Starting phenix.real_space_refine on Sun Jun 22 07:27:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9azm_44016/06_2025/9azm_44016.cif Found real_map, /net/cci-nas-00/data/ceres_data/9azm_44016/06_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_44016/06_2025/9azm_44016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9azm_44016/06_2025/9azm_44016.map" model { file = "/net/cci-nas-00/data/ceres_data/9azm_44016/06_2025/9azm_44016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9azm_44016/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.37, per 1000 atoms: 0.67 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: 8.10 Conformation dependent library (CDL) restraints added in 3.5 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: 12.25 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: 15.81 Time building geometry restraints manager: 8.89 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: 13.410 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: 0.060 Extract box with map and model: 0.980 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 74.490 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.100 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:14.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.180 ------------------------------------------------------------------------------- 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 : 2.157 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: 1.2694 time to fit residues: 630.4396 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 : 3.143 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.055800 restraints weight = 77238.946| |-----------------------------------------------------------------------------| 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: 0.2792 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 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 : 2.235 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: 0.9304 (OUTLIER) cc_final: 0.8817 (mm) REVERT: SD 56 GLN cc_start: 0.9176 (tp-100) cc_final: 0.8939 (tp-100) REVERT: SD 74 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8872 (tm-30) REVERT: SD 94 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8653 (ptp90) REVERT: SF 27 ASP cc_start: 0.8405 (p0) cc_final: 0.8190 (p0) REVERT: SF 29 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8446 (mm-40) REVERT: SF 36 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: SF 106 GLU cc_start: 0.8346 (pp20) cc_final: 0.7850 (pp20) REVERT: SF 127 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6434 (tpp-160) REVERT: SF 136 ARG cc_start: 0.7039 (mtp180) cc_final: 0.6737 (mtp85) REVERT: SK 29 MET cc_start: 0.9305 (ttm) cc_final: 0.8937 (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: 0.8825 (pm20) REVERT: SP 34 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8128 (mtm) REVERT: SP 65 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8858 (tptp) REVERT: SP 69 PRO cc_start: 0.9481 (Cg_exo) cc_final: 0.8736 (Cg_endo) REVERT: SQ 107 GLU cc_start: 0.8778 (pp20) cc_final: 0.8507 (pp20) REVERT: SQ 116 ASP cc_start: 0.8184 (t0) cc_final: 0.7856 (t0) REVERT: SS 50 ILE cc_start: 0.8697 (pt) cc_final: 0.8080 (pp) REVERT: SS 63 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.7468 (mm-30) REVERT: SS 73 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8640 (p0) REVERT: SS 92 ASP cc_start: 0.8519 (t0) cc_final: 0.8131 (t0) REVERT: ST 114 GLU cc_start: 0.8502 (pm20) cc_final: 0.8103 (pm20) REVERT: ST 126 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8357 (tm-30) REVERT: ST 143 LYS cc_start: 0.9152 (tppt) cc_final: 0.8950 (tppt) REVERT: SU 111 GLU cc_start: 0.8431 (tt0) cc_final: 0.8197 (tt0) REVERT: SU 113 GLU cc_start: 0.7996 (mp0) cc_final: 0.7664 (mp0) REVERT: Sc 41 SER cc_start: 0.8497 (p) cc_final: 0.8283 (t) REVERT: Sc 60 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6381 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5017 (OUTLIER) cc_final: 0.4812 (tt0) REVERT: Sc 66 ARG cc_start: 0.7449 (mpp80) cc_final: 0.7213 (mtm-85) REVERT: Sg 14 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.7417 (p90) REVERT: Sg 195 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8433 (mm) REVERT: Sg 228 TYR cc_start: 0.7498 (t80) cc_final: 0.7259 (t80) REVERT: SM 88 TRP cc_start: 0.9313 (m-10) cc_final: 0.9107 (m-10) REVERT: SZ 50 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8434 (p90) REVERT: Sf 103 LEU cc_start: 0.6795 (pt) cc_final: 0.6544 (pp) REVERT: Sf 113 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8409 (mmtt) outliers start: 162 outliers final: 61 residues processed: 464 average time/residue: 1.3500 time to fit residues: 728.8549 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 : 2.247 ------------------------------------------------------------------------------- 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: 0.9990 chunk 194 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 74 optimal weight: 0.0970 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.074098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055767 restraints weight = 77240.557| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.20 r_work: 0.2905 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27254 Z= 0.158 Angle : 0.683 12.624 39102 Z= 0.344 Chirality : 0.040 0.229 4767 Planarity : 0.005 0.127 3185 Dihedral : 22.417 168.943 9788 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.55 % Favored : 90.24 % Rotamer: Outliers : 8.98 % Allowed : 33.09 % Favored : 57.93 % 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: -1.83 (0.19), residues: 1916 helix: 0.07 (0.21), residues: 588 sheet: -1.26 (0.29), residues: 310 loop : -2.02 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPSg 219 HIS 0.012 0.001 HISSg 188 PHE 0.033 0.002 PHESF 61 TYR 0.017 0.001 TYRSf 140 ARG 0.011 0.001 ARGSg 118 Details of bonding type rmsd hydrogen bonds : bond 0.06319 ( 952) hydrogen bonds : angle 4.43296 ( 2152) covalent geometry : bond 0.00331 (27254) covalent geometry : angle 0.68335 (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 504 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 354 time to evaluate : 2.108 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: 0.7578 (tpt) cc_final: 0.7233 (tpt) REVERT: CD 287 TRP cc_start: 0.9040 (t-100) cc_final: 0.8696 (t60) REVERT: SD 56 GLN cc_start: 0.9125 (tp-100) cc_final: 0.8852 (tp-100) REVERT: SD 74 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8757 (tm-30) REVERT: SD 94 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8680 (ptp90) REVERT: SF 29 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8419 (mm-40) REVERT: SF 127 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6410 (tpp-160) REVERT: SK 13 GLU cc_start: 0.8304 (pm20) cc_final: 0.8053 (pm20) REVERT: SK 29 MET cc_start: 0.9288 (ttm) cc_final: 0.8931 (ttp) REVERT: SK 89 ILE cc_start: 0.9021 (mp) cc_final: 0.8424 (mp) REVERT: SP 23 ASP cc_start: 0.8988 (m-30) cc_final: 0.8723 (m-30) REVERT: SP 65 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8869 (tptp) REVERT: SP 69 PRO cc_start: 0.9222 (Cg_exo) cc_final: 0.9004 (Cg_endo) REVERT: SQ 41 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7327 (mpp) REVERT: SQ 107 GLU cc_start: 0.8856 (pp20) cc_final: 0.8621 (pp20) REVERT: SQ 116 ASP cc_start: 0.8338 (t0) cc_final: 0.7944 (t0) REVERT: SS 50 ILE cc_start: 0.8605 (pt) cc_final: 0.8004 (pp) REVERT: SS 63 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: SS 73 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8499 (p0) REVERT: ST 114 GLU cc_start: 0.8374 (pm20) cc_final: 0.7971 (pm20) REVERT: ST 143 LYS cc_start: 0.9164 (tppt) cc_final: 0.8904 (tppt) REVERT: SU 113 GLU cc_start: 0.7966 (mp0) cc_final: 0.7630 (mp0) REVERT: Sc 18 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9165 (mt) REVERT: Sc 31 ARG cc_start: 0.8556 (tpp80) cc_final: 0.8263 (tpp80) REVERT: Sc 41 SER cc_start: 0.8620 (p) cc_final: 0.8379 (t) REVERT: Sc 60 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6260 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5143 (OUTLIER) cc_final: 0.4891 (tt0) REVERT: Sg 14 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.7375 (p90) REVERT: Sg 195 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8488 (mm) REVERT: Sg 228 TYR cc_start: 0.7337 (t80) cc_final: 0.7107 (t80) REVERT: Sg 282 GLU cc_start: 0.9003 (mp0) cc_final: 0.8666 (pm20) REVERT: SM 37 GLU cc_start: 0.8282 (mp0) cc_final: 0.8032 (mp0) REVERT: SM 58 GLU cc_start: 0.8998 (tp30) cc_final: 0.8455 (tp30) REVERT: SM 61 TYR cc_start: 0.8589 (t80) cc_final: 0.8382 (t80) REVERT: SM 88 TRP cc_start: 0.9324 (m-10) cc_final: 0.9077 (m-10) REVERT: SZ 50 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8353 (p90) REVERT: Sf 103 LEU cc_start: 0.6690 (pt) cc_final: 0.6463 (pp) REVERT: Sf 107 LYS cc_start: 0.8583 (tptp) cc_final: 0.8330 (tptp) outliers start: 150 outliers final: 56 residues processed: 458 average time/residue: 1.2861 time to fit residues: 685.5722 Evaluate side-chains 401 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 334 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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 26 ASP Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 127 ARG Chi-restraints excluded: chain SF residue 141 VAL 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 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 92 SER Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 41 MET Chi-restraints excluded: chain SQ residue 67 ASP Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 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 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 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 46 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 62 GLU Chi-restraints excluded: chain Sg residue 14 HIS Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 144 ASP Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 195 LEU Chi-restraints excluded: chain Sg residue 287 THR Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 312 VAL Chi-restraints excluded: chain SM residue 14 VAL Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain SZ residue 47 LEU Chi-restraints excluded: chain SZ residue 50 PHE Chi-restraints excluded: chain SZ residue 58 LEU Chi-restraints excluded: chain SZ residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 18 optimal weight: 7.9990 chunk 206 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** SM 48 HIS ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.073218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.054788 restraints weight = 77656.720| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.22 r_work: 0.2878 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27254 Z= 0.175 Angle : 0.686 13.412 39102 Z= 0.344 Chirality : 0.040 0.229 4767 Planarity : 0.005 0.118 3185 Dihedral : 22.366 169.026 9782 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.28 % Favored : 89.56 % Rotamer: Outliers : 8.44 % Allowed : 33.33 % Favored : 58.23 % 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: -1.71 (0.19), residues: 1916 helix: 0.25 (0.21), residues: 583 sheet: -1.15 (0.29), residues: 314 loop : -2.01 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPSg 219 HIS 0.011 0.001 HISSg 188 PHE 0.030 0.002 PHESf 136 TYR 0.016 0.002 TYRSZ 65 ARG 0.006 0.000 ARGSc 66 Details of bonding type rmsd hydrogen bonds : bond 0.06237 ( 952) hydrogen bonds : angle 4.25196 ( 2152) covalent geometry : bond 0.00368 (27254) covalent geometry : angle 0.68571 (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 497 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 356 time to evaluate : 2.095 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: 0.7644 (tpt) cc_final: 0.7400 (tpt) REVERT: CD 287 TRP cc_start: 0.9085 (t-100) cc_final: 0.8647 (t-100) REVERT: SD 50 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8721 (mm) REVERT: SD 56 GLN cc_start: 0.9160 (tp-100) cc_final: 0.8881 (tp-100) REVERT: SD 74 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8718 (tm-30) REVERT: SD 127 MET cc_start: 0.9205 (mmm) cc_final: 0.8985 (mmt) REVERT: SF 25 THR cc_start: 0.8873 (m) cc_final: 0.8529 (t) REVERT: SF 29 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8363 (mm-40) REVERT: SF 136 ARG cc_start: 0.7233 (mtp180) cc_final: 0.6870 (mtp85) REVERT: SK 18 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7888 (pp20) REVERT: SK 29 MET cc_start: 0.9270 (ttm) cc_final: 0.8915 (ttp) REVERT: SK 80 ARG cc_start: 0.9066 (tpp80) cc_final: 0.8669 (tpp80) REVERT: SK 89 ILE cc_start: 0.9080 (mp) cc_final: 0.8330 (mp) REVERT: SP 34 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8191 (mtm) REVERT: SP 65 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8950 (tptp) REVERT: SQ 43 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: SQ 84 ILE cc_start: 0.9698 (OUTLIER) cc_final: 0.9422 (mp) REVERT: SQ 107 GLU cc_start: 0.8924 (pp20) cc_final: 0.8654 (pp20) REVERT: SQ 116 ASP cc_start: 0.8478 (t0) cc_final: 0.8036 (t0) REVERT: SS 50 ILE cc_start: 0.8661 (pt) cc_final: 0.8020 (pp) REVERT: SS 63 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: ST 114 GLU cc_start: 0.8351 (pm20) cc_final: 0.8007 (pm20) REVERT: ST 121 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8428 (ptp-170) REVERT: ST 143 LYS cc_start: 0.9129 (tppt) cc_final: 0.8888 (tppt) REVERT: SU 111 GLU cc_start: 0.8381 (tt0) cc_final: 0.8157 (tt0) REVERT: SU 113 GLU cc_start: 0.7930 (mp0) cc_final: 0.7235 (mp0) REVERT: Sc 18 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9211 (mt) REVERT: Sc 29 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: Sc 60 GLU cc_start: 0.6825 (tm-30) cc_final: 0.6270 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5178 (OUTLIER) cc_final: 0.4881 (tt0) REVERT: Sd 5 GLN cc_start: 0.8721 (mp10) cc_final: 0.8345 (mp10) REVERT: Sg 14 HIS cc_start: 0.8669 (OUTLIER) cc_final: 0.7430 (p90) REVERT: Sg 140 TYR cc_start: 0.8193 (t80) cc_final: 0.7870 (t80) REVERT: Sg 195 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8453 (mm) REVERT: Sg 228 TYR cc_start: 0.7472 (t80) cc_final: 0.7239 (t80) REVERT: Sg 282 GLU cc_start: 0.9001 (mp0) cc_final: 0.8656 (pm20) REVERT: SM 37 GLU cc_start: 0.8347 (mp0) cc_final: 0.8069 (mp0) REVERT: SM 63 LYS cc_start: 0.9127 (ptmt) cc_final: 0.8731 (pptt) REVERT: SM 78 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8876 (mmmm) REVERT: SM 83 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8815 (mmmt) REVERT: SM 88 TRP cc_start: 0.9271 (m-10) cc_final: 0.8914 (m-10) REVERT: Sf 103 LEU cc_start: 0.6735 (pt) cc_final: 0.6525 (pp) REVERT: Sf 110 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6820 (pp20) REVERT: Sf 113 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8236 (mmtt) outliers start: 141 outliers final: 68 residues processed: 453 average time/residue: 1.3604 time to fit residues: 713.2783 Evaluate side-chains 419 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 338 time to evaluate : 2.394 ------------------------------------------------------------------------------- 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 170 THR Chi-restraints excluded: chain SD residue 181 VAL 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 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 SK residue 96 ARG Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 65 LYS Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SQ residue 26 LYS Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 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 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 63 GLU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 83 PHE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain 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 121 ARG Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain 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 46 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 62 GLU Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 14 HIS Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 64 HIS Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 144 ASP Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 168 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 195 LEU Chi-restraints excluded: chain Sg residue 287 THR Chi-restraints excluded: chain Sg residue 306 LEU Chi-restraints excluded: chain Sg residue 309 VAL Chi-restraints excluded: chain Sg residue 312 VAL Chi-restraints excluded: chain Sg residue 313 THR Chi-restraints excluded: chain SM residue 14 VAL Chi-restraints excluded: chain SM residue 104 VAL Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain SZ residue 47 LEU Chi-restraints excluded: chain SZ residue 58 LEU Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 65 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 48 GLN SQ 97 GLN SU 92 HIS ** Sg 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sg 143 GLN ** Sg 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 48 HIS ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.067711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.048952 restraints weight = 77858.730| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.23 r_work: 0.2712 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 27254 Z= 0.411 Angle : 0.843 17.034 39102 Z= 0.427 Chirality : 0.049 0.250 4767 Planarity : 0.006 0.121 3185 Dihedral : 22.534 162.363 9782 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.28 % Favored : 89.35 % Rotamer: Outliers : 10.23 % Allowed : 31.72 % Favored : 58.05 % 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: -1.80 (0.19), residues: 1916 helix: 0.18 (0.21), residues: 579 sheet: -1.41 (0.28), residues: 346 loop : -1.99 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPSg 219 HIS 0.032 0.002 HISSg 64 PHE 0.035 0.003 PHESF 61 TYR 0.028 0.002 TYRSZ 65 ARG 0.009 0.001 ARGSc 66 Details of bonding type rmsd hydrogen bonds : bond 0.07678 ( 952) hydrogen bonds : angle 4.35852 ( 2152) covalent geometry : bond 0.00847 (27254) covalent geometry : angle 0.84312 (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 526 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 355 time to evaluate : 2.096 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: 0.7835 (tpt) cc_final: 0.7498 (tpt) REVERT: CD 283 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7705 (t) REVERT: CD 287 TRP cc_start: 0.9222 (t-100) cc_final: 0.8749 (t-100) REVERT: SD 50 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.8963 (mm) REVERT: SD 56 GLN cc_start: 0.9237 (tp-100) cc_final: 0.8889 (tp-100) REVERT: SD 74 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8860 (tm-30) REVERT: SD 117 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8418 (ttt90) REVERT: SF 83 ASN cc_start: 0.9046 (OUTLIER) cc_final: 0.8822 (m-40) REVERT: SK 5 LYS cc_start: 0.8884 (ttpm) cc_final: 0.8681 (ttmm) REVERT: SK 89 ILE cc_start: 0.9185 (mp) cc_final: 0.8672 (mp) REVERT: SK 95 ARG cc_start: 0.7832 (tmm160) cc_final: 0.7546 (tmm-80) REVERT: SP 31 GLU cc_start: 0.9154 (mp0) cc_final: 0.8857 (mp0) REVERT: SP 34 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8366 (mtm) REVERT: SP 66 GLU cc_start: 0.8596 (mp0) cc_final: 0.8316 (mp0) REVERT: SP 106 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7859 (tp30) REVERT: SQ 43 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: SQ 107 GLU cc_start: 0.8997 (pp20) cc_final: 0.8728 (pp20) REVERT: SQ 116 ASP cc_start: 0.8578 (t0) cc_final: 0.8065 (t0) REVERT: ST 114 GLU cc_start: 0.8439 (pm20) cc_final: 0.7990 (pm20) REVERT: ST 143 LYS cc_start: 0.9158 (tppt) cc_final: 0.8908 (tppt) REVERT: SU 107 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7719 (tp30) REVERT: SU 113 GLU cc_start: 0.8013 (mp0) cc_final: 0.7585 (mp0) REVERT: Sc 18 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9340 (mt) REVERT: Sc 33 GLU cc_start: 0.8458 (pp20) cc_final: 0.7888 (pp20) REVERT: Sc 51 ARG cc_start: 0.8165 (tpt-90) cc_final: 0.7940 (tpt-90) REVERT: Sc 60 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6670 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.5084 (tt0) REVERT: Sd 5 GLN cc_start: 0.8876 (mp10) cc_final: 0.8314 (mp10) REVERT: Sg 14 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.7443 (p90) REVERT: Sg 145 GLU cc_start: 0.8501 (mp0) cc_final: 0.8163 (mp0) REVERT: Sg 195 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8611 (mm) REVERT: Sg 217 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7215 (pmt) REVERT: Sg 228 TYR cc_start: 0.7590 (t80) cc_final: 0.7301 (t80) REVERT: Sg 282 GLU cc_start: 0.9099 (mp0) cc_final: 0.8764 (pm20) REVERT: SM 48 HIS cc_start: 0.8010 (m170) cc_final: 0.7798 (m90) REVERT: SM 63 LYS cc_start: 0.9135 (ptmt) cc_final: 0.8840 (pptt) REVERT: SM 78 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8817 (mmmm) REVERT: SM 88 TRP cc_start: 0.9248 (m-10) cc_final: 0.8852 (m-10) REVERT: SM 91 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8632 (tm) REVERT: Sf 107 LYS cc_start: 0.8945 (tppt) cc_final: 0.8691 (ttpp) REVERT: Sf 117 LEU cc_start: 0.9229 (mp) cc_final: 0.9008 (mp) outliers start: 171 outliers final: 78 residues processed: 478 average time/residue: 1.3304 time to fit residues: 743.6477 Evaluate side-chains 431 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 340 time to evaluate : 2.105 ------------------------------------------------------------------------------- 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 117 ARG Chi-restraints excluded: chain SD residue 153 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 173 ARG Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 79 HIS Chi-restraints excluded: chain SF residue 83 ASN Chi-restraints excluded: chain SF residue 141 VAL Chi-restraints excluded: chain SK residue 13 GLU Chi-restraints excluded: chain SK residue 35 LEU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 85 LEU Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 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 SP residue 106 GLU 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 100 VAL Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SQ residue 111 ILE Chi-restraints excluded: chain SQ residue 118 THR Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SS residue 12 ILE Chi-restraints excluded: chain SS residue 13 LEU Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 45 LEU Chi-restraints excluded: chain SS residue 59 LEU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 8 ASP Chi-restraints excluded: chain ST residue 28 LEU Chi-restraints excluded: chain ST residue 34 VAL Chi-restraints excluded: chain ST residue 36 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 121 ARG Chi-restraints excluded: chain SU residue 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 21 THR Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 41 SER 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 Sc residue 64 GLU Chi-restraints excluded: chain Sg residue 14 HIS Chi-restraints excluded: chain Sg residue 21 ILE Chi-restraints excluded: chain Sg residue 52 TYR Chi-restraints excluded: chain Sg residue 63 SER Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 144 ASP Chi-restraints excluded: chain Sg residue 147 HIS 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 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 58 LEU Chi-restraints excluded: chain SZ residue 59 CYS Chi-restraints excluded: chain SZ residue 62 VAL Chi-restraints excluded: chain SZ residue 72 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 118 optimal weight: 8.9990 chunk 225 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 99 optimal weight: 0.0010 chunk 91 optimal weight: 0.6980 chunk 210 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- 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 SP 54 HIS SQ 48 GLN SQ 97 GLN SU 92 HIS Sc 29 GLN Sg 62 HIS Sg 64 HIS ** Sg 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 244 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.070872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.052437 restraints weight = 77768.269| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.21 r_work: 0.2816 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27254 Z= 0.167 Angle : 0.712 14.089 39102 Z= 0.358 Chirality : 0.041 0.236 4767 Planarity : 0.005 0.116 3185 Dihedral : 22.445 167.458 9782 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.81 % Favored : 90.03 % Rotamer: Outliers : 8.38 % Allowed : 34.89 % Favored : 56.73 % 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: -1.65 (0.19), residues: 1916 helix: 0.36 (0.22), residues: 586 sheet: -1.13 (0.29), residues: 314 loop : -2.02 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPSg 219 HIS 0.012 0.001 HISSg 188 PHE 0.023 0.002 PHESF 61 TYR 0.016 0.002 TYRSD 107 ARG 0.007 0.000 ARGSc 31 Details of bonding type rmsd hydrogen bonds : bond 0.06098 ( 952) hydrogen bonds : angle 4.15924 ( 2152) covalent geometry : bond 0.00352 (27254) covalent geometry : angle 0.71173 (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 505 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 365 time to evaluate : 2.002 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 283 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7654 (t) REVERT: CD 287 TRP cc_start: 0.9141 (t-100) cc_final: 0.8729 (t-100) REVERT: SD 56 GLN cc_start: 0.9199 (tp-100) cc_final: 0.8855 (tp-100) REVERT: SD 74 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8634 (tm-30) REVERT: SD 117 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8186 (ttm-80) REVERT: SF 45 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8052 (p90) REVERT: SF 83 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8474 (m110) REVERT: SF 146 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8386 (ttt90) REVERT: SK 5 LYS cc_start: 0.8852 (ttpm) cc_final: 0.8644 (ttmm) REVERT: SK 29 MET cc_start: 0.9304 (ttm) cc_final: 0.8939 (ttp) REVERT: SK 31 LYS cc_start: 0.9396 (mptp) cc_final: 0.9072 (mptp) REVERT: SK 89 ILE cc_start: 0.9210 (mp) cc_final: 0.8836 (mp) REVERT: SP 31 GLU cc_start: 0.9049 (mp0) cc_final: 0.8774 (mp0) REVERT: SP 34 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8251 (mtm) REVERT: SQ 84 ILE cc_start: 0.9708 (OUTLIER) cc_final: 0.9462 (mp) REVERT: SQ 107 GLU cc_start: 0.9001 (pp20) cc_final: 0.8700 (pp20) REVERT: SQ 116 ASP cc_start: 0.8524 (t0) cc_final: 0.8053 (t0) REVERT: ST 35 ASP cc_start: 0.9170 (p0) cc_final: 0.8945 (p0) REVERT: ST 36 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8068 (p) REVERT: ST 108 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8496 (mt-10) REVERT: ST 111 LYS cc_start: 0.9421 (mmmm) cc_final: 0.9169 (mppt) REVERT: ST 114 GLU cc_start: 0.8377 (pm20) cc_final: 0.7931 (pm20) REVERT: ST 143 LYS cc_start: 0.9117 (tppt) cc_final: 0.8913 (tppt) REVERT: SU 44 LYS cc_start: 0.9434 (mmmt) cc_final: 0.9220 (mmmm) REVERT: SU 92 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.7157 (t-90) REVERT: SU 113 GLU cc_start: 0.7922 (mp0) cc_final: 0.7439 (mp0) REVERT: Sc 18 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9295 (mt) REVERT: Sc 33 GLU cc_start: 0.8429 (pp20) cc_final: 0.8187 (pp20) REVERT: Sc 60 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6692 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5297 (OUTLIER) cc_final: 0.5071 (tt0) REVERT: Sd 5 GLN cc_start: 0.8829 (mp10) cc_final: 0.8258 (mp10) REVERT: Sg 14 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.7247 (p90) REVERT: Sg 42 MET cc_start: 0.8794 (ttm) cc_final: 0.8323 (ptm) REVERT: Sg 140 TYR cc_start: 0.8265 (t80) cc_final: 0.7976 (t80) REVERT: Sg 228 TYR cc_start: 0.7509 (t80) cc_final: 0.7271 (t80) REVERT: Sg 282 GLU cc_start: 0.8992 (mp0) cc_final: 0.8709 (pm20) REVERT: SM 48 HIS cc_start: 0.8141 (m170) cc_final: 0.7938 (m90) REVERT: SM 58 GLU cc_start: 0.8865 (tp30) cc_final: 0.8186 (tp30) REVERT: SM 60 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.9051 (pmm) REVERT: SM 63 LYS cc_start: 0.9209 (ptmt) cc_final: 0.8823 (pptt) REVERT: SM 78 LYS cc_start: 0.9169 (mmmm) cc_final: 0.8887 (mmmm) REVERT: SM 84 LYS cc_start: 0.9234 (tppt) cc_final: 0.8961 (tppp) REVERT: SM 91 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8559 (tm) REVERT: SZ 50 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8309 (p90) REVERT: Sf 118 ARG cc_start: 0.8570 (mmt90) cc_final: 0.8257 (mpt-90) outliers start: 140 outliers final: 65 residues processed: 459 average time/residue: 1.3024 time to fit residues: 697.5982 Evaluate side-chains 426 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 346 time to evaluate : 2.173 ------------------------------------------------------------------------------- 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 117 ARG Chi-restraints excluded: chain SD residue 153 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SF residue 19 LEU 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 83 ASN Chi-restraints excluded: chain SF residue 146 ARG Chi-restraints excluded: chain SF residue 185 SER Chi-restraints excluded: chain SK residue 13 GLU Chi-restraints excluded: chain SK residue 35 LEU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 85 LEU Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 76 VAL Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SQ residue 26 LYS Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 67 ASP Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 84 ILE Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SQ residue 110 ASP Chi-restraints excluded: chain SQ residue 127 CYS Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SS residue 12 ILE Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 59 LEU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 28 LEU Chi-restraints excluded: chain ST residue 36 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 121 ARG Chi-restraints excluded: chain SU residue 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 SU residue 112 VAL Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 62 GLU Chi-restraints excluded: chain 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 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 91 LEU Chi-restraints excluded: chain SM residue 104 VAL 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 94 LYS Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 130 VAL Chi-restraints excluded: chain Sf residue 143 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 197 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SP 24 GLN SP 46 ASN SQ 97 GLN SU 92 HIS Sc 29 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 = 0.3379 r_free = 0.3379 target = 0.069417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.050827 restraints weight = 78094.848| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.20 r_work: 0.2772 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27254 Z= 0.230 Angle : 0.741 14.703 39102 Z= 0.372 Chirality : 0.043 0.222 4767 Planarity : 0.005 0.115 3185 Dihedral : 22.372 166.080 9782 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.54 % Favored : 89.30 % Rotamer: Outliers : 8.32 % Allowed : 35.43 % Favored : 56.25 % 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: -1.62 (0.19), residues: 1916 helix: 0.44 (0.22), residues: 582 sheet: -1.16 (0.29), residues: 323 loop : -2.02 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPSg 219 HIS 0.020 0.002 HISSU 92 PHE 0.027 0.002 PHESF 61 TYR 0.019 0.002 TYRSZ 65 ARG 0.008 0.001 ARGSK 95 Details of bonding type rmsd hydrogen bonds : bond 0.06395 ( 952) hydrogen bonds : angle 4.09985 ( 2152) covalent geometry : bond 0.00478 (27254) covalent geometry : angle 0.74064 (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 492 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 353 time to evaluate : 2.926 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 287 TRP cc_start: 0.9137 (t-100) cc_final: 0.8731 (t-100) REVERT: SD 50 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8777 (mm) REVERT: SD 56 GLN cc_start: 0.9212 (tp-100) cc_final: 0.8872 (tp-100) REVERT: SD 74 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8689 (tm-30) REVERT: SD 117 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8211 (ttm-80) REVERT: SF 45 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8086 (p90) REVERT: SF 60 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8546 (mtp180) REVERT: SF 83 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8572 (m-40) REVERT: SF 146 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8367 (ttt90) REVERT: SK 5 LYS cc_start: 0.8920 (ttpm) cc_final: 0.8707 (ttmm) REVERT: SK 29 MET cc_start: 0.9341 (ttm) cc_final: 0.8965 (ttp) REVERT: SK 31 LYS cc_start: 0.9422 (mptp) cc_final: 0.9048 (mptp) REVERT: SK 89 ILE cc_start: 0.9171 (mp) cc_final: 0.8600 (mp) REVERT: SP 31 GLU cc_start: 0.9049 (mp0) cc_final: 0.8773 (mp0) REVERT: SP 34 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8347 (mtm) REVERT: SQ 107 GLU cc_start: 0.9034 (pp20) cc_final: 0.8778 (pp20) REVERT: SQ 116 ASP cc_start: 0.8563 (t0) cc_final: 0.8108 (t0) REVERT: ST 35 ASP cc_start: 0.9193 (p0) cc_final: 0.8960 (p0) REVERT: ST 114 GLU cc_start: 0.8379 (pm20) cc_final: 0.7911 (pm20) REVERT: ST 143 LYS cc_start: 0.9124 (tppt) cc_final: 0.8918 (tppt) REVERT: SU 21 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7693 (ttm170) REVERT: SU 44 LYS cc_start: 0.9452 (mmmt) cc_final: 0.9234 (mmmm) REVERT: SU 113 GLU cc_start: 0.7907 (mp0) cc_final: 0.7593 (mp0) REVERT: Sc 18 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9348 (mt) REVERT: Sc 29 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8205 (mt0) REVERT: Sc 33 GLU cc_start: 0.8453 (pp20) cc_final: 0.7834 (pp20) REVERT: Sc 51 ARG cc_start: 0.7915 (tpt-90) cc_final: 0.7684 (tpt-90) REVERT: Sc 60 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6812 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5473 (OUTLIER) cc_final: 0.5205 (tt0) REVERT: Sd 5 GLN cc_start: 0.8944 (mp10) cc_final: 0.8414 (mp10) REVERT: Sg 14 HIS cc_start: 0.8744 (OUTLIER) cc_final: 0.7361 (p90) REVERT: Sg 27 PHE cc_start: 0.9429 (m-80) cc_final: 0.9181 (m-80) REVERT: Sg 140 TYR cc_start: 0.8264 (t80) cc_final: 0.7956 (t80) REVERT: Sg 228 TYR cc_start: 0.7565 (t80) cc_final: 0.7266 (t80) REVERT: Sg 282 GLU cc_start: 0.8954 (mp0) cc_final: 0.8665 (pm20) REVERT: SM 23 LYS cc_start: 0.9599 (mmmm) cc_final: 0.9152 (mmtp) REVERT: SM 37 GLU cc_start: 0.8315 (mp0) cc_final: 0.8072 (mp0) REVERT: SM 63 LYS cc_start: 0.9282 (ptmt) cc_final: 0.8936 (pptt) REVERT: SM 78 LYS cc_start: 0.9152 (mmmm) cc_final: 0.8940 (mmmm) REVERT: SM 88 TRP cc_start: 0.9183 (m-10) cc_final: 0.8787 (m-10) REVERT: SM 91 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8580 (tm) REVERT: SZ 50 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8350 (p90) REVERT: SZ 75 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8536 (tp30) REVERT: Sf 107 LYS cc_start: 0.8870 (tptp) cc_final: 0.8541 (ttpp) outliers start: 139 outliers final: 74 residues processed: 450 average time/residue: 1.3869 time to fit residues: 726.7292 Evaluate side-chains 432 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 344 time to evaluate : 2.358 ------------------------------------------------------------------------------- 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 117 ARG Chi-restraints excluded: chain SD residue 153 VAL Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SF residue 17 ILE Chi-restraints excluded: chain SF residue 19 LEU Chi-restraints excluded: chain SF residue 45 TYR Chi-restraints excluded: chain SF residue 60 ARG Chi-restraints excluded: chain SF residue 79 HIS Chi-restraints excluded: chain SF residue 83 ASN Chi-restraints excluded: chain SF residue 141 VAL Chi-restraints excluded: chain SF residue 146 ARG Chi-restraints excluded: chain SF residue 185 SER Chi-restraints excluded: chain SK residue 13 GLU Chi-restraints excluded: chain SK residue 35 LEU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 85 LEU Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 24 GLN Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 76 VAL Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SQ residue 26 LYS Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 67 ASP Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 78 VAL Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 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 36 VAL Chi-restraints excluded: chain SS residue 59 LEU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 28 LEU Chi-restraints excluded: chain ST residue 36 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 121 ARG Chi-restraints excluded: chain SU residue 21 ARG Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 112 VAL Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 29 GLN 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 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 168 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 249 CYS 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 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 50 PHE Chi-restraints excluded: chain SZ residue 61 GLU Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 94 LYS Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sf residue 98 VAL Chi-restraints excluded: chain Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 130 VAL Chi-restraints excluded: chain Sf residue 143 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 133 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 94 optimal weight: 0.0040 chunk 26 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- 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 SU 92 HIS Sc 29 GLN Sg 62 HIS ** Sg 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sg 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.068926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.050138 restraints weight = 77703.036| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.22 r_work: 0.2756 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27254 Z= 0.244 Angle : 0.754 14.863 39102 Z= 0.378 Chirality : 0.043 0.216 4767 Planarity : 0.005 0.113 3185 Dihedral : 22.354 165.726 9782 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.23 % Favored : 89.61 % Rotamer: Outliers : 7.72 % Allowed : 36.56 % Favored : 55.72 % 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: -1.63 (0.19), residues: 1916 helix: 0.44 (0.22), residues: 580 sheet: -1.14 (0.29), residues: 319 loop : -2.03 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPSg 219 HIS 0.011 0.001 HISSg 188 PHE 0.025 0.002 PHESF 61 TYR 0.020 0.002 TYRSZ 65 ARG 0.006 0.001 ARGSc 51 Details of bonding type rmsd hydrogen bonds : bond 0.06388 ( 952) hydrogen bonds : angle 4.08349 ( 2152) covalent geometry : bond 0.00510 (27254) covalent geometry : angle 0.75382 (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 487 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 358 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CD 283 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7630 (t) REVERT: CD 287 TRP cc_start: 0.9075 (t-100) cc_final: 0.8730 (t-100) REVERT: SD 50 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8803 (mm) REVERT: SD 56 GLN cc_start: 0.9220 (tp-100) cc_final: 0.8779 (tp-100) REVERT: SD 74 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8822 (tm-30) REVERT: SD 117 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8238 (ttt90) REVERT: SF 45 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8044 (p90) REVERT: SF 60 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8564 (mtp180) REVERT: SF 83 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8590 (m-40) REVERT: SF 146 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8366 (ttt90) REVERT: SK 5 LYS cc_start: 0.8968 (ttpm) cc_final: 0.8751 (ttmm) REVERT: SK 29 MET cc_start: 0.9322 (ttm) cc_final: 0.8944 (ttp) REVERT: SK 31 LYS cc_start: 0.9438 (mptp) cc_final: 0.9095 (mptp) REVERT: SK 89 ILE cc_start: 0.9191 (mp) cc_final: 0.8531 (mp) REVERT: SP 31 GLU cc_start: 0.9027 (mp0) cc_final: 0.8751 (mp0) REVERT: SP 34 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8385 (mtm) REVERT: SQ 87 SER cc_start: 0.9425 (t) cc_final: 0.9117 (p) REVERT: SQ 107 GLU cc_start: 0.9042 (pp20) cc_final: 0.8790 (pp20) REVERT: SQ 116 ASP cc_start: 0.8513 (t0) cc_final: 0.8080 (t0) REVERT: ST 35 ASP cc_start: 0.9207 (p0) cc_final: 0.8954 (p0) REVERT: ST 114 GLU cc_start: 0.8398 (pm20) cc_final: 0.8015 (pm20) REVERT: SU 21 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7740 (ttm170) REVERT: SU 44 LYS cc_start: 0.9470 (mmmt) cc_final: 0.9260 (mmmm) REVERT: SU 49 LYS cc_start: 0.8937 (tppp) cc_final: 0.8300 (ttpt) REVERT: SU 92 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.7019 (t70) REVERT: SU 113 GLU cc_start: 0.7906 (mp0) cc_final: 0.7599 (mp0) REVERT: Sc 18 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9343 (mt) REVERT: Sc 33 GLU cc_start: 0.8448 (pp20) cc_final: 0.7781 (pp20) REVERT: Sc 51 ARG cc_start: 0.7953 (tpt-90) cc_final: 0.7744 (tpt-90) REVERT: Sc 60 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6932 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5490 (OUTLIER) cc_final: 0.5012 (tt0) REVERT: Sd 5 GLN cc_start: 0.9025 (mp10) cc_final: 0.8737 (mp10) REVERT: Sg 14 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.7414 (p90) REVERT: Sg 27 PHE cc_start: 0.9450 (m-80) cc_final: 0.9193 (m-80) REVERT: Sg 42 MET cc_start: 0.8726 (ttm) cc_final: 0.8275 (ptm) REVERT: Sg 140 TYR cc_start: 0.8339 (t80) cc_final: 0.8047 (t80) REVERT: Sg 145 GLU cc_start: 0.8736 (mp0) cc_final: 0.8508 (mp0) REVERT: Sg 228 TYR cc_start: 0.7577 (t80) cc_final: 0.7248 (t80) REVERT: Sg 282 GLU cc_start: 0.8947 (mp0) cc_final: 0.8686 (pm20) REVERT: SM 23 LYS cc_start: 0.9587 (mmmm) cc_final: 0.9264 (mppt) REVERT: SM 37 GLU cc_start: 0.8295 (mp0) cc_final: 0.8040 (mp0) REVERT: SM 58 GLU cc_start: 0.8870 (tp30) cc_final: 0.8229 (tp30) REVERT: SM 60 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8943 (pmm) REVERT: SM 63 LYS cc_start: 0.9275 (ptmt) cc_final: 0.8984 (pptt) REVERT: SM 78 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8834 (mmmm) REVERT: SM 84 LYS cc_start: 0.9188 (tppt) cc_final: 0.8478 (ttpp) REVERT: SM 88 TRP cc_start: 0.9177 (m-10) cc_final: 0.8645 (m-10) REVERT: SM 91 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8496 (tm) REVERT: SZ 50 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8371 (p90) REVERT: Sf 107 LYS cc_start: 0.8973 (tptp) cc_final: 0.8719 (ttpp) REVERT: Sf 113 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8454 (mmtp) REVERT: Sf 119 ARG cc_start: 0.8312 (mtm180) cc_final: 0.8087 (mmm-85) outliers start: 129 outliers final: 76 residues processed: 450 average time/residue: 1.5136 time to fit residues: 796.3706 Evaluate side-chains 445 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 353 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 117 ARG Chi-restraints excluded: chain SD residue 153 VAL Chi-restraints excluded: chain SD residue 169 ASP Chi-restraints excluded: chain SD residue 170 THR Chi-restraints excluded: chain SD residue 181 VAL Chi-restraints excluded: chain SF residue 17 ILE Chi-restraints excluded: chain SF residue 19 LEU 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 83 ASN 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 185 SER Chi-restraints excluded: chain SK residue 13 GLU Chi-restraints excluded: chain SK residue 35 LEU Chi-restraints excluded: chain SK residue 58 VAL Chi-restraints excluded: chain SK residue 85 LEU Chi-restraints excluded: chain SP residue 20 VAL Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 76 VAL Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SQ residue 26 LYS Chi-restraints excluded: chain SQ residue 32 ILE Chi-restraints excluded: chain SQ residue 51 LEU 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 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 36 VAL Chi-restraints excluded: chain SS residue 59 LEU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 28 LEU Chi-restraints excluded: chain ST residue 36 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 121 ARG Chi-restraints excluded: chain SU residue 21 ARG Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 92 HIS Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 112 VAL Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sc residue 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 168 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 249 CYS 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 60 MET 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 50 PHE Chi-restraints excluded: chain SZ residue 61 GLU Chi-restraints excluded: chain SZ residue 66 LYS Chi-restraints excluded: chain SZ residue 94 LYS Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sf residue 98 VAL Chi-restraints excluded: chain Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 130 VAL Chi-restraints excluded: chain Sf residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 219 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 204 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 SU 92 HIS Sc 29 GLN Sg 62 HIS ** Sg 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.069648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.051218 restraints weight = 78157.215| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.15 r_work: 0.2785 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27254 Z= 0.194 Angle : 0.746 14.301 39102 Z= 0.373 Chirality : 0.041 0.220 4767 Planarity : 0.005 0.113 3185 Dihedral : 22.347 167.728 9782 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.70 % Favored : 89.14 % Rotamer: Outliers : 7.18 % Allowed : 36.86 % Favored : 55.95 % 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: -1.64 (0.19), residues: 1916 helix: 0.43 (0.22), residues: 582 sheet: -1.20 (0.29), residues: 321 loop : -2.01 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPSg 219 HIS 0.013 0.001 HISSg 188 PHE 0.022 0.002 PHESF 61 TYR 0.022 0.002 TYRSM 61 ARG 0.006 0.000 ARGSc 31 Details of bonding type rmsd hydrogen bonds : bond 0.06100 ( 952) hydrogen bonds : angle 4.04491 ( 2152) covalent geometry : bond 0.00411 (27254) covalent geometry : angle 0.74631 (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 474 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 354 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CD 282 MET cc_start: 0.7187 (tpt) cc_final: 0.5708 (tpt) REVERT: CD 283 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.6222 (t) REVERT: CD 287 TRP cc_start: 0.9042 (t-100) cc_final: 0.8817 (t-100) REVERT: SD 50 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8744 (mm) REVERT: SD 56 GLN cc_start: 0.9245 (tp-100) cc_final: 0.8803 (tp-100) REVERT: SD 74 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8628 (tm-30) REVERT: SD 117 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8202 (ttt90) REVERT: SF 45 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.7996 (p90) REVERT: SF 60 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8585 (mtp180) REVERT: SF 83 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8418 (m-40) REVERT: SF 146 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8364 (ttt90) REVERT: SK 5 LYS cc_start: 0.8987 (ttpm) cc_final: 0.8771 (ttmm) REVERT: SK 29 MET cc_start: 0.9311 (ttm) cc_final: 0.8935 (ttp) REVERT: SK 31 LYS cc_start: 0.9443 (mptp) cc_final: 0.9114 (mptp) REVERT: SK 89 ILE cc_start: 0.9175 (mp) cc_final: 0.8929 (mp) REVERT: SP 31 GLU cc_start: 0.9084 (mp0) cc_final: 0.8770 (mp0) REVERT: SP 34 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8331 (mtm) REVERT: SQ 87 SER cc_start: 0.9379 (t) cc_final: 0.9044 (p) REVERT: SQ 107 GLU cc_start: 0.9049 (pp20) cc_final: 0.8777 (pp20) REVERT: SQ 116 ASP cc_start: 0.8465 (t0) cc_final: 0.8068 (t0) REVERT: ST 35 ASP cc_start: 0.9170 (p0) cc_final: 0.8915 (p0) REVERT: ST 36 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7895 (p) REVERT: ST 114 GLU cc_start: 0.8365 (pm20) cc_final: 0.7973 (pm20) REVERT: SU 21 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7768 (ttm170) REVERT: SU 49 LYS cc_start: 0.8901 (tppp) cc_final: 0.8245 (ttpt) REVERT: SU 92 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.7221 (m90) REVERT: SU 113 GLU cc_start: 0.7904 (mp0) cc_final: 0.7585 (mp0) REVERT: Sc 18 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9316 (mt) REVERT: Sc 33 GLU cc_start: 0.8430 (pp20) cc_final: 0.8172 (pp20) REVERT: Sc 51 ARG cc_start: 0.7872 (tpt-90) cc_final: 0.7566 (tpt-90) REVERT: Sc 60 GLU cc_start: 0.7558 (tm-30) cc_final: 0.6946 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5518 (OUTLIER) cc_final: 0.4960 (tt0) REVERT: Sd 3 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8339 (p90) REVERT: Sd 5 GLN cc_start: 0.9004 (mp10) cc_final: 0.8447 (mp10) REVERT: Sg 14 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.7210 (p90) REVERT: Sg 27 PHE cc_start: 0.9465 (m-80) cc_final: 0.9188 (m-80) REVERT: Sg 42 MET cc_start: 0.8718 (ttm) cc_final: 0.8312 (ptm) REVERT: Sg 140 TYR cc_start: 0.8360 (t80) cc_final: 0.8134 (t80) REVERT: Sg 145 GLU cc_start: 0.8682 (mp0) cc_final: 0.8332 (mp0) REVERT: Sg 228 TYR cc_start: 0.7585 (t80) cc_final: 0.7216 (t80) REVERT: Sg 282 GLU cc_start: 0.9006 (mp0) cc_final: 0.8712 (pm20) REVERT: SM 23 LYS cc_start: 0.9589 (mmmm) cc_final: 0.9264 (mppt) REVERT: SM 58 GLU cc_start: 0.8875 (tp30) cc_final: 0.8192 (tp30) REVERT: SM 60 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8935 (pmm) REVERT: SM 63 LYS cc_start: 0.9305 (ptmt) cc_final: 0.9022 (pptt) REVERT: SM 78 LYS cc_start: 0.9162 (mmmm) cc_final: 0.8879 (mmmm) REVERT: SM 84 LYS cc_start: 0.9201 (tppt) cc_final: 0.8925 (tppp) REVERT: SM 91 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8595 (tm) REVERT: Sf 107 LYS cc_start: 0.9008 (tptp) cc_final: 0.8766 (ttpp) REVERT: Sf 119 ARG cc_start: 0.8521 (mtm180) cc_final: 0.8296 (mmm-85) outliers start: 120 outliers final: 67 residues processed: 442 average time/residue: 1.2927 time to fit residues: 666.6143 Evaluate side-chains 430 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 346 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CD residue 283 THR 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 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 45 TYR Chi-restraints excluded: chain SF residue 60 ARG Chi-restraints excluded: chain SF residue 79 HIS Chi-restraints excluded: chain SF residue 83 ASN Chi-restraints excluded: chain SF residue 141 VAL Chi-restraints excluded: chain SF residue 146 ARG Chi-restraints excluded: chain SF residue 185 SER 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 SP residue 20 VAL Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 76 VAL Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SQ residue 26 LYS 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 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 36 VAL Chi-restraints excluded: chain SS residue 59 LEU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 28 LEU Chi-restraints excluded: chain ST residue 36 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 121 ARG Chi-restraints excluded: chain SU residue 21 ARG Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 92 HIS Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain 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 3 HIS 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 168 CYS Chi-restraints excluded: chain Sg residue 174 VAL Chi-restraints excluded: chain Sg residue 249 CYS 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 60 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 144 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 88 optimal weight: 0.0770 chunk 226 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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** ** SM 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.068618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.050039 restraints weight = 77932.750| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.20 r_work: 0.2750 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3033 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= 0.246 Angle : 0.776 14.807 39102 Z= 0.391 Chirality : 0.043 0.243 4767 Planarity : 0.005 0.117 3185 Dihedral : 22.345 165.814 9782 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.70 % Favored : 89.14 % Rotamer: Outliers : 6.22 % Allowed : 38.18 % Favored : 55.60 % 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: -1.59 (0.19), residues: 1916 helix: 0.45 (0.22), residues: 581 sheet: -1.12 (0.29), residues: 324 loop : -2.00 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPSg 219 HIS 0.014 0.001 HISSg 188 PHE 0.023 0.002 PHESF 61 TYR 0.026 0.002 TYRSM 61 ARG 0.005 0.001 ARGSc 31 Details of bonding type rmsd hydrogen bonds : bond 0.06429 ( 952) hydrogen bonds : angle 4.10233 ( 2152) covalent geometry : bond 0.00513 (27254) covalent geometry : angle 0.77591 (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 453 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 349 time to evaluate : 2.457 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: 0.7498 (tpt) cc_final: 0.7197 (tpp) REVERT: SD 50 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8780 (mm) REVERT: SD 56 GLN cc_start: 0.9224 (tp-100) cc_final: 0.8836 (tp-100) REVERT: SD 74 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8686 (tm-30) REVERT: SD 117 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8239 (ttt90) REVERT: SF 45 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8049 (p90) REVERT: SF 60 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8602 (mtp180) REVERT: SF 146 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8382 (ttt90) REVERT: SK 5 LYS cc_start: 0.9029 (ttpm) cc_final: 0.8806 (ttmm) REVERT: SK 29 MET cc_start: 0.9319 (ttm) cc_final: 0.8939 (ttp) REVERT: SK 31 LYS cc_start: 0.9439 (mptp) cc_final: 0.9110 (mptp) REVERT: SK 89 ILE cc_start: 0.9088 (mp) cc_final: 0.8881 (mp) REVERT: SP 31 GLU cc_start: 0.9022 (mp0) cc_final: 0.8728 (mp0) REVERT: SP 34 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8363 (mtm) REVERT: SQ 107 GLU cc_start: 0.9062 (pp20) cc_final: 0.8798 (pp20) REVERT: SQ 116 ASP cc_start: 0.8510 (t0) cc_final: 0.8156 (t0) REVERT: SS 10 GLN cc_start: 0.8832 (mm110) cc_final: 0.8584 (mm-40) REVERT: ST 35 ASP cc_start: 0.9188 (p0) cc_final: 0.8930 (p0) REVERT: ST 114 GLU cc_start: 0.8342 (pm20) cc_final: 0.8024 (pm20) REVERT: SU 49 LYS cc_start: 0.8914 (tppp) cc_final: 0.8450 (tmtt) REVERT: SU 113 GLU cc_start: 0.7918 (mp0) cc_final: 0.7599 (mp0) REVERT: Sc 18 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9281 (mt) REVERT: Sc 51 ARG cc_start: 0.7859 (tpt-90) cc_final: 0.7601 (tpt-90) REVERT: Sc 60 GLU cc_start: 0.7539 (tm-30) cc_final: 0.6891 (tm-30) REVERT: Sc 62 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5194 (tt0) REVERT: Sd 3 HIS cc_start: 0.8598 (OUTLIER) cc_final: 0.8393 (p90) REVERT: Sd 5 GLN cc_start: 0.9024 (mp10) cc_final: 0.8477 (mp10) REVERT: Sg 14 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.7442 (p90) REVERT: Sg 27 PHE cc_start: 0.9492 (m-80) cc_final: 0.9238 (m-80) REVERT: Sg 42 MET cc_start: 0.8720 (ttm) cc_final: 0.8230 (ptm) REVERT: Sg 140 TYR cc_start: 0.8376 (t80) cc_final: 0.8156 (t80) REVERT: Sg 145 GLU cc_start: 0.8596 (mp0) cc_final: 0.8278 (mp0) REVERT: Sg 228 TYR cc_start: 0.7668 (t80) cc_final: 0.7284 (t80) REVERT: Sg 282 GLU cc_start: 0.8935 (mp0) cc_final: 0.8676 (pm20) REVERT: SM 23 LYS cc_start: 0.9592 (mmmm) cc_final: 0.9259 (mppt) REVERT: SM 58 GLU cc_start: 0.8892 (tp30) cc_final: 0.8206 (tp30) REVERT: SM 63 LYS cc_start: 0.9308 (ptmt) cc_final: 0.9028 (pptt) REVERT: SM 78 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8848 (mmmm) REVERT: SM 84 LYS cc_start: 0.9162 (tppt) cc_final: 0.8867 (tppp) REVERT: SM 91 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8577 (tm) REVERT: Sf 107 LYS cc_start: 0.9039 (tptp) cc_final: 0.8821 (ttpp) REVERT: Sf 119 ARG cc_start: 0.8430 (mtm180) cc_final: 0.8182 (mmm-85) outliers start: 104 outliers final: 69 residues processed: 427 average time/residue: 1.5824 time to fit residues: 800.5362 Evaluate side-chains 425 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 345 time to evaluate : 2.684 ------------------------------------------------------------------------------- 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 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 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 185 SER 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 SP residue 20 VAL Chi-restraints excluded: chain SP residue 34 MET Chi-restraints excluded: chain SP residue 76 VAL Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SP residue 101 THR Chi-restraints excluded: chain SQ residue 26 LYS Chi-restraints excluded: chain SQ residue 51 LEU 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 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 SS residue 12 ILE Chi-restraints excluded: chain SS residue 36 VAL Chi-restraints excluded: chain SS residue 59 LEU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 84 LEU Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 6 VAL Chi-restraints excluded: chain ST residue 28 LEU Chi-restraints excluded: chain ST residue 36 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 121 ARG Chi-restraints excluded: chain SU residue 22 ILE Chi-restraints excluded: chain SU residue 23 THR Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain Sc residue 18 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sc residue 62 GLU Chi-restraints excluded: chain Sd residue 3 HIS Chi-restraints excluded: chain Sd residue 25 SER Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 5 MET 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 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 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 48 VAL Chi-restraints excluded: chain SZ residue 61 GLU Chi-restraints excluded: chain SZ residue 66 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 172 optimal weight: 0.1980 chunk 224 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 27 optimal weight: 0.0030 chunk 130 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 SU 92 HIS Sc 29 GLN Sg 62 HIS ** Sg 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.072030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.054150 restraints weight = 78673.106| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.19 r_work: 0.2875 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3234 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= 0.138 Angle : 0.739 13.550 39102 Z= 0.369 Chirality : 0.040 0.241 4767 Planarity : 0.005 0.111 3185 Dihedral : 22.330 172.461 9780 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.39 % Favored : 89.46 % Rotamer: Outliers : 4.73 % Allowed : 39.62 % Favored : 55.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 1.37 % Twisted General : 0.11 % 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: -1.50 (0.19), residues: 1916 helix: 0.50 (0.22), residues: 579 sheet: -0.95 (0.28), residues: 338 loop : -1.97 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPCD 287 HIS 0.013 0.001 HISSg 188 PHE 0.037 0.002 PHESf 136 TYR 0.028 0.001 TYRSM 61 ARG 0.006 0.000 ARGSf 118 Details of bonding type rmsd hydrogen bonds : bond 0.05764 ( 952) hydrogen bonds : angle 4.03778 ( 2152) covalent geometry : bond 0.00300 (27254) covalent geometry : angle 0.73933 (39102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25503.37 seconds wall clock time: 440 minutes 2.74 seconds (26402.74 seconds total)