Starting phenix.real_space_refine on Tue Jun 17 08:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc2_19045/06_2025/8rc2_19045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc2_19045/06_2025/8rc2_19045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rc2_19045/06_2025/8rc2_19045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc2_19045/06_2025/8rc2_19045.map" model { file = "/net/cci-nas-00/data/ceres_data/8rc2_19045/06_2025/8rc2_19045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc2_19045/06_2025/8rc2_19045.cif" } resolution = 3.1 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= 0.098 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 93 5.49 5 S 66 5.16 5 C 12143 2.51 5 N 3484 2.21 5 O 3968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19755 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2639 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain: "B" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2639 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain: "C" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2639 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain: "D" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2587 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain breaks: 1 Chain: "E" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1866 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain breaks: 2 Chain: "F" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1792 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 215} Chain: "G" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2090 Classifications: {'peptide': 263} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 246} Chain: "H" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 787 Classifications: {'RNA': 37} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 13, 'rna3p': 23} Chain: "I" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 792 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "J" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1551 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 3 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14394 SG CYS G 30 44.527 42.695 165.563 1.00131.74 S ATOM 14412 SG CYS G 33 43.647 46.091 165.784 1.00146.67 S ATOM 14609 SG CYS G 58 41.811 43.588 168.122 1.00125.99 S ATOM 14633 SG CYS G 61 40.910 43.718 164.521 1.00124.64 S Time building chain proxies: 12.96, per 1000 atoms: 0.66 Number of scatterers: 19755 At special positions: 0 Unit cell: (110, 117.7, 188.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 66 16.00 P 93 15.00 O 3968 8.00 N 3484 7.00 C 12143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.10 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 33 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 30 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 61 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 58 " Number of angles added : 6 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4188 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 29 sheets defined 41.7% alpha, 20.7% beta 33 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 7.21 Creating SS restraints... Processing helix chain 'A' and resid 44 through 65 removed outlier: 3.613A pdb=" N ILE A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.580A pdb=" N ASP A 153 " --> pdb=" O MET A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 161 through 199 removed outlier: 3.993A pdb=" N LYS A 197 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.894A pdb=" N GLN A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 273 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'B' and resid 44 through 65 removed outlier: 3.625A pdb=" N ILE B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 83 Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.548A pdb=" N GLU B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 196 Processing helix chain 'B' and resid 200 through 225 removed outlier: 3.579A pdb=" N LYS B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 273 Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.584A pdb=" N PHE B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 65 removed outlier: 3.699A pdb=" N ILE C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 110 through 116 Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.821A pdb=" N GLU C 158 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 194 removed outlier: 3.609A pdb=" N ASP C 166 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 200 through 224 removed outlier: 4.174A pdb=" N ALA C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 273 Processing helix chain 'C' and resid 282 through 286 removed outlier: 4.083A pdb=" N CYS C 286 " --> pdb=" O ASN C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 334 removed outlier: 3.512A pdb=" N PHE C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 65 removed outlier: 3.728A pdb=" N ILE D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 84 Processing helix chain 'D' and resid 102 through 110 Processing helix chain 'D' and resid 110 through 116 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 154 through 160 removed outlier: 3.740A pdb=" N GLU D 158 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 196 removed outlier: 3.614A pdb=" N MET D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 224 Processing helix chain 'D' and resid 258 through 273 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 322 through 335 Processing helix chain 'E' and resid 44 through 65 removed outlier: 3.805A pdb=" N ILE E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 100 Processing helix chain 'E' and resid 101 through 110 removed outlier: 3.737A pdb=" N GLU E 105 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 116 Processing helix chain 'E' and resid 258 through 273 Processing helix chain 'E' and resid 322 through 335 removed outlier: 3.562A pdb=" N PHE E 326 " --> pdb=" O GLY E 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 38 Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 158 through 163 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'G' and resid 3 through 12 removed outlier: 3.656A pdb=" N SER G 7 " --> pdb=" O HIS G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 40 Processing helix chain 'G' and resid 58 through 63 removed outlier: 3.576A pdb=" N THR G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 68 through 73 Processing helix chain 'G' and resid 85 through 89 removed outlier: 3.804A pdb=" N TRP G 89 " --> pdb=" O PHE G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 115 Processing helix chain 'G' and resid 116 through 123 removed outlier: 4.281A pdb=" N PHE G 120 " --> pdb=" O PRO G 116 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 131 No H-bonds generated for 'chain 'G' and resid 129 through 131' Processing helix chain 'G' and resid 132 through 140 Processing helix chain 'G' and resid 155 through 162 Processing helix chain 'G' and resid 191 through 203 removed outlier: 3.651A pdb=" N LYS G 203 " --> pdb=" O HIS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 222 Processing helix chain 'G' and resid 226 through 238 Processing helix chain 'G' and resid 239 through 244 Processing helix chain 'G' and resid 249 through 263 removed outlier: 3.517A pdb=" N LYS G 262 " --> pdb=" O HIS G 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 64 removed outlier: 3.553A pdb=" N ILE L 48 " --> pdb=" O PRO L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 110 Processing helix chain 'L' and resid 110 through 116 Processing helix chain 'L' and resid 258 through 273 removed outlier: 3.535A pdb=" N PHE L 265 " --> pdb=" O GLU L 261 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE L 266 " --> pdb=" O ALA L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132 removed outlier: 6.014A pdb=" N VAL A 125 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 255 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE A 127 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER A 253 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN A 129 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A 251 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 256 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG A 2 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR A 3 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP A 298 " --> pdb=" O THR A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 132 removed outlier: 6.014A pdb=" N VAL A 125 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 255 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE A 127 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER A 253 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN A 129 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A 251 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 256 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG A 2 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR A 3 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP A 298 " --> pdb=" O THR A 3 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.710A pdb=" N GLU B 247 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 12 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER B 249 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE B 10 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG B 251 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY B 8 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER B 253 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 6 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS B 255 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU B 4 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR B 297 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N THR B 307 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 141 Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 132 removed outlier: 6.059A pdb=" N VAL C 125 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS C 255 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE C 127 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N SER C 253 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASN C 129 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG C 251 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN C 256 " --> pdb=" O ARG C 2 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG C 2 " --> pdb=" O ASN C 256 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR C 297 " --> pdb=" O THR C 307 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR C 307 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 138 through 141 Processing sheet with id=AB2, first strand: chain 'C' and resid 144 through 146 Processing sheet with id=AB3, first strand: chain 'D' and resid 125 through 127 Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 127 removed outlier: 6.676A pdb=" N GLU D 247 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR D 12 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER D 249 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE D 10 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG D 251 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLY D 8 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER D 253 " --> pdb=" O PHE D 6 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N PHE D 6 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS D 255 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 4 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR D 297 " --> pdb=" O THR D 307 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N THR D 307 " --> pdb=" O THR D 297 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 138 through 141 Processing sheet with id=AB6, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AB7, first strand: chain 'E' and resid 125 through 127 Processing sheet with id=AB8, first strand: chain 'E' and resid 125 through 127 removed outlier: 3.537A pdb=" N ASN E 256 " --> pdb=" O ARG E 2 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG E 2 " --> pdb=" O ASN E 256 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR E 297 " --> pdb=" O THR E 307 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N THR E 307 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 138 through 141 Processing sheet with id=AC1, first strand: chain 'F' and resid 167 through 174 removed outlier: 5.545A pdb=" N ASN F 169 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER F 12 " --> pdb=" O ASN F 169 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS F 5 " --> pdb=" O GLY F 139 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE F 70 " --> pdb=" O GLN F 227 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AC3, first strand: chain 'F' and resid 79 through 85 Processing sheet with id=AC4, first strand: chain 'F' and resid 103 through 104 Processing sheet with id=AC5, first strand: chain 'F' and resid 182 through 183 Processing sheet with id=AC6, first strand: chain 'F' and resid 191 through 192 Processing sheet with id=AC7, first strand: chain 'G' and resid 24 through 25 Processing sheet with id=AC8, first strand: chain 'G' and resid 124 through 127 removed outlier: 6.840A pdb=" N SER G 103 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE G 126 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU G 105 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N LEU G 146 " --> pdb=" O TYR G 173 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N CYS G 175 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR G 148 " --> pdb=" O CYS G 175 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 127 Processing sheet with id=AD1, first strand: chain 'L' and resid 125 through 127 removed outlier: 3.666A pdb=" N ASN L 256 " --> pdb=" O ARG L 2 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG L 2 " --> pdb=" O ASN L 256 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR L 297 " --> pdb=" O THR L 307 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR L 307 " --> pdb=" O THR L 297 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 138 through 141 907 hydrogen bonds defined for protein. 2535 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 182 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 7.07 Time building geometry restraints manager: 5.79 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: 5210 1.33 - 1.45: 4006 1.45 - 1.57: 10828 1.57 - 1.69: 184 1.69 - 1.81: 119 Bond restraints: 20347 Sorted by residual: bond pdb=" C ILE F 38 " pdb=" N PRO F 39 " ideal model delta sigma weight residual 1.334 1.259 0.074 2.34e-02 1.83e+03 1.01e+01 bond pdb=" N LYS A 193 " pdb=" CA LYS A 193 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.56e+00 bond pdb=" N LYS A 204 " pdb=" CA LYS A 204 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.33e-02 5.65e+03 5.24e+00 bond pdb=" N ASP A 200 " pdb=" CA ASP A 200 " ideal model delta sigma weight residual 1.453 1.482 -0.029 1.31e-02 5.83e+03 4.89e+00 bond pdb=" N LYS G 235 " pdb=" CA LYS G 235 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.46e+00 ... (remaining 20342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 27446 1.99 - 3.98: 454 3.98 - 5.96: 41 5.96 - 7.95: 5 7.95 - 9.94: 2 Bond angle restraints: 27948 Sorted by residual: angle pdb=" CA ASP A 200 " pdb=" CB ASP A 200 " pdb=" CG ASP A 200 " ideal model delta sigma weight residual 112.60 116.26 -3.66 1.00e+00 1.00e+00 1.34e+01 angle pdb=" CA GLN C 184 " pdb=" CB GLN C 184 " pdb=" CG GLN C 184 " ideal model delta sigma weight residual 114.10 121.35 -7.25 2.00e+00 2.50e-01 1.31e+01 angle pdb=" N HIS C 284 " pdb=" CA HIS C 284 " pdb=" C HIS C 284 " ideal model delta sigma weight residual 113.72 109.10 4.62 1.52e+00 4.33e-01 9.24e+00 angle pdb=" C4' DG I -7 " pdb=" O4' DG I -7 " pdb=" C1' DG I -7 " ideal model delta sigma weight residual 109.70 105.15 4.55 1.50e+00 4.44e-01 9.19e+00 angle pdb=" CA LEU F 89 " pdb=" CB LEU F 89 " pdb=" CG LEU F 89 " ideal model delta sigma weight residual 116.30 106.36 9.94 3.50e+00 8.16e-02 8.06e+00 ... (remaining 27943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 11592 34.96 - 69.92: 436 69.92 - 104.89: 40 104.89 - 139.85: 6 139.85 - 174.81: 4 Dihedral angle restraints: 12078 sinusoidal: 5570 harmonic: 6508 Sorted by residual: dihedral pdb=" O4' U H 30 " pdb=" C1' U H 30 " pdb=" N1 U H 30 " pdb=" C2 U H 30 " ideal model delta sinusoidal sigma weight residual 200.00 45.21 154.79 1 1.50e+01 4.44e-03 8.13e+01 dihedral pdb=" O4' C H 19 " pdb=" C1' C H 19 " pdb=" N1 C H 19 " pdb=" C2 C H 19 " ideal model delta sinusoidal sigma weight residual -160.00 -100.59 -59.41 1 1.50e+01 4.44e-03 2.10e+01 dihedral pdb=" C4' DC I -9 " pdb=" C3' DC I -9 " pdb=" O3' DC I -9 " pdb=" P DC I -8 " ideal model delta sinusoidal sigma weight residual -140.00 34.81 -174.81 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 12075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2233 0.043 - 0.086: 694 0.086 - 0.129: 186 0.129 - 0.172: 22 0.172 - 0.215: 1 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CB VAL L 18 " pdb=" CA VAL L 18 " pdb=" CG1 VAL L 18 " pdb=" CG2 VAL L 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1' G H 25 " pdb=" O4' G H 25 " pdb=" C2' G H 25 " pdb=" N9 G H 25 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" C1' C H 1 " pdb=" O4' C H 1 " pdb=" C2' C H 1 " pdb=" N1 C H 1 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 3133 not shown) Planarity restraints: 3336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 116 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO F 117 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 117 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 117 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 234 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO A 235 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 234 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO D 235 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " -0.036 5.00e-02 4.00e+02 ... (remaining 3333 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 222 2.62 - 3.19: 17423 3.19 - 3.76: 31757 3.76 - 4.33: 45178 4.33 - 4.90: 74099 Nonbonded interactions: 168679 Sorted by model distance: nonbonded pdb=" OG1 THR D 46 " pdb=" OP1 C H 19 " model vdw 2.046 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" OP1 A H 5 " model vdw 2.166 3.120 nonbonded pdb=" OG1 THR E 46 " pdb=" OP1 G H 25 " model vdw 2.186 3.040 nonbonded pdb=" NH2 ARG A 107 " pdb=" O SER A 122 " model vdw 2.192 3.120 nonbonded pdb=" NH1 ARG C 49 " pdb=" OP1 A H 11 " model vdw 2.200 3.120 ... (remaining 168674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 197 or resid 205 through 341)) selection = (chain 'B' and (resid 1 through 197 or resid 205 through 341)) selection = (chain 'C' and (resid 1 through 197 or resid 205 through 341)) selection = chain 'D' } 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: 3.370 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: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.200 Process input model: 55.430 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.110 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.006 0.074 20351 Z= 0.281 Angle : 0.621 10.692 27954 Z= 0.325 Chirality : 0.044 0.215 3136 Planarity : 0.005 0.073 3336 Dihedral : 17.109 174.812 7890 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.42 % Allowed : 7.69 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2276 helix: 1.51 (0.17), residues: 832 sheet: 0.92 (0.26), residues: 350 loop : -0.25 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 119 HIS 0.006 0.001 HIS A 29 PHE 0.027 0.002 PHE A 80 TYR 0.029 0.002 TYR G 51 ARG 0.010 0.001 ARG F 234 Details of bonding type rmsd hydrogen bonds : bond 0.16693 ( 972) hydrogen bonds : angle 7.10500 ( 2717) metal coordination : bond 0.01233 ( 4) metal coordination : angle 5.48519 ( 6) covalent geometry : bond 0.00648 (20347) covalent geometry : angle 0.61556 (27948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 285 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASN cc_start: 0.9090 (m110) cc_final: 0.8859 (m-40) REVERT: A 184 GLN cc_start: 0.7178 (mt0) cc_final: 0.6925 (mm110) REVERT: A 189 GLN cc_start: 0.7491 (tt0) cc_final: 0.7185 (tt0) REVERT: A 193 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6813 (mmtt) REVERT: A 196 MET cc_start: 0.8111 (tpt) cc_final: 0.6511 (tpt) REVERT: A 213 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7982 (mm-30) REVERT: A 216 GLU cc_start: 0.8853 (mp0) cc_final: 0.8562 (mp0) REVERT: B 78 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6861 (mt-10) REVERT: B 190 ASP cc_start: 0.8042 (p0) cc_final: 0.7825 (p0) REVERT: B 216 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7717 (mp0) REVERT: B 336 GLN cc_start: 0.8914 (mt0) cc_final: 0.8618 (mm110) REVERT: C 7 ASN cc_start: 0.8776 (t0) cc_final: 0.8519 (t0) REVERT: D 58 LYS cc_start: 0.8186 (mttt) cc_final: 0.7939 (mppt) REVERT: D 87 ASP cc_start: 0.8232 (p0) cc_final: 0.7850 (p0) REVERT: D 101 ASN cc_start: 0.8485 (t0) cc_final: 0.8177 (t0) REVERT: D 158 GLU cc_start: 0.7569 (mp0) cc_final: 0.6866 (tm-30) REVERT: E 9 LYS cc_start: 0.8972 (mttm) cc_final: 0.8573 (mtpp) REVERT: E 109 LYS cc_start: 0.8214 (mttt) cc_final: 0.7982 (pttp) REVERT: E 135 ASP cc_start: 0.7838 (t70) cc_final: 0.7512 (t70) REVERT: E 275 GLU cc_start: 0.8224 (tp30) cc_final: 0.7958 (tt0) REVERT: F 59 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8360 (mp0) REVERT: F 105 ARG cc_start: 0.7443 (mtt180) cc_final: 0.6963 (mtt180) REVERT: G 100 ASP cc_start: 0.8980 (m-30) cc_final: 0.8627 (m-30) REVERT: G 132 GLN cc_start: 0.8640 (mt0) cc_final: 0.8140 (mt0) REVERT: G 164 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.7640 (mtp180) REVERT: G 189 MET cc_start: 0.8174 (ttm) cc_final: 0.7932 (tmm) REVERT: L 18 VAL cc_start: 0.8606 (p) cc_final: 0.8301 (p) REVERT: L 19 THR cc_start: 0.7645 (m) cc_final: 0.7230 (p) REVERT: L 124 LYS cc_start: 0.8529 (mmtp) cc_final: 0.8259 (mmtp) REVERT: L 260 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7377 (tp30) REVERT: L 277 ARG cc_start: 0.6732 (mtp180) cc_final: 0.6478 (mtp180) REVERT: L 299 LYS cc_start: 0.9018 (tppp) cc_final: 0.8611 (tmmt) REVERT: L 302 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8310 (mt-10) REVERT: L 328 MET cc_start: 0.9322 (mtp) cc_final: 0.8898 (mtp) REVERT: L 334 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7782 (mp0) outliers start: 8 outliers final: 1 residues processed: 292 average time/residue: 0.3897 time to fit residues: 162.2258 Evaluate side-chains 205 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain G residue 89 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 120 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 184 optimal weight: 0.0030 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 224 GLN C 292 HIS C 335 ASN D 84 GLN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 HIS L 336 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.086818 restraints weight = 27662.803| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.18 r_work: 0.2851 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20351 Z= 0.142 Angle : 0.581 8.548 27954 Z= 0.308 Chirality : 0.042 0.166 3136 Planarity : 0.005 0.067 3336 Dihedral : 19.339 175.027 3635 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.84 % Allowed : 8.17 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 2276 helix: 1.99 (0.18), residues: 836 sheet: 1.01 (0.26), residues: 355 loop : -0.01 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 119 HIS 0.005 0.001 HIS E 57 PHE 0.017 0.001 PHE L 6 TYR 0.017 0.001 TYR G 51 ARG 0.006 0.001 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 972) hydrogen bonds : angle 5.32719 ( 2717) metal coordination : bond 0.00578 ( 4) metal coordination : angle 5.80215 ( 6) covalent geometry : bond 0.00303 (20347) covalent geometry : angle 0.57514 (27948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLN cc_start: 0.7554 (tt0) cc_final: 0.7292 (tt0) REVERT: A 208 GLN cc_start: 0.7953 (mp10) cc_final: 0.7697 (mp10) REVERT: A 213 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8110 (mm-30) REVERT: A 216 GLU cc_start: 0.8905 (mp0) cc_final: 0.8568 (mp0) REVERT: A 330 LYS cc_start: 0.8245 (ttpp) cc_final: 0.7962 (ttpp) REVERT: B 174 GLU cc_start: 0.7998 (tt0) cc_final: 0.7739 (tt0) REVERT: B 190 ASP cc_start: 0.7952 (p0) cc_final: 0.7747 (p0) REVERT: B 217 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8360 (mtmt) REVERT: C 157 MET cc_start: 0.9008 (mmm) cc_final: 0.8802 (mmm) REVERT: C 227 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6933 (mt-10) REVERT: D 78 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: D 196 MET cc_start: 0.3445 (OUTLIER) cc_final: 0.3040 (ptm) REVERT: E 9 LYS cc_start: 0.9117 (mttm) cc_final: 0.8860 (mttm) REVERT: E 14 GLU cc_start: 0.8807 (mp0) cc_final: 0.8542 (mp0) REVERT: E 109 LYS cc_start: 0.8461 (mttt) cc_final: 0.8230 (pttp) REVERT: E 135 ASP cc_start: 0.7994 (t70) cc_final: 0.7765 (t70) REVERT: E 258 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7965 (p) REVERT: E 275 GLU cc_start: 0.8236 (tp30) cc_final: 0.7999 (tt0) REVERT: F 3 ASN cc_start: 0.7160 (p0) cc_final: 0.6960 (p0) REVERT: F 42 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8472 (tp30) REVERT: F 75 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8709 (mp0) REVERT: F 201 LYS cc_start: 0.8823 (mttp) cc_final: 0.8560 (mmtm) REVERT: G 16 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7620 (pp) REVERT: L 19 THR cc_start: 0.7670 (OUTLIER) cc_final: 0.7392 (p) REVERT: L 127 ILE cc_start: 0.7995 (mm) cc_final: 0.7737 (mm) REVERT: L 137 GLN cc_start: 0.8351 (mp10) cc_final: 0.7991 (mp10) REVERT: L 288 LEU cc_start: 0.8584 (tt) cc_final: 0.8262 (mm) REVERT: L 299 LYS cc_start: 0.8994 (tppp) cc_final: 0.8759 (tmmt) REVERT: L 334 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7648 (mp0) outliers start: 35 outliers final: 19 residues processed: 276 average time/residue: 0.3934 time to fit residues: 155.5978 Evaluate side-chains 214 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 42 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 216 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS A 151 GLN A 219 GLN A 250 HIS C 226 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 HIS G 3 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.130917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.085635 restraints weight = 27486.313| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.17 r_work: 0.2834 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20351 Z= 0.167 Angle : 0.556 7.890 27954 Z= 0.293 Chirality : 0.042 0.251 3136 Planarity : 0.004 0.064 3336 Dihedral : 19.271 172.417 3631 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.37 % Allowed : 8.43 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.17), residues: 2276 helix: 2.01 (0.18), residues: 848 sheet: 0.87 (0.26), residues: 357 loop : 0.03 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 119 HIS 0.004 0.001 HIS E 57 PHE 0.019 0.001 PHE L 37 TYR 0.015 0.001 TYR G 51 ARG 0.006 0.001 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 972) hydrogen bonds : angle 5.04851 ( 2717) metal coordination : bond 0.00659 ( 4) metal coordination : angle 5.07826 ( 6) covalent geometry : bond 0.00375 (20347) covalent geometry : angle 0.55144 (27948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 2.143 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.9080 (mmt90) cc_final: 0.8717 (mmt-90) REVERT: A 208 GLN cc_start: 0.7948 (mp10) cc_final: 0.7735 (mp10) REVERT: A 213 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8160 (mm-30) REVERT: A 216 GLU cc_start: 0.8874 (mp0) cc_final: 0.8567 (mp0) REVERT: B 105 GLU cc_start: 0.8032 (tt0) cc_final: 0.7670 (tp30) REVERT: B 190 ASP cc_start: 0.7954 (p0) cc_final: 0.7750 (p0) REVERT: C 157 MET cc_start: 0.9018 (mmm) cc_final: 0.8789 (mmm) REVERT: C 227 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6678 (mt-10) REVERT: D 78 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: D 196 MET cc_start: 0.3588 (OUTLIER) cc_final: 0.3053 (ptm) REVERT: E 9 LYS cc_start: 0.9100 (mttm) cc_final: 0.8828 (mttm) REVERT: E 14 GLU cc_start: 0.8833 (mp0) cc_final: 0.8488 (mp0) REVERT: E 109 LYS cc_start: 0.8467 (mttt) cc_final: 0.8232 (pttp) REVERT: E 119 TRP cc_start: 0.9025 (t-100) cc_final: 0.8701 (t-100) REVERT: E 258 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8046 (p) REVERT: E 275 GLU cc_start: 0.8315 (tp30) cc_final: 0.8060 (tt0) REVERT: E 334 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8382 (pp20) REVERT: F 42 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8489 (tp30) REVERT: F 75 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8706 (mp0) REVERT: G 16 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7666 (pp) REVERT: L 9 LYS cc_start: 0.6852 (mtpp) cc_final: 0.6380 (mmtt) REVERT: L 19 THR cc_start: 0.7289 (OUTLIER) cc_final: 0.7005 (p) REVERT: L 127 ILE cc_start: 0.8057 (mm) cc_final: 0.7850 (mm) REVERT: L 137 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8157 (mm-40) REVERT: L 288 LEU cc_start: 0.8562 (tt) cc_final: 0.8272 (mm) REVERT: L 299 LYS cc_start: 0.9001 (tppp) cc_final: 0.8366 (tmmt) outliers start: 45 outliers final: 26 residues processed: 237 average time/residue: 0.4032 time to fit residues: 138.6460 Evaluate side-chains 223 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 137 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 99 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 142 optimal weight: 0.0670 chunk 122 optimal weight: 30.0000 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.084350 restraints weight = 27865.982| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.17 r_work: 0.2803 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20351 Z= 0.201 Angle : 0.568 8.738 27954 Z= 0.297 Chirality : 0.043 0.247 3136 Planarity : 0.004 0.059 3336 Dihedral : 19.342 172.424 3631 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.90 % Allowed : 9.54 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2276 helix: 2.00 (0.18), residues: 847 sheet: 0.75 (0.26), residues: 350 loop : 0.03 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 119 HIS 0.006 0.001 HIS E 57 PHE 0.015 0.001 PHE A 80 TYR 0.014 0.001 TYR G 51 ARG 0.004 0.001 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 972) hydrogen bonds : angle 4.97161 ( 2717) metal coordination : bond 0.00796 ( 4) metal coordination : angle 5.02409 ( 6) covalent geometry : bond 0.00459 (20347) covalent geometry : angle 0.56312 (27948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 2.108 Fit side-chains REVERT: A 30 ARG cc_start: 0.9084 (mmt90) cc_final: 0.8738 (mmt-90) REVERT: A 210 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8195 (mttp) REVERT: A 213 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8098 (mm-30) REVERT: A 216 GLU cc_start: 0.8942 (mp0) cc_final: 0.8368 (mp0) REVERT: B 190 ASP cc_start: 0.7974 (p0) cc_final: 0.7773 (p0) REVERT: C 157 MET cc_start: 0.8994 (mmm) cc_final: 0.8694 (mmm) REVERT: C 227 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6842 (mt-10) REVERT: D 78 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: E 14 GLU cc_start: 0.8840 (mp0) cc_final: 0.8491 (mp0) REVERT: E 109 LYS cc_start: 0.8467 (mttt) cc_final: 0.8223 (pttp) REVERT: E 258 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8089 (p) REVERT: E 275 GLU cc_start: 0.8374 (tp30) cc_final: 0.8157 (tt0) REVERT: E 334 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8402 (pp20) REVERT: F 3 ASN cc_start: 0.7198 (p0) cc_final: 0.6905 (t0) REVERT: F 42 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8511 (tp30) REVERT: F 105 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7265 (mtt180) REVERT: F 201 LYS cc_start: 0.8950 (mttp) cc_final: 0.8672 (mmtm) REVERT: G 16 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7718 (pp) REVERT: L 9 LYS cc_start: 0.6933 (mtpp) cc_final: 0.6412 (mmtt) REVERT: L 19 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6830 (p) REVERT: L 124 LYS cc_start: 0.8880 (mmtp) cc_final: 0.8673 (mttp) REVERT: L 249 SER cc_start: 0.8321 (t) cc_final: 0.7691 (m) REVERT: L 299 LYS cc_start: 0.8985 (tppp) cc_final: 0.8370 (tmmt) outliers start: 36 outliers final: 22 residues processed: 225 average time/residue: 0.3874 time to fit residues: 126.7117 Evaluate side-chains 218 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 177 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 180 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN C 226 GLN C 335 ASN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 HIS L 256 ASN L 281 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.085123 restraints weight = 27954.939| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.17 r_work: 0.2820 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20351 Z= 0.169 Angle : 0.553 10.460 27954 Z= 0.288 Chirality : 0.042 0.265 3136 Planarity : 0.004 0.052 3336 Dihedral : 19.309 171.285 3631 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.21 % Allowed : 10.06 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2276 helix: 2.00 (0.18), residues: 848 sheet: 0.63 (0.25), residues: 352 loop : 0.08 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 119 HIS 0.007 0.001 HIS E 57 PHE 0.014 0.001 PHE L 37 TYR 0.007 0.001 TYR G 173 ARG 0.006 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 972) hydrogen bonds : angle 4.85055 ( 2717) metal coordination : bond 0.00606 ( 4) metal coordination : angle 5.12164 ( 6) covalent geometry : bond 0.00385 (20347) covalent geometry : angle 0.54827 (27948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 2.330 Fit side-chains REVERT: A 213 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8136 (mm-30) REVERT: A 216 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8263 (mp0) REVERT: A 328 MET cc_start: 0.8998 (mtt) cc_final: 0.8774 (mtt) REVERT: B 190 ASP cc_start: 0.7982 (p0) cc_final: 0.7779 (p0) REVERT: C 157 MET cc_start: 0.9014 (mmm) cc_final: 0.8693 (mmm) REVERT: C 227 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6912 (mt-10) REVERT: D 78 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: E 14 GLU cc_start: 0.8813 (mp0) cc_final: 0.8455 (mp0) REVERT: E 109 LYS cc_start: 0.8463 (mttt) cc_final: 0.8227 (pttp) REVERT: E 258 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8034 (p) REVERT: E 275 GLU cc_start: 0.8358 (tp30) cc_final: 0.8141 (tt0) REVERT: E 290 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8283 (pt0) REVERT: E 330 LYS cc_start: 0.9141 (tppt) cc_final: 0.8878 (tptp) REVERT: E 334 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8417 (pp20) REVERT: F 42 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8515 (tp30) REVERT: F 84 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7953 (tmt) REVERT: F 166 GLU cc_start: 0.9100 (tp30) cc_final: 0.8836 (tt0) REVERT: F 201 LYS cc_start: 0.8967 (mttp) cc_final: 0.8686 (mmtm) REVERT: G 16 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7683 (pp) REVERT: G 228 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7923 (tp30) REVERT: L 9 LYS cc_start: 0.6878 (mtpp) cc_final: 0.6550 (mmtt) REVERT: L 19 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.6826 (p) REVERT: L 288 LEU cc_start: 0.8497 (tt) cc_final: 0.8215 (mm) REVERT: L 299 LYS cc_start: 0.8981 (tppp) cc_final: 0.8391 (tmmt) outliers start: 42 outliers final: 22 residues processed: 236 average time/residue: 0.3786 time to fit residues: 130.2624 Evaluate side-chains 217 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 37 PHE Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 167 optimal weight: 4.9990 chunk 200 optimal weight: 0.5980 chunk 121 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 225 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 226 GLN C 335 ASN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN G 84 GLN G 251 HIS L 250 HIS L 281 HIS L 336 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.083709 restraints weight = 27858.120| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.17 r_work: 0.2798 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20351 Z= 0.209 Angle : 0.575 10.384 27954 Z= 0.299 Chirality : 0.043 0.292 3136 Planarity : 0.004 0.047 3336 Dihedral : 19.298 173.867 3631 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.48 % Allowed : 10.54 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2276 helix: 2.03 (0.18), residues: 842 sheet: 0.62 (0.25), residues: 354 loop : 0.08 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 119 HIS 0.008 0.001 HIS E 57 PHE 0.027 0.001 PHE L 6 TYR 0.013 0.001 TYR G 51 ARG 0.004 0.000 ARG L 33 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 972) hydrogen bonds : angle 4.88660 ( 2717) metal coordination : bond 0.00802 ( 4) metal coordination : angle 5.11350 ( 6) covalent geometry : bond 0.00482 (20347) covalent geometry : angle 0.56979 (27948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 1.925 Fit side-chains REVERT: A 30 ARG cc_start: 0.9122 (mmt90) cc_final: 0.8769 (mmt-90) REVERT: A 210 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8171 (mttp) REVERT: A 213 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8094 (mm-30) REVERT: A 216 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8301 (mp0) REVERT: A 328 MET cc_start: 0.9037 (mtt) cc_final: 0.8800 (mtt) REVERT: B 105 GLU cc_start: 0.8116 (tt0) cc_final: 0.7803 (tp30) REVERT: B 213 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8571 (pp20) REVERT: B 217 LYS cc_start: 0.8669 (ptpt) cc_final: 0.8248 (ptpt) REVERT: C 227 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6959 (mt-10) REVERT: D 78 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: D 196 MET cc_start: 0.3181 (OUTLIER) cc_final: 0.2792 (ptm) REVERT: E 14 GLU cc_start: 0.8810 (mp0) cc_final: 0.8468 (mp0) REVERT: E 106 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8590 (tp) REVERT: E 109 LYS cc_start: 0.8484 (mttt) cc_final: 0.8246 (pttp) REVERT: E 135 ASP cc_start: 0.8079 (t70) cc_final: 0.7790 (t70) REVERT: E 258 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8066 (p) REVERT: E 290 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8350 (pt0) REVERT: E 330 LYS cc_start: 0.9146 (tppt) cc_final: 0.8889 (tptp) REVERT: E 334 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8404 (pp20) REVERT: F 3 ASN cc_start: 0.7191 (p0) cc_final: 0.6884 (t0) REVERT: F 84 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7940 (tmt) REVERT: F 105 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7440 (mtt180) REVERT: F 201 LYS cc_start: 0.8958 (mttp) cc_final: 0.8677 (mmtm) REVERT: G 16 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7754 (pp) REVERT: G 191 ASP cc_start: 0.9190 (t0) cc_final: 0.8961 (t0) REVERT: L 19 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.6824 (p) REVERT: L 124 LYS cc_start: 0.8857 (mttp) cc_final: 0.8472 (mttt) REVERT: L 137 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8239 (mm-40) REVERT: L 299 LYS cc_start: 0.8980 (tppp) cc_final: 0.8396 (tmmt) outliers start: 47 outliers final: 28 residues processed: 233 average time/residue: 0.3717 time to fit residues: 125.1934 Evaluate side-chains 223 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 37 PHE Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.085597 restraints weight = 27742.429| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.17 r_work: 0.2835 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20351 Z= 0.146 Angle : 0.541 9.165 27954 Z= 0.282 Chirality : 0.042 0.294 3136 Planarity : 0.004 0.047 3336 Dihedral : 19.249 179.826 3631 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.21 % Allowed : 10.59 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.17), residues: 2276 helix: 2.17 (0.18), residues: 833 sheet: 0.55 (0.24), residues: 371 loop : 0.17 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 119 HIS 0.008 0.001 HIS E 57 PHE 0.022 0.001 PHE L 6 TYR 0.007 0.001 TYR G 173 ARG 0.007 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 972) hydrogen bonds : angle 4.77142 ( 2717) metal coordination : bond 0.00487 ( 4) metal coordination : angle 4.89219 ( 6) covalent geometry : bond 0.00328 (20347) covalent geometry : angle 0.53622 (27948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 2.217 Fit side-chains revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8072 (mttp) REVERT: A 213 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8076 (mm-30) REVERT: A 216 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8272 (mp0) REVERT: A 328 MET cc_start: 0.8942 (mtt) cc_final: 0.8725 (mtt) REVERT: B 213 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8632 (pp20) REVERT: C 99 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7359 (mt-10) REVERT: C 227 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6971 (mt-10) REVERT: C 335 ASN cc_start: 0.8603 (t0) cc_final: 0.8291 (t0) REVERT: D 78 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: D 196 MET cc_start: 0.3313 (OUTLIER) cc_final: 0.2922 (ptm) REVERT: E 9 LYS cc_start: 0.8880 (mttm) cc_final: 0.8536 (mtpp) REVERT: E 14 GLU cc_start: 0.8828 (mp0) cc_final: 0.8492 (mp0) REVERT: E 106 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8534 (tp) REVERT: E 109 LYS cc_start: 0.8458 (mttt) cc_final: 0.8216 (pttp) REVERT: E 258 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8092 (p) REVERT: E 290 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8313 (pt0) REVERT: E 330 LYS cc_start: 0.9148 (tppt) cc_final: 0.8905 (tptp) REVERT: E 334 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8408 (pp20) REVERT: F 3 ASN cc_start: 0.7082 (p0) cc_final: 0.6750 (t0) REVERT: F 42 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8511 (tp30) REVERT: F 84 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.8027 (tmt) REVERT: F 166 GLU cc_start: 0.9095 (tp30) cc_final: 0.8840 (tt0) REVERT: F 201 LYS cc_start: 0.8959 (mttp) cc_final: 0.8691 (mmtm) REVERT: G 16 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7603 (pp) REVERT: G 191 ASP cc_start: 0.9178 (t0) cc_final: 0.8937 (t0) REVERT: G 228 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: L 19 THR cc_start: 0.6864 (OUTLIER) cc_final: 0.6595 (p) REVERT: L 124 LYS cc_start: 0.8850 (mttp) cc_final: 0.8596 (mttt) REVERT: L 137 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8300 (mm-40) REVERT: L 288 LEU cc_start: 0.8508 (tt) cc_final: 0.8213 (mm) REVERT: L 299 LYS cc_start: 0.8965 (tppp) cc_final: 0.8393 (tmmt) outliers start: 42 outliers final: 24 residues processed: 242 average time/residue: 0.3823 time to fit residues: 134.5310 Evaluate side-chains 229 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 254 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 181 optimal weight: 0.0020 chunk 162 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN C 335 ASN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.086465 restraints weight = 27978.963| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.18 r_work: 0.2839 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20351 Z= 0.138 Angle : 0.535 8.785 27954 Z= 0.278 Chirality : 0.042 0.300 3136 Planarity : 0.004 0.048 3336 Dihedral : 19.183 170.742 3631 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.11 % Allowed : 10.59 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.17), residues: 2276 helix: 2.25 (0.18), residues: 832 sheet: 0.57 (0.24), residues: 371 loop : 0.19 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 119 HIS 0.008 0.001 HIS E 57 PHE 0.019 0.001 PHE L 6 TYR 0.013 0.001 TYR G 9 ARG 0.006 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 972) hydrogen bonds : angle 4.71952 ( 2717) metal coordination : bond 0.00254 ( 4) metal coordination : angle 4.57521 ( 6) covalent geometry : bond 0.00310 (20347) covalent geometry : angle 0.53127 (27948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 2.080 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.9116 (mmt90) cc_final: 0.8763 (mmt-90) REVERT: A 106 LEU cc_start: 0.8850 (tp) cc_final: 0.8607 (tp) REVERT: A 213 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8127 (mm-30) REVERT: A 216 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8264 (mp0) REVERT: A 328 MET cc_start: 0.8939 (mtt) cc_final: 0.8686 (mtt) REVERT: C 99 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7009 (mt-10) REVERT: C 153 ASP cc_start: 0.7727 (t0) cc_final: 0.7381 (p0) REVERT: C 184 GLN cc_start: 0.8085 (tp40) cc_final: 0.7753 (tp-100) REVERT: C 227 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6927 (mt-10) REVERT: D 78 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: D 196 MET cc_start: 0.3308 (OUTLIER) cc_final: 0.3022 (ptm) REVERT: E 9 LYS cc_start: 0.8855 (mttm) cc_final: 0.8625 (mttm) REVERT: E 14 GLU cc_start: 0.8826 (mp0) cc_final: 0.8469 (mp0) REVERT: E 106 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8507 (tp) REVERT: E 109 LYS cc_start: 0.8459 (mttt) cc_final: 0.8206 (pttp) REVERT: E 258 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8025 (p) REVERT: E 290 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8333 (pt0) REVERT: F 84 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8058 (tmt) REVERT: F 166 GLU cc_start: 0.9106 (tp30) cc_final: 0.8862 (tt0) REVERT: F 201 LYS cc_start: 0.8947 (mttp) cc_final: 0.8673 (mmtm) REVERT: G 16 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7550 (pp) REVERT: G 191 ASP cc_start: 0.9110 (t0) cc_final: 0.8900 (t0) REVERT: L 9 LYS cc_start: 0.6340 (mtpp) cc_final: 0.5914 (mmtt) REVERT: L 124 LYS cc_start: 0.8806 (mttp) cc_final: 0.8378 (mttt) REVERT: L 137 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8273 (mm-40) REVERT: L 261 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: L 288 LEU cc_start: 0.8532 (tt) cc_final: 0.8244 (mm) REVERT: L 299 LYS cc_start: 0.8969 (tppp) cc_final: 0.8365 (tmmt) outliers start: 40 outliers final: 21 residues processed: 236 average time/residue: 0.3814 time to fit residues: 131.2756 Evaluate side-chains 220 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 261 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 199 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 144 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN C 335 ASN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 GLN L 281 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.130837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.085839 restraints weight = 27830.371| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.16 r_work: 0.2828 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20351 Z= 0.158 Angle : 0.556 9.085 27954 Z= 0.288 Chirality : 0.042 0.353 3136 Planarity : 0.004 0.048 3336 Dihedral : 19.154 171.133 3631 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.69 % Allowed : 11.28 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.17), residues: 2276 helix: 2.24 (0.18), residues: 833 sheet: 0.57 (0.24), residues: 366 loop : 0.22 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 119 HIS 0.009 0.001 HIS E 57 PHE 0.020 0.001 PHE L 6 TYR 0.008 0.001 TYR F 128 ARG 0.006 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 972) hydrogen bonds : angle 4.74305 ( 2717) metal coordination : bond 0.00579 ( 4) metal coordination : angle 4.72597 ( 6) covalent geometry : bond 0.00360 (20347) covalent geometry : angle 0.55163 (27948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.9129 (mmt90) cc_final: 0.8787 (mmt-90) REVERT: A 106 LEU cc_start: 0.8866 (tp) cc_final: 0.8621 (tp) REVERT: A 210 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8286 (mttp) REVERT: A 213 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8095 (mm-30) REVERT: A 216 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8265 (mp0) REVERT: A 328 MET cc_start: 0.8951 (mtt) cc_final: 0.8690 (mtt) REVERT: C 99 GLU cc_start: 0.7855 (mm-30) cc_final: 0.6993 (mt-10) REVERT: C 149 MET cc_start: 0.8334 (ttm) cc_final: 0.7967 (ttt) REVERT: C 153 ASP cc_start: 0.7776 (t0) cc_final: 0.7311 (p0) REVERT: C 184 GLN cc_start: 0.8084 (tp40) cc_final: 0.7757 (tp-100) REVERT: C 227 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6923 (mt-10) REVERT: D 78 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: D 157 MET cc_start: 0.7735 (mmm) cc_final: 0.7349 (mmt) REVERT: D 196 MET cc_start: 0.3480 (OUTLIER) cc_final: 0.3260 (ptm) REVERT: E 9 LYS cc_start: 0.8871 (mttm) cc_final: 0.8634 (mttm) REVERT: E 14 GLU cc_start: 0.8826 (mp0) cc_final: 0.8482 (mp0) REVERT: E 106 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8507 (tp) REVERT: E 109 LYS cc_start: 0.8459 (mttt) cc_final: 0.8204 (pttp) REVERT: E 258 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8029 (p) REVERT: E 290 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8350 (pt0) REVERT: F 42 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8518 (tp30) REVERT: F 84 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.8028 (tmt) REVERT: F 87 ASP cc_start: 0.8894 (m-30) cc_final: 0.8678 (m-30) REVERT: F 166 GLU cc_start: 0.9115 (tp30) cc_final: 0.8861 (tt0) REVERT: F 201 LYS cc_start: 0.8945 (mttp) cc_final: 0.8669 (mmtm) REVERT: G 16 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7648 (pp) REVERT: G 191 ASP cc_start: 0.9146 (t0) cc_final: 0.8908 (t0) REVERT: L 9 LYS cc_start: 0.6250 (mtpp) cc_final: 0.5964 (mmtt) REVERT: L 53 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7768 (mmm-85) REVERT: L 124 LYS cc_start: 0.8809 (mttp) cc_final: 0.8539 (mttt) REVERT: L 137 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8312 (mm-40) REVERT: L 261 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: L 288 LEU cc_start: 0.8549 (tt) cc_final: 0.8257 (mm) REVERT: L 299 LYS cc_start: 0.8971 (tppp) cc_final: 0.8740 (tppt) outliers start: 32 outliers final: 21 residues processed: 230 average time/residue: 0.3672 time to fit residues: 123.6996 Evaluate side-chains 226 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 261 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN L 281 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.128630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.083137 restraints weight = 27853.098| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.17 r_work: 0.2791 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20351 Z= 0.221 Angle : 0.594 10.288 27954 Z= 0.306 Chirality : 0.044 0.344 3136 Planarity : 0.004 0.048 3336 Dihedral : 19.184 172.404 3631 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.74 % Allowed : 11.59 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2276 helix: 2.10 (0.18), residues: 839 sheet: 0.56 (0.24), residues: 361 loop : 0.18 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 119 HIS 0.010 0.001 HIS E 57 PHE 0.019 0.001 PHE L 6 TYR 0.017 0.002 TYR G 9 ARG 0.006 0.001 ARG L 49 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 972) hydrogen bonds : angle 4.86493 ( 2717) metal coordination : bond 0.00862 ( 4) metal coordination : angle 4.83417 ( 6) covalent geometry : bond 0.00511 (20347) covalent geometry : angle 0.58990 (27948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 2.086 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.9131 (mmt90) cc_final: 0.8773 (mmt-90) REVERT: A 210 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8134 (mttp) REVERT: A 213 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8088 (mm-30) REVERT: A 216 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8260 (mp0) REVERT: A 328 MET cc_start: 0.9038 (mtt) cc_final: 0.8806 (mtt) REVERT: C 99 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7061 (mt-10) REVERT: C 153 ASP cc_start: 0.7883 (t0) cc_final: 0.7376 (p0) REVERT: C 184 GLN cc_start: 0.8124 (tp40) cc_final: 0.7787 (tp-100) REVERT: C 227 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6924 (mt-10) REVERT: D 78 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: D 196 MET cc_start: 0.3510 (OUTLIER) cc_final: 0.3221 (ptm) REVERT: E 14 GLU cc_start: 0.8819 (mp0) cc_final: 0.8509 (mp0) REVERT: E 106 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8565 (tp) REVERT: E 109 LYS cc_start: 0.8468 (mttt) cc_final: 0.8232 (pttp) REVERT: E 258 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8085 (p) REVERT: E 290 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8352 (pt0) REVERT: E 330 LYS cc_start: 0.9170 (tppt) cc_final: 0.8888 (tptp) REVERT: F 84 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7998 (tmt) REVERT: F 201 LYS cc_start: 0.8956 (mttp) cc_final: 0.8685 (mmtm) REVERT: G 16 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7828 (pp) REVERT: L 53 ARG cc_start: 0.8020 (mmm-85) cc_final: 0.7736 (mmm-85) REVERT: L 137 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8321 (mm-40) REVERT: L 261 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7946 (pt0) REVERT: L 299 LYS cc_start: 0.8974 (tppp) cc_final: 0.8743 (tppt) outliers start: 33 outliers final: 20 residues processed: 221 average time/residue: 0.3744 time to fit residues: 119.8658 Evaluate side-chains 214 residues out of total 1898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 89 TRP Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain L residue 261 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 99 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 281 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.086121 restraints weight = 27794.435| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.53 r_work: 0.2812 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20351 Z= 0.153 Angle : 0.568 12.574 27954 Z= 0.291 Chirality : 0.042 0.342 3136 Planarity : 0.004 0.070 3336 Dihedral : 19.143 170.748 3631 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.58 % Allowed : 11.96 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.17), residues: 2276 helix: 2.13 (0.18), residues: 842 sheet: 0.40 (0.24), residues: 382 loop : 0.18 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 119 HIS 0.011 0.001 HIS E 57 PHE 0.020 0.001 PHE L 6 TYR 0.009 0.001 TYR F 128 ARG 0.011 0.000 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 972) hydrogen bonds : angle 4.79813 ( 2717) metal coordination : bond 0.00932 ( 4) metal coordination : angle 6.46554 ( 6) covalent geometry : bond 0.00348 (20347) covalent geometry : angle 0.55986 (27948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11802.93 seconds wall clock time: 202 minutes 13.77 seconds (12133.77 seconds total)