 0.9137 (pm20) cc_final: 0.8690 (pm20) REVERT: SP 57 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9168 (mp) REVERT: SP 66 GLU cc_start: 0.8663 (mp0) cc_final: 0.8419 (mp0) REVERT: SQ 107 GLU cc_start: 0.9004 (pp20) cc_final: 0.8697 (pp20) REVERT: SQ 116 ASP cc_start: 0.8545 (t0) cc_final: 0.8035 (t0) REVERT: ST 111 LYS cc_start: 0.9459 (mmmm) cc_final: 0.9178 (mppt) REVERT: ST 114 GLU cc_start: 0.8312 (pm20) cc_final: 0.7927 (pm20) REVERT: SU 21 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7681 (ttm170) REVERT: SU 113 GLU cc_start: 0.7835 (mp0) cc_final: 0.7407 (mp0) REVERT: Sc 18 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9216 (mt) REVERT: Sc 33 GLU cc_start: 0.8304 (pp20) cc_final: 0.8101 (pp20) REVERT: Sc 40 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7542 (ppp80) REVERT: Sc 60 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6618 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5587 (OUTLIER) cc_final: 0.5283 (tt0) REVERT: Sd 5 GLN cc_start: 0.8980 (mp10) cc_final: 0.8660 (mp10) REVERT: Sg 14 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.7144 (p90) REVERT: Sg 42 MET cc_start: 0.8734 (ttm) cc_final: 0.8280 (ptm) REVERT: Sg 113 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8984 (m-80) REVERT: Sg 140 TYR cc_start: 0.8285 (t80) cc_final: 0.7997 (t80) REVERT: Sg 145 GLU cc_start: 0.8595 (mp0) cc_final: 0.8252 (mp0) REVERT: Sg 228 TYR cc_start: 0.7570 (t80) cc_final: 0.7227 (t80) REVERT: Sg 282 GLU cc_start: 0.8941 (mp0) cc_final: 0.8647 (pm20) REVERT: SM 37 GLU cc_start: 0.8232 (mp0) cc_final: 0.7918 (mp0) REVERT: SM 48 HIS cc_start: 0.8064 (m170) cc_final: 0.7829 (m90) REVERT: SM 60 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8926 (pmm) REVERT: SM 63 LYS cc_start: 0.9249 (ptmt) cc_final: 0.8949 (pptt) REVERT: SM 78 LYS cc_start: 0.9195 (mmmm) cc_final: 0.8985 (mmmm) REVERT: SM 84 LYS cc_start: 0.9201 (tppt) cc_final: 0.8926 (tppp) REVERT: SZ 60 LYS cc_start: 0.9276 (tmmm) cc_final: 0.9026 (ttpp) REVERT: Sf 118 ARG cc_start: 0.8383 (mmt90) cc_final: 0.7967 (mmm-85) outliers start: 123 outliers final: 53 residues processed: 445 average time/residue: 1.2715 time to fit residues: 657.0249 Evaluate side-chains 407 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 344 time to evaluate : 1.938 ------------------------------------------------------------------------------- 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 181 VAL Chi-restraints excluded: chain SF residue 19 LEU Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 124 ASP 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 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 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 99 LEU 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 88 LEU 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 40 ARG Chi-restraints excluded: chain Sc residue 42 ILE 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 21 ILE Chi-restraints excluded: chain Sg residue 52 TYR Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 113 PHE 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 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 48 VAL Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 68 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 133 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SF 29 GLN SP 24 GLN SP 32 GLN SP 46 ASN SQ 97 GLN Sg 62 HIS ** Sg 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.068715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.050019 restraints weight = 77987.552| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.26 r_work: 0.2752 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 27254 Z= 0.253 Angle : 0.747 14.684 39102 Z= 0.375 Chirality : 0.043 0.207 4767 Planarity : 0.005 0.121 3185 Dihedral : 22.328 166.300 9782 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.23 % Favored : 89.61 % Rotamer: Outliers : 7.00 % Allowed : 36.62 % Favored : 56.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.19), residues: 1916 helix: 0.39 (0.22), residues: 579 sheet: -1.15 (0.28), residues: 321 loop : -1.95 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPSg 219 HIS 0.011 0.001 HISSg 188 PHE 0.021 0.002 PHESF 61 TYR 0.025 0.002 TYRSF 188 ARG 0.006 0.001 ARGSc 31 Details of bonding type rmsd hydrogen bonds : bond 0.06439 ( 952) hydrogen bonds : angle 4.10220 ( 2152) covalent geometry : bond 0.00529 (27254) covalent geometry : angle 0.74673 (39102) *********************** 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 471 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 354 time to evaluate : 1.965 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: 0.7620 (tpt) cc_final: 0.6908 (tpt) REVERT: CD 287 TRP cc_start: 0.9083 (t-100) cc_final: 0.8581 (t-100) REVERT: CD 349 GLN cc_start: 0.8986 (pm20) cc_final: 0.8453 (pm20) REVERT: SD 50 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8755 (mm) REVERT: SD 56 GLN cc_start: 0.9250 (tp-100) cc_final: 0.8806 (tp-100) REVERT: SD 74 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8688 (tm-30) REVERT: SD 117 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8210 (ttt90) REVERT: SF 45 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8096 (p90) REVERT: SK 3 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.8527 (ptm) REVERT: SK 29 MET cc_start: 0.9323 (ttm) cc_final: 0.8952 (ttp) REVERT: SK 31 LYS cc_start: 0.9477 (mptp) cc_final: 0.9134 (mptp) REVERT: SK 80 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8789 (tpp80) REVERT: SK 89 ILE cc_start: 0.9217 (mp) cc_final: 0.8543 (mp) REVERT: SP 23 ASP cc_start: 0.9104 (m-30) cc_final: 0.8761 (m-30) REVERT: SP 27 ASP cc_start: 0.8993 (m-30) cc_final: 0.8700 (m-30) REVERT: SP 31 GLU cc_start: 0.9099 (mp0) cc_final: 0.8812 (mp0) REVERT: SP 32 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8917 (mp10) REVERT: SP 34 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8358 (mmm) REVERT: SP 66 GLU cc_start: 0.8613 (mp0) cc_final: 0.8357 (mp0) REVERT: SQ 107 GLU cc_start: 0.9033 (pp20) cc_final: 0.8774 (pp20) REVERT: SQ 116 ASP cc_start: 0.8539 (t0) cc_final: 0.8044 (t0) REVERT: ST 114 GLU cc_start: 0.8300 (pm20) cc_final: 0.7914 (pm20) REVERT: SU 21 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7800 (ttm170) REVERT: SU 113 GLU cc_start: 0.7951 (mp0) cc_final: 0.7629 (mp0) REVERT: Sc 18 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9272 (mt) REVERT: Sc 40 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7458 (ptm160) REVERT: Sc 60 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6746 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5287 (tt0) REVERT: Sd 5 GLN cc_start: 0.9029 (mp10) cc_final: 0.8512 (mp10) REVERT: Sg 14 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.7375 (p90) REVERT: Sg 27 PHE cc_start: 0.9447 (m-80) cc_final: 0.9215 (m-80) REVERT: Sg 140 TYR cc_start: 0.8356 (t80) cc_final: 0.8079 (t80) REVERT: Sg 145 GLU cc_start: 0.8621 (mp0) cc_final: 0.8315 (mp0) REVERT: Sg 217 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.6595 (pmt) REVERT: Sg 228 TYR cc_start: 0.7587 (t80) cc_final: 0.7256 (t80) REVERT: Sg 282 GLU cc_start: 0.8968 (mp0) cc_final: 0.8677 (pm20) REVERT: SM 37 GLU cc_start: 0.8422 (mp0) cc_final: 0.8142 (mp0) REVERT: SM 48 HIS cc_start: 0.8059 (m170) cc_final: 0.7828 (m90) REVERT: SM 63 LYS cc_start: 0.9287 (ptmt) cc_final: 0.9023 (pptt) REVERT: SM 78 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8874 (mmmm) REVERT: SM 84 LYS cc_start: 0.9224 (tppt) cc_final: 0.8936 (tppp) REVERT: SM 91 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8225 (tm) outliers start: 117 outliers final: 64 residues processed: 435 average time/residue: 1.3130 time to fit residues: 663.0354 Evaluate side-chains 422 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 344 time to evaluate : 2.103 ------------------------------------------------------------------------------- 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 SD residue 211 VAL Chi-restraints excluded: chain SF residue 19 LEU Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 79 HIS Chi-restraints excluded: chain SF residue 149 GLN Chi-restraints excluded: chain SK residue 3 MET 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 32 GLN Chi-restraints excluded: chain SP residue 34 MET 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 32 ILE Chi-restraints excluded: chain SQ residue 67 ASP Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 104 SER 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 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 84 LEU 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 21 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 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 40 ARG 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 25 SER 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 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 217 MET 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 91 LEU Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain SZ residue 47 LEU Chi-restraints excluded: chain SZ residue 48 VAL Chi-restraints excluded: chain SZ residue 61 GLU Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 68 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 219 optimal weight: 5.9990 chunk 172 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 30 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 217 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SF 82 ASN SP 46 ASN SQ 97 GLN Sc 29 GLN Sg 62 HIS ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.071988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053856 restraints weight = 78468.355| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.26 r_work: 0.2862 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27254 Z= 0.138 Angle : 0.747 15.066 39102 Z= 0.372 Chirality : 0.040 0.241 4767 Planarity : 0.005 0.143 3185 Dihedral : 22.349 171.958 9782 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.60 % Favored : 90.24 % Rotamer: Outliers : 5.45 % Allowed : 37.88 % Favored : 56.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.19), residues: 1916 helix: 0.43 (0.22), residues: 579 sheet: -1.08 (0.29), residues: 307 loop : -1.94 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPCD 287 HIS 0.016 0.001 HISSg 188 PHE 0.035 0.002 PHESf 136 TYR 0.024 0.001 TYRSM 61 ARG 0.009 0.001 ARGSc 51 Details of bonding type rmsd hydrogen bonds : bond 0.05752 ( 952) hydrogen bonds : angle 4.07057 ( 2152) covalent geometry : bond 0.00303 (27254) covalent geometry : angle 0.74704 (39102) *********************** 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 448 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 357 time to evaluate : 2.068 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 56 GLN cc_start: 0.9179 (tp-100) cc_final: 0.8735 (tp-100) REVERT: SD 74 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8622 (tm-30) REVERT: SD 117 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8104 (ttt90) REVERT: SD 189 MET cc_start: 0.9273 (ttt) cc_final: 0.9069 (ttt) REVERT: SF 45 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8069 (p90) REVERT: SK 29 MET cc_start: 0.9301 (ttm) cc_final: 0.8962 (ttp) REVERT: SK 31 LYS cc_start: 0.9438 (mptp) cc_final: 0.9110 (mptp) REVERT: SK 80 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8767 (tpp80) REVERT: SP 23 ASP cc_start: 0.9072 (m-30) cc_final: 0.8733 (m-30) REVERT: SP 27 ASP cc_start: 0.8946 (m-30) cc_final: 0.8663 (m-30) REVERT: SP 32 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8532 (mp10) REVERT: SP 34 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8361 (mmm) REVERT: SP 57 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9158 (mp) REVERT: SP 66 GLU cc_start: 0.8650 (mp0) cc_final: 0.8399 (mp0) REVERT: SQ 107 GLU cc_start: 0.9019 (pp20) cc_final: 0.8758 (pp20) REVERT: SQ 116 ASP cc_start: 0.8469 (t0) cc_final: 0.8038 (t0) REVERT: ST 114 GLU cc_start: 0.8294 (pm20) cc_final: 0.7971 (pm20) REVERT: SU 113 GLU cc_start: 0.7840 (mp0) cc_final: 0.7518 (mp0) REVERT: Sc 18 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9230 (mt) REVERT: Sc 33 GLU cc_start: 0.8386 (pp20) cc_final: 0.8111 (pp20) REVERT: Sc 60 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6932 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5201 (tt0) REVERT: Sd 5 GLN cc_start: 0.9052 (mp10) cc_final: 0.8750 (mp10) REVERT: Sg 14 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.7191 (p90) REVERT: Sg 27 PHE cc_start: 0.9434 (m-80) cc_final: 0.9211 (m-80) REVERT: Sg 42 MET cc_start: 0.8696 (ttm) cc_final: 0.8317 (ptm) REVERT: Sg 140 TYR cc_start: 0.8312 (t80) cc_final: 0.8104 (t80) REVERT: Sg 145 GLU cc_start: 0.8560 (mp0) cc_final: 0.8257 (mp0) REVERT: Sg 228 TYR cc_start: 0.7619 (t80) cc_final: 0.7266 (t80) REVERT: Sg 282 GLU cc_start: 0.8878 (mp0) cc_final: 0.8628 (pm20) REVERT: SM 23 LYS cc_start: 0.9491 (mmmm) cc_final: 0.9195 (mppt) REVERT: SM 37 GLU cc_start: 0.8220 (mp0) cc_final: 0.7916 (mp0) REVERT: SM 48 HIS cc_start: 0.8048 (m170) cc_final: 0.7828 (m90) REVERT: SM 63 LYS cc_start: 0.9288 (ptmt) cc_final: 0.8970 (pptt) REVERT: SM 78 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8897 (mmmm) REVERT: SM 84 LYS cc_start: 0.9199 (tppt) cc_final: 0.8902 (tppp) REVERT: SM 91 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8231 (tm) outliers start: 91 outliers final: 51 residues processed: 413 average time/residue: 1.2866 time to fit residues: 618.9151 Evaluate side-chains 406 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 345 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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 117 ARG Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SF residue 19 LEU 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 32 GLN Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 57 LEU 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 104 SER Chi-restraints excluded: chain SS residue 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 84 LEU 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 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 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 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 287 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 313 THR Chi-restraints excluded: chain SM residue 91 LEU 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 48 VAL Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 68 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 144 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SF 29 GLN SF 82 ASN SP 24 GLN SP 46 ASN SQ 97 GLN Sc 29 GLN Sg 62 HIS ** Sg 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.068983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.050379 restraints weight = 77926.483| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.19 r_work: 0.2761 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3102 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= 0.251 Angle : 0.765 14.516 39102 Z= 0.384 Chirality : 0.043 0.205 4767 Planarity : 0.006 0.143 3185 Dihedral : 22.291 166.541 9779 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.49 % Favored : 89.35 % Rotamer: Outliers : 5.03 % Allowed : 38.48 % Favored : 56.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.19), residues: 1916 helix: 0.44 (0.22), residues: 586 sheet: -1.07 (0.28), residues: 319 loop : -1.93 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPCD 287 HIS 0.013 0.001 HISSg 188 PHE 0.028 0.002 PHESF 61 TYR 0.024 0.002 TYRSf 140 ARG 0.008 0.001 ARGSf 119 Details of bonding type rmsd hydrogen bonds : bond 0.06373 ( 952) hydrogen bonds : angle 4.08048 ( 2152) covalent geometry : bond 0.00524 (27254) covalent geometry : angle 0.76462 (39102) ********************** 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 431 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 347 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SD 56 GLN cc_start: 0.9232 (tp-100) cc_final: 0.8841 (tp-100) REVERT: SD 74 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8668 (tm-30) REVERT: SD 117 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8204 (ttt90) REVERT: SD 189 MET cc_start: 0.9337 (ttt) cc_final: 0.9119 (ttt) REVERT: SF 45 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.8002 (p90) REVERT: SK 29 MET cc_start: 0.9329 (ttm) cc_final: 0.8967 (ttp) REVERT: SK 31 LYS cc_start: 0.9439 (mptp) cc_final: 0.9109 (mptp) REVERT: SK 80 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8662 (tpp80) REVERT: SP 23 ASP cc_start: 0.9041 (m-30) cc_final: 0.8591 (m-30) REVERT: SP 27 ASP cc_start: 0.8991 (m-30) cc_final: 0.8683 (m-30) REVERT: SP 34 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8280 (mmm) REVERT: SP 66 GLU cc_start: 0.8568 (mp0) cc_final: 0.8282 (mp0) REVERT: SQ 107 GLU cc_start: 0.9064 (pp20) cc_final: 0.8798 (pp20) REVERT: SQ 116 ASP cc_start: 0.8487 (t0) cc_final: 0.8031 (t0) REVERT: SS 10 GLN cc_start: 0.8799 (mm110) cc_final: 0.8587 (mm-40) REVERT: ST 114 GLU cc_start: 0.8353 (pm20) cc_final: 0.7967 (pm20) REVERT: SU 113 GLU cc_start: 0.7903 (mp0) cc_final: 0.7594 (mp0) REVERT: Sc 18 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9279 (mt) REVERT: Sc 62 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5193 (tt0) REVERT: Sd 5 GLN cc_start: 0.9056 (mp10) cc_final: 0.8775 (mp10) REVERT: Sg 14 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.7377 (p90) REVERT: Sg 27 PHE cc_start: 0.9473 (m-80) cc_final: 0.9270 (m-80) REVERT: Sg 42 MET cc_start: 0.8682 (ttm) cc_final: 0.8230 (ptm) REVERT: Sg 140 TYR cc_start: 0.8356 (t80) cc_final: 0.8112 (t80) REVERT: Sg 145 GLU cc_start: 0.8539 (mp0) cc_final: 0.8222 (mp0) REVERT: Sg 195 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8427 (mm) REVERT: Sg 228 TYR cc_start: 0.7686 (t80) cc_final: 0.7285 (t80) REVERT: Sg 282 GLU cc_start: 0.8932 (mp0) cc_final: 0.8670 (pm20) REVERT: SM 23 LYS cc_start: 0.9539 (mmmm) cc_final: 0.9265 (mppt) REVERT: SM 37 GLU cc_start: 0.8394 (mp0) cc_final: 0.8108 (mp0) REVERT: SM 48 HIS cc_start: 0.8037 (m170) cc_final: 0.7811 (m90) REVERT: SM 63 LYS cc_start: 0.9280 (ptmt) cc_final: 0.9041 (pptt) REVERT: SM 78 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8875 (mmmm) REVERT: SM 84 LYS cc_start: 0.9230 (tppt) cc_final: 0.8922 (tppp) REVERT: SM 91 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8301 (tm) REVERT: SZ 50 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8329 (p90) REVERT: SZ 75 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8612 (tp30) outliers start: 84 outliers final: 58 residues processed: 400 average time/residue: 1.3224 time to fit residues: 613.9752 Evaluate side-chains 406 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 338 time to evaluate : 2.011 ------------------------------------------------------------------------------- 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 117 ARG Chi-restraints excluded: chain SD residue 181 VAL 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 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 SP residue 20 VAL Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 52 LYS Chi-restraints excluded: chain SP residue 57 LEU 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 104 SER 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 SS residue 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 84 LEU 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 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 50 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 62 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 313 THR Chi-restraints excluded: chain SM residue 91 LEU 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 48 VAL Chi-restraints excluded: chain SZ residue 50 PHE Chi-restraints excluded: chain SZ residue 61 GLU Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 68 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 172 optimal weight: 0.6980 chunk 224 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 227 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 177 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.071510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.053165 restraints weight = 78213.711| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.22 r_work: 0.2846 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27254 Z= 0.143 Angle : 0.750 14.233 39102 Z= 0.372 Chirality : 0.039 0.227 4767 Planarity : 0.005 0.152 3185 Dihedral : 22.327 170.783 9779 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.18 % Favored : 89.67 % Rotamer: Outliers : 4.67 % Allowed : 38.84 % Favored : 56.49 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.19), residues: 1916 helix: 0.54 (0.22), residues: 583 sheet: -1.10 (0.28), residues: 321 loop : -1.90 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPCD 287 HIS 0.013 0.001 HISSg 188 PHE 0.035 0.002 PHESf 136 TYR 0.023 0.001 TYRSf 140 ARG 0.007 0.000 ARGSc 66 Details of bonding type rmsd hydrogen bonds : bond 0.05757 ( 952) hydrogen bonds : angle 4.03687 ( 2152) covalent geometry : bond 0.00313 (27254) covalent geometry : angle 0.74953 (39102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23551.25 seconds wall clock time: 406 minutes 19.08 seconds (24379.08 seconds total)